I helped with the arXiv in its early days, initially doing things like scripting the
auto-TeXing. I invented hyperTeX that allowed TeX to produce fully hyperlinked pdf and
wrote the first design of hyperref LaTeX package. I also helped in the first design of
Ghostview displaying hyperlinked postscript and pdf, as well as in an unrelated device
driver, and in the development of the webserver that became Apache. Now, I am one of
the moderators of the hep-lat arXiv.
I used to be a regular contributor to comp.lang.c, comp.lang.fortran, and comp.std.c
newsgroups, and had contributed an example to ISO C defect reports. I am currently on
the design team of International Society of Genetic Genealogy,
which maintains the current Y chromosome phylogenetic tree.
I was the secretary of the LANL Fellows in 2023 and am now the coordinator.
Patents and Patent Applications
In Chinese patent applications, my name is spelt 坦莫伊·巴塔查里亚,
and in Japanese as バッタチャルヤ, タンモイ.
In Devanagari script it is written as तन्मय भट्टाचार्य and
I spell my name in Bengali as তন্ময় ভট্টাচার্য্য.
This is a roughly reverse time-ordered list of my publications. See my academic interests page
for a brief description of the context in which this research sits. I have
a LinkedIn profile,
but this page is likely to be more complete and updated, and an Academia.edu
profile. My ORCID is
0000-0002-1060-652X (QR code on right),
Researcher id is J-8956-2013,
Scopus Author ID is 7006308075, MR author
ID is 730531, Semantic Scholar ID is 144296799, loop ID is 767051, DBLP id is 29/5903, and VIAF id is 39029408.
My High Energy Physics Output according to the InSpire database.
The links below from the author names go to their home pages.
The ori links go directly to the papers. Note that on-line journals may need
subscription. The pmid links go to pub med which provides a detailed metadata
for the paper, whereas PMC's and NIHMS's go to the Pubmed Central and the NIH Manuscript Submission system which makes
US government funded biomedical work available for free after an embargo
period. A list of my papers on the publicly accessible e-print arXiv, which covers my physics
interests, can be obtained using my arXiv public identifier bhattacharya_t_1;
the arXiv identifiers on the individual entries link to the abstract of the
paper on the arXiv allowing retrieval of the full text; it might be more
convenient to access one of its mirror sites instead. Though every
attempt is made to update them, the versions on the arXiv are not always
completely up to date.
The altmetric links, if visible, provide a measure the online impact of the work and hovering
over the plumx links will also provide impact measures; clicking either will provide details.
The inspire links go to the InSpire HEP
database, which allows a citation search in high energy physics. The InSpire
publication summary page
provides statistics of my career in HEP publication; and my InSpire ID is INSPIRE-00066839.
Citation count
Google scholar automatically
maintains a
citation count and the currently unmaintained site Impact Story
used to maintain all kind of impact statistics resulting from a recent
100 of my publications. According to Google,
on May29, 2024, the
seven most cited articles of mine had 4696, 2320, 1535, 1617, 1598, 1293,
and 1073 citations. With 54 more articles with 100 citations or more and yet
29 others with 50 or more citations, overall my 354 articles had garnered
30430 citations by that date, and I had
an h index of
70.
Helped by the analysis of my Google Scholar profile by
the Publish or Perish
program, on Mar5, 2017, I had
calculated that I had 222 papers written over 32 years,
resulting in an average of 398.09 citations per year and 57.38
citations per paper.
The Hirsch a
coefficient was 4.71, the rate m was 1.62, and the excess given by
an e_index
of 92.82. The average number of citations in the Hirsch core, A, was
215.7923,
the median, m, was
124, and the r-index
was 105.91, so that
the q^2
index was 80.30.
The hc_index
was
37. The g_index
was 112, so
the hg-index
was
107.7. The age-weighted
citation rate was 1607.7, and
the AW_index
was 40.1.
The h(2) index was 14.
On average, the cites per author were 2240.85, the papers per
author 57.64 and authors per paper were 5.06. The individualized
metric, hI-index
was 8.69,
the hI
normalized index was 26, and
the hm-index
was 18.26.
The AWCR
per Author was 258.47.
I had used similar data on Oct18, 2013 to
calculate my h index as 40, h(2) index to be 13, g index to be 86, a
index to be 164.175, m index to be 103.5 and r index to be 6567.
My
ResearchGate
profile had a score of 42.19
on Mar6, 2017.
It was 42.08 with 823.55 impact points
on Feb22, 2016. I
don't quite understand this site since I find duplicate listings of my
papers there and treatment of my non-biology publications used to be
distinctly odd.
Since like all automatic programs, it is difficult to know the accuracy of
the google scholar results, I have also manually counted the number of
citations each publication had on April13, 2011. The number I quote below
is the larger of the result from ISI
Web of Knowledge and from the INSPIRE databases, and is an underestimate
because these databases have a very uneven coverage of the various fields
I work in. Also, comparing them across fields is a bit
problematic. Nevertheless, the count stood at two papers with over
300 citations (317 and 395, not counting citations to responses), four
more with over 100, 11 further with greater than 50 citations, 15 more
with greater than 25 citations. A more robust measure is that I had
over 28 (30 to be exact) papers with 28 citations or more, so my h index was 28.
Similarly, my g
index was 55, my w
index was 9, and my E
and P indices were 919 and about 677 respectively.
Miscellaneous
My Erdös number is
at most 3, Dijkstra and Einstein numbers at most 5, and Wolfgang Pauli and Eugene Wigner numbers
at most 4, as detailed here. My academic
genealogy is traced here; the internet physics tree
might be more accurate.
Publications in preparation or under review
Here is a list of papers I am currently working on. Papers meant for anonymous review suppress their titles to avoid corrupting the review process.
CP-violating pion-nucleon coupling(FangchengHe,
TanmoyBhattacharya,
EmanueleMereghetti, and
RajanGupta)Los Alamos reports
LA-UR-24-28427,
In preparation.
Flavor diagonal charges of the nucleon and the sigma term(RajanGupta,
SungwooPark, and
TanmoyBhattacharya)Los Alamos reports
LA-UR-24-,
In preparation.
Gauge-Invariant Formulation of SU(N) Lattice Gauge Theories with Schwinger Fermions(HanqingLiu,
TanmoyBhattacharya,
ShaileshChandrasekharan, and
RajanGupta)Los Alamos reports
LA-UR-24-25480,
LA-UR-24-25481,
LA-UR-24-,
In preparation.
Gradient Flow of the Weinberg Operator(TanmoyBhattacharya,
ShohiniBhattacharya,
VincenzoCirigliano,
RajanGupta,
EmanueleMereghetti,
SungwooPark,
Jun-SikYoo, and
BoramYoon)Los Alamos reports
LA-UR-24-28189,
LA-UR-24-29084,
In preparation.
On the claimed dependence of extracted dipole moment on the nucleon interpolating field used(TanmoyBhattacharya,
VincenzoCirigliano, and
EmanueleMereghetti)Los Alamos report
LA-UR-24-24974,
In preparation.
Impact of VRC01 on the genotypic and phenotypic properties of viruses that establish infection in the Phase 2b antibody mediated prevention (AMP) studyIn preparation.
Bayesian Combination Methods Applied to Diagnostic and
Sequence Timing Methods Provide a Posterior Probability by Day for Possible Dates of HIV
Acquisition which is Useful in Clinical Trials. or Use of acute
HIV-1 sequence and diagnostic data from the FRESH and RV217 cohorts to evaluate acquisition
timing estimation with application to the Antibody Mediated Prevention (AMP) trials
(RaabyaRossenkhan,
Elena E.
Giorgi,
DanicaShao,
JamesLudwig,
PhillipLabuschagne,
Craig A.
Margaret,
ThumbiNdung'u,
DanielMuema,
KaminiGounder,
Krista L.
Dong,
Bruce D.
Walker,
MorganeRolland,
Merlin L.
Robb,
Leigh AnneEller,
FredrickSawe,
SorachaiNitayaphan,
EduardGrebe,
Michael P.
Busch,
Kevin P.
Delaney,
ShellyFacente,
Lindsay N.
Carpp,
Allan C.
deCamp,
YundaHuang,
BetteKorber,
MichalJuraska,
ErikaRudnicki,
EwelinaKosmider,
Daniel B.
Reeves,
Bryan T.
Mayer,
JohnHural,
WenjieDeng,
Dylan H.
Westfall,
AnnaYssel,
TanmoyBhattacharya,
DavidMatten,
LawrenceCorey,
Peter B.
Gilbert,
CarolynWilliamson,
James I.
Mullins, and
Paul T.
Edlefsen)
Los Alamos report
LA-UR-24-23873.
In preparation.
Explainability through linear projection of keywords
from saliency maps (ELiPKeSaM)
(SayeraDhaubhadel,
JamaludinMohd-Yusof,
KumkumGanguly,
BenjaminMcMahon, and
TanmoyBhattacharya)
In preparation.
Comment on the claim of physical irrelevance of the QCD topological termLos Alamos report
LA-UR-22-29996,
In preparation.
Predicting fifteen year all-cause mortality from VA medical records
(SayeraDhaubhadel,
LeticiaCuellar-Hengartner,
NicolasHengartner,
KumkumGanguly,
Ruy M.
Ribeiro,
TanmoyBhattacharya,
RebeccaHehl,
Judith D.
Cohn,
Nathan A.
Kimbrel,
Jean C.
Beckham,
KellyCho,
LaurenCosta,
Yuk-LamHo,
IonaDanciu,
Amy C.
Justice,
Janet P.
Tate, and
BenjaminMcMahon)Los Alamos report
LA-UR-21-26945 and
LA-UR-22-29759;
In preparation.
Strange and Charm Moments from Nf = 2 + 1 + 1 HISQ Lattices
(
(Precision Neutron Decay Matrix Element (PNDME) Collaboration))
In preparation.
Contribution of the gluon chromo-EDM to nucleon electric dipole moment
(TanmoyBhattacharya,
VincenzoCirigliano,
RajanGupta,
EmanueleMereghetti,
Jun-SikYoo, and
BoramYoon)Los Alamos report
LA-UR-21-22073.
In preparation.
Phases of 2d massless QCD with qubit regularization or
Infrared Phases of 2d QCD from Qubit Regularization(HanqingLiu,
TanmoyBhattacharya,
ShaileshChandrasekharan, and
RajanGupta)Los Alamos report
LA-UR-22-28886,
ori:oai:arXiv.org:2312.17734 [hep-lat]
[inspire]
Topological terms with qubit regularization and relativistic quantum circuits
(TanmoyBhattacharya,
ShaileshChandrasekharan,
RajanGupta,
Thomas R.
Richardson, and
HershSingh)
Los Alamos report
LA-UR-22-27102.
Mainz Institute of Theoretical Physics preprint
MITP-23-013.
ori:oai:arXiv.org:2310.06805 [hep-lat]
[inspire].
Comparison of diverse machine learning (ML) models of Major Adverse
Cardiovascular Events (MACE) in 4.2 million US Veterans or
MACE prediction using high-dimensional machine learning and mechanistic
interpretation: A longitudinal cohort study in US veterans
(SayeraDhaubhadel,
Ruy M.
Ribeiro,
KumkumGanguly,
Nicolas W.
Hengartner,
TanmoyBhattacharya,
BeautyKolade,
Judith D.
Cohn,
James M.
Hyman,
KhushbuAgarwal,
KellyCho,
LaurenCosta,
Yuk-LamHo,
Allison E.
Murata,
Glen H.
Murata,
Jason L.
Vassy,
Daniel C.
Posner,
J. MichaelGaziano,
Yan V.
Sun,
Peter W.
Wilson,
RaviMadduri,
Amy C.
Justice,
PhilTsao,
Christopher J.
O'Donnel,
ScottDamrauer, and
Benjamin H.
McMahon)Los Alamos report
LA-UR-22-29761;
medRxiv 2022.10.31.22281742 ori:doi:10.1101/2022.10.31.22281742In revision.
Vacuum Entanglement Harvesting in the Ising Model
(HershSingh,
TanmoyBhattacharya,
ShaileshChandrasekharan, and
RajanGupta)Los Alamos report
LA-UR-21-26805.
ori:oai:arXiv.org:2302.12858 [hep-lat].
In revision.
[inspire].
An explainability module for analysis of DAC extraction from cancer pathology reports
(SayeraDhaubhadel,
JamaludinMohd-Yusof,
KumkumGanguly,
BenjaminMcMahon, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-23-21470.
In review.
Papers and refereed conference papers
These are my publications published (or in press) in peer-reviewed venues or resulting from peer-reviewed conference submissions.
Theoretical tools for neutrino scattering: interplay between lattice QCD, EFTs, nuclear physics, phenomenology, and neutrino event generators
(L. Alvarez Ruso,
A. M. Ankowski,
S. Bacca,
A. B. Balantekin,
J. Carlson,
S. Gardener,
R. González-Jiménez,
R. Gupta,
T. J. Hobbs,
M. Hoferichter,
J. Isaacson,
N. Jachowicz,
W. I. Jay,
T. Katori,
F. Kling,
A. S. Kronfeld,
S. W. Li,
H.-W. Lin,
K.-F. Liu,
A. Lovato,
K. Mahn,
J. Menéndez,
A. S. Meyer,
J. Morfin,
S. Pastori,
N. Rocco,
M. Sajjad Athar,
T. Sato,
A. Schwenk,
P. E. Shanahan,
L. E. Strigari,
M. Wagman,
X. Zhang,
Y. Zhao,
B. Acharya,
L. Andreoli,
C. Andreopoulos,
J. L. Barrow,
T. Bhattacharya,
V. Brdar,
Z. Davoudi,
C. Giusti,
Y. Hayato,
A. N. Khan,
D. Kim,
Y. F. Li,
M. Lin,
P. Machado,
M. Martini,
K. Niewczas,
P. Pandey,
A. Papadopolou,
R. Plestid,
M. Roda,
I. Ruiz Simo,
J. N. Simone,
R. S. Sufian,
J. Tena-Vidal,
O. Tomalak,
Y.-D. Tsai, and
J. M. Udías)
DESY report DESY-22-05,
Fermilab report FERMILAB-FN-1161-T,
MIT report MITP-22-027,
Los Alamos National Laboratory report
LA-UR-22-22647ori:oai:arXiv.org:2203.09030 [hep-ph]Journal of PhysicsGIn press.
[inspire].
High dimensional predictions
of suicide risk in 4.2 million US Veterans using ensemble transfer learning or
High dimensional predictions
of suicide risk in millions of US Veterans
(SayeraDhaubhadel,
KumkumGanguly,
Ruy M.
Ribeiro,
Judith D.
Cohn,
James M.
Hyman,
Nicolas W.
Hengartner,
BeautyKolade,
AnnaSingley,
TanmoyBhattacharya,
PatrickFinley,
DrewLevin,
HaediThelen,
KellyCho,
LaurenCosta,
Yuk-LamHo,
Amy C.
Justice,
JohnPestian,
DanielSantel,
RafaelZamora-Resendiz,
SilviaCrivelli,
SuzanneTamang,
SusanaMartins,
JodieTrafton,
David W.
Oslin,
Jean C.
Beckham,
Nathaniel A.
Kimbrel,
Million Veteran Program
Suicide Exemplar Work Group
(KhushbuAgarwal,
Allison E.
Ashley-Koch,
MihaelaAslan,
Jean C.
Beckham,
EdmondBegoli,
TanmoyBhattacharya,
BenBrown,
Patrick S.
Calhoun,
Kei-HoiCheung,
SutanayChoudhury,
Ashley M.
Cliff,
Judith D.
Cohn,
SilviaCrivelli,
LeticiaCuellar-Hengartner,
Haedi E.
Deangelis,
Michelle F.
Dennis,
SayeraDhaubhadel,
Patrick D.
Finley,
KumkumGanguly,
Michael R.
Garvin,
Joel E.
Gelernter,
Lauren P.
Hair,
ColbyHam,
Phillip D.
Harvey,
Elizabeth R.
Hauser,
Michael A.
Hauser,
Nick W.
Hengartner,
Daniel A.
Jacobson,
JessicaJones,
Piet C.
Jones,
DavidKainer,
Alan D.
Kaplan,
Ira R.
Katz,
Rachel L.
Kember,
Nathan A.
Kimbrel,
Angela C.
Kirby,
John C.
Ko,
BeautyKolade,
JohnLagergren,
MatthewLane,
Daniel F.
Levey,
DrewLevin,
Jennifer H.
Lindquist,
XianlianLiu,
Ravi K.
Madduri,
CarrieManore,
CarianneMartinez,
Susana B.
Martins,
John F.
McCarthy,
MikaelaMcDevitt Cashman,
Benjamin H.
McMahon,
J. IzaakMiller,
DestineeMorrow,
David W.
Oslin,
MirkoPavicic-Venegas,
John P.
Pestian,
SaijuPyarajan,
Xue J.
Qin,
NallakkandiRajeevan,
Christine M.
Ramsey,
RuyRibeiro,
AlexRodriguez,
JonathonRomero,
DanielSantel,
YunlingShi,
Murray B.
Stein,
Kyle A.
Sullivan,
NingSun,
Suzanne R.
Tamang,
AliceTownsend,
Jodie A.
Trafton,
AngelicaWalker,
XiangeWang,
VictoriaWangia-Anderson,
RenjiYang,
ShinjaeYoo,
RafaelZamora-Resendiz, and
HongyuZhao), and
Benjamin H.
McMahon)Los Alamos report
LA-UR-22-29760;
Research Square 24August2023, preprint (Version 1)
ori:doi:10.21203/rs.3.rs-3276492/v1Scientific Reports14
(January20, 2024)
1793;
ori:doi:10.1038/s41598-024-51762-9;
pmid:38245528,
PMC10799879.
A broadly neutralizing antibody’s prevention efficacy depends on HIV-1 envelope sequence features in the Antibody Mediated Prevention trials or
Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features(MichalJuraska,
HongjunBai,
Allan C.
deCamp,
Craig A.
Margaret,
LiLi,
KevinGillespie,
Lindsay N.
Carpp,
Elena E.
Giorgi,
JamesLudwig,
CindyMolitor,
AaronHudson,
Brian D.
Williamson,
NicoleEspy,
BrianSimpkins,
ErikaRudnicki,
DanicaShao,
RaabyaRossenkhan,
Paul T.
Edlefsen,
Dylan H.
Westfall,
WenjieDeng,
LennieChen,
HongZhao,
TanmoyBhattacharya,
AlecPankow,
BenMurrell,
AnnaYssel,
DavidMatten,
TalitaYork,
NicolasBeaume,
AsandaGwashu-Nyangiwe,
NonkululekoNdabambi,
RuwayhidaThebus,
Shelly T.
Karuna,
LynnMorris,
David C.
Montefiori,
John A.
Hural,
Myron S.
Cohen,
LawrenceCorey,
MorganeRolland,
Peter B.
Gilbert,
CarolynWilliamson,
James I.
Mullins)Los Alamos report
LA-UR-23-25710May 2023.
Proceedings of National Academy of Sciences121:4
(January19, 2024)
e2308942121;
ori:doi:10.1073/pnas.2308942121;
pmid:38241441.
PMC10823214
Deep learning uncertainty quantification for clinical text classification or
Uncertainty quantification for deep learning models for clinical text classification
(AlinaPeluso,
IoanaDanciu,
Hong-JunYoon,
JamaludinMohd Yusof,
TanmoyBhattacharya,
AdamSpannaus,
NoahSchaefferkoetter,
Eric B.
Durbin,
Xiao-ChengWu,
AntonietteStroup,
JenniferDoherty,
StephenSchwarz,
CharlesWiggins,
LindaCoyle,
LynnePenberthy,
Georgia D.
Tourassi, and
ShangGao)
Los Alamos report
LA-UR-22-23086Journal of Biomedical Informatics149
(January2024)
104576;
ori:doi:10.1016/j.jbi.2023.104576;
pmid:38101690.
Available online 13December2023
Quark Chromo-Electric Dipole Moment Operator on the Lattice
(TanmoyBhattacharya,
VincenzoCirigliano,
RajanGupta,
EmanueleMereghetti,
Jun-SikYoo, and
BoramYoon)Los Alamos report
LA-UR-21-21913,
Institute of Nuclear Theory preprint
INT-PUB-23-013.
ori:oai:arXiv.org:2304.09929 [hep-lat]Physical ReviewD108:7
(2023)
074507;
ori:doi:10.1103/PhysRevD.108.074507Published October10, 2023.
[inspire].
Quantum Simulations for High-energy Physics
(Christian W.
Bauer,
ZohrehDavoudi,
A. BahaBalantekin,
TanmoyBhattacharya,
MarcelaCarena,
Wibe A.
de Jong,
PatrickDraper,
AidaEl-Khadra,
NateGemelke,
MasanoriHanada,
DmitriKharzeev,
HenryLamm,
Ying-YingLi,
JunyuLiu,
MikhailLukin,
YannickMeurice,
ChristopherMonroe,
BenjaminNachman,
GuidoPagano,
JohnPreskill,
EnricoRinaldi,
AlessandroRoggero,
David I.
Santiago,
Martin J.
Savage,
IrfanSiddiqi,
GeorgeSiopsis,
NathanWiebe,
DavidVan Zanten,
YukariYamauchi,
KübraYeter-Aydeniz, and
SilviaZorzetti)
University of Maryland report
UMD-PP-022-04;
Los Alamos report
LA-UR-22-22100;
RIKEN report
RIKEN-iTHEMS-Report-22;
Fermilab report
FERMILAB-PUB-22-249-SQMS-T;
InQubator for Quantum Simulation report
IQuS@UW-21-027;
The MITRE Corporation report
MITRE-21-03848-2;
ori:oai:arXiv.org:2204.03381 [quant-ph]Physical Review X Quantum4:2
(1May2023)
027001;
ori:doi:10.1103/PRXQuantum.4.027001.
[inspire].
Why I'm not Answering: Understanding Determinants of Classification of an Abstaining Classifier for Cancer Pathology Reports
(SayeraDhaubhadel,
JamaludinMohd-Yusof,
KumkumGanguly,
GopinathChennupati,
SunilThulasidasan,
NicolasHengartner,
Brent J.
Mumphrey,
Eric B.
Durban,
Jennifer A.
Doherty,
MireilleLemieux,
NoahSchaefferkoetter,
GeorgiaTourassi,
LindaCoyle,
LynnePenberthy,
BenjaminMcMahon,
TanmoyBhattacharya)
Los Alamos report
LA-UR-20-27364ori:oai:arXiv.org:2009.05094 [cs.LG]BMC SupplementsIn press.
Spacetime symmetric qubit regularization of the asymptotically free two-dimensional O(4) model or
Space-time symmetric qubit regularization of the asymptotically free two-dimensional O(4) model(JunzheZhou,
HershSingh,
TanmoyBhattacharya,
ShaileshChandrasekharan, and
RajanGupta)Los Alamos report
LA-UR-21-30982,
Institute for Nuclear Theory report
INT-PUB-21-023,
InQubator for Quantum Simulations report
IQS@UW-21-013.
ori:oai:arXiv.org:2111.13780 [hep-lat]Physical ReviewD105:5
(1March2022)
054510;
ori:doi:10.1103/PhysRevD.105.054510.
Published 21March2022.
[inspire].
Precision Nucleon Charges and Form Factors Using (2+1)-flavor Lattice QCD
(SungwooPark,
RajanGupta,
BoramYoon,
SantanuMondal,
TanmoyBhattacharya,
Yong-ChullJang,
BálintJoó, and
FrankWinter
(Nucleon Matrix Elements (NME) Collaboration))
Los Alamos report
LA-UR-21-20526;
ori:oai:arXiv.org:2103.05599 [hep-lat]Physical ReviewD105:05
(2022)
054505;
ori:doi:10.1103/PhysRevD.105.054505Published March10, 2022.
[inspire].
A Simple and Effective Baseline for Out-of-Distribution
Detection using Abstention or
An Effective Baseline for Robustness to Distributional Shift
(SushilThapa,
SunilThulasidasan,
SayeraDhaubhadel,
GopinathChennupati,
TanmoyBhattacharya, and
JeffreyBilmes)
Los Alamos report
LA-UR-20-25378 and
LA-UR-21-30506.
Proceedings of
20th IEEE International Conference on Machine Learning and Applications (ICMLA2021),
Virtually online13–16December, 2021,
278–285;
ori:doi:10.1109/ICMLA52953.2021.00050;
Conference Paper 408.
Published December15, 2021.
(Rejected from ICLR 2021 Paper 2981,Rejected from UAI 2021 paper 508.)
ori:oai:arXiv.org:2105.07107 [cs.LG]
Uncertainty Bounds for Multivariate Machine Learning Predictions on High-Strain Brittle Fracture
(CristinaGarcia-Cardona,
M. GiselleFernández-Godino,
DanielO’Malley, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-20-30015,
Livermore report
LLNL-JRNL-817876;
ori:oai:arXiv.org:2012.15739 [cond-mat.mtrl-sci]Computational Materials Science,
201
(January2022)
110883;
ori:doi:10.1016/j.commatsci.2021.110883.
Published online September30, 2021.
HIV-1 and SARS-CoV-2: Patterns in the Evolution of Two Pandemic Pathogens
(WillFischer,
Elena E.
Giorgi,
SrirupaChakraborty,
KienNguyen,
TanmoyBhattacharya,
JamesTheiler,
Pablo A.
Goloboff,
HyejinYoon,
WernerAbfalterer,
Brian T.
Foley,
HouriiyahTegally,
James Emmanuel
San,
Tuliode Oliveira,
Network for Genomic Surveillance
in South Africa (NGS-SA)
(EduanWilkinson,
NokukhanyaMsomi,
ArashIranzadeh,
VagnerFonseca,
DeelanDoolabh,
Emmanuel James
San,
KolekaMlisana,
Annevon Gottberg,
SibongileWalaza,
MushalAllam,
ArshadIsmail,
ThaboMohale,
Allison J.
Glass,
SusanEngelbrecht,
GertVan Zyl,
WolfgangPreiser,
FrancescoPetruccione,
AlexSigal,
DianaHardie,
GertMarais,
MarvinHsiao,
StephenKorsman,
Mary-AnnDavies,
LynnTyers,
InnocentMudau,
DenisYork,
CarolineMaslo,
DominiqueGoedhals,
ShareefAbrahams,
OluwakemiLaguda-Akingba,
ArghavanAlisoltani-Dehkordi,
AdamGodzik,
Constantinos Kurt
Wibmer,
Bryan Trevor
Sewell,
JoséLourenço,
Sergei L
Kosakovsky Pond,
StevenWeaver,
MartaGiovanetti,
Luiz Carlos Junior
Alcantara,
DarrenMartin,
Jinal N.
Bhiman,
Carlolyn D.
Williamson),
S
Gnanakaran, and
BetteKorber)Los Alamos report
LA-UR-21-23163;
Cell Host and Microbe29:7
(July14, 2021)
1093–1110;
ori:doi:10.1016/j.chom.2021.05.012.
pmid:34242582;
PMC8173590.
Published online June3, 2021.
Uncertainty Quantification for Deep Learning Regression Models in the Low Data Limit
(CristinaGarcia-Cardona,
Yen TingLin, and
TanmoyBhattacharya)
Los Alamos reports
LA-UR-21-21550,
LA-UR-21-22482.
Proceedings of the
4th International Conference on Uncertainty Quantification in Computational Sciences and Engineering (UNCECOMP 2021),
Streamed from Athens, Greece27–30June, 2021,
Eds.
M. Papadrakakis,
V. Papadopoulos, and
G. Stefanou,
article 19145.
European Community on Computational Methods in Applied Sciences (ECCOMAS) Proceedia8045
(2021)
379–393;
ori:doi:10.7712/120221.8045.19145Published September2021.
Nucleon Momentum Fraction, Helicity and Transversity from 2+1-flavor Lattice QCD
(SantanuMondal,
RajanGupta,
SungwooPark,
BoramYoon,
TanmoyBhattacharya,
BálintJoó, and
FrankWinter
(Nucleon Matrix Elements (NME) Collaboration))
Los Alamos report
LA-UR-20-28586;
ori:oai:arXiv.org:2011.12787 [hep-lat]Journal of High Energy Physics2021:04
(2021)
44;
ori:doi:10.1007/JHEP04(2021)044Published April07, 2021.
[inspire].
State preparation and measurement in a quantum simulation of the O(3)
sigma model or
Quantum simulation of the qubit-regularized O(3)-sigma model
(Alexander J.
Buser,
TanmoyBhattacharya,
LukaszCincio, and
RajanGupta)
Los Alamos report
LA-UR-20-24538;
ori:oai:arXiv.org:2006.15746 [quant-ph]Physical ReviewD102:11
(2020)
114514;
ori:doi:10.1103/PhysRevD.102.114514Published December21, 2020.
[inspire].
Moments of nucleon isovector structure in 2+1+1-flavor QCD
(SantanuMondal,
RajanGupta,
SungwooPark,
BoramYoon,
TanmoyBhattacharya, and
Huey-WenLin
(Precision Neutron Decay Matrix Element (PNDME) Collaboration))
Los Alamos report
LA-UR-20-23801;
MSU report
MSUHEP-20-009;
ori:oai:arXiv.org:2005.13779 [hep-lat]Physical ReviewD102:05
(2020)
054512;
ori:doi:10.1103/PhysRevD.102.054512Published September22, 2020.
[inspire].
Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus or
Tracking SARS-CoV-2 Spike mutations: evidence that D614G increases infectivity of the COVID-19 virus or
Spike mutation pipeline reveals the emergene of a more transmissible form of
SARS CoV-2
(BetteKorber,
William M
Fischer,
S
Gnanakaran,
HyejinYoon,
JamesTheiler,
WernerAbfalterer,
NicholasHengartner,
Elena E
Giorgi,
TanmoyBhattacharya,
BrianFoley,
Kathryn M
Hastie,
Matthew D
Parker,
David G
Partridge,
Cariad M
Evans,
Timothy M
Freeman,
Thushan I
de Silva
(on behalf of the Sheffield COVID-19 Genomics
group:
AdrienneAngyal,
Rebecca L.
Brown,
LauraCarrilero,
Luke R.
Green,
Danielle C.
Groves,
Katie J.
Johnson,
Alexander J.
Keeley,
Benjamin B.
Lindsey,
Paul J.
Parsons,
MohammadRaza,
SarahRowland-Jones,
NikkiSmith,
Rachel M.
Tucker,
DennisWang, and
Matthew D.
Wyles),
CharleneMcDanal,
Lautaro G
Perez,
HailiTang,
AlexMoon-Walker,
Sean P
Whelan,
Celia C
La Branche,
Erica O
Saphire, and
David C
Montefiori)Los Alamos report
LA-UR-20-23199;
bioRxiv 2020.04.29.069054 ori:doi:10.1101/2020.04.29.069054Cell182:4
(August20, 2020)
819–827.E19;
ori:doi:10.1016/j.cell.2020.06.043.
pmid:32697968;
PMC7332439.
Published online July2, 2020.
The Role of Lattice QCD in Searches for Violations of Fundamental Symmetries and Signals for New Physics(United States Quantum Chromodynamics (USQCD) Collaboration:
VincenzoCirigliano,
ZohrehDavoudi,
TanmoyBhattacharya,
TakuIzubuchi,
Phiala E. Shanahan,
SergeySyritsin,
Michael L. Wagman)ori:oai:arXiv.org:1904.09704 [hep-lat]European Physics JournalA55:11
(2019)
197;
ori:doi:10.1140/epja/i2019-12889-8.
First online November14, 2019.
[inspire]
AI Meets Exascale Computing: Advancing Cancer Research with Large-Scale High Performance Computing
(TanmoyBhattacharya,
ThomasBrettin,
James H.
Doroshow,
Yvonne A.
Evrard,
Emily J.
Greenspan,
Amy L.
Gryshuk,
Thuc T.
Hoang,
Carolyn B.
Vea Lauzon,
DwightNissley,
LynnePenberthy,
EricStahlberg,
RickStevens,
FredStreitz,
GeorgiaTourassi,
FangfangXia, and
GeorgeZaki)Los Alamos report
LA-UR-19-24131;
Frontiers in Oncology9
(2019)
984;
ori:doi:10.3389/fonc.2019.00984;
pmid:31632915;
PMC6783509.
Published October2, 2019.
Estimating the timing of early simian-human immunodeficiency virus infections: a comparison between Poisson Fitter and BEAST
(Elena E.
Giorgi,
HuiLi,
TanmoyBhattacharya,
George M.
Shaw, and
BetteKorber)Los Alamos report
LA-UR-19-26789;
mBio11:2
(Mar/Apr 2020)
e00324-20;
ori:doi:10.1128/mBio.00324-20pmid:32209678;
PMC7157514.
Published March24, 2020.
On Mixup Training: Improved Calibration and Predictive Uncertainty for Deep Neural Networks
(SunilThulasidasan,
GopinathChennupati,
Jeff A.
Bilmes,
TanmoyBhattacharya,
SarahMichalak)
ori:oai:arXiv.org:1905.11001 [stat.ML]36th International Conference on Machine Learning (Workshop on Uncertainty Quantification and Robustness in Deep Learning),
Long Beach, California, USA11–13June, 2019UDL-2019-paper-43.
and
33rd Conference on Neural Information Processing Systems,
Vancouver, Canada10–12December, 2019.
Advances in Neural Information Processing Systems32
(2019)
13888–13899.
Combating Label Noise in Deep Learning using Abstention
(SunilThulasidasan,
TanmoyBhattacharya,
JeffBilmes,
GopinathChennupati, and
JamalMohd-Yusof)
ori:oai:arXiv.org:1905.10964 [stat.ML]36th International Conference on Machine Learning,
Long Beach, California, USA11–13June, 2019.
Paper ID 3320.Proceedings of Machine Learning Research97
(2019)
6234–6243.
CAT: Computer Aided Triage Improving upon the Bayes Risk through ε-refusal triage rules
(NicolasHengartner,
LeticiaCuellar,
Xiao-ChengWu,
GeorgiaTourassi,
JohnQiu,
BlairChristian, and
TanmoyBhattacharya)
BMC Bioinformtics19:Suppl 18
(2018)
485;
ori:doi:10.1186/s12859-018-2503-9;
pmid:30577756;
PMC6302364.
Published December21, 2018.
The need for uncertainty quantification in machine-assisted medical decision making
(EdmonBegoli,
TanmoyBhattacharya, and
DimitriKusnezov)
Los Alamos report
LA-UR-18-28661Nature Machine Intelligence1:1
(2019)
20–23;
ori:doi:10.1038/s42256-018-0004-1Published on January7, 2019.
Isovector Charges of the Nucleon from 2+1+1-flavor Lattice QCD
(RajanGupta,
Yong-ChullJang,
BoramYoon,
Huey-WenLin,
VincenzoCirigliano, and
TanmoyBhattacharya
(Precision Neutron Decay Matrix Element (PNDME) Collaboration))
Los Alamos report
LA-UR-18-25535;
MSU publication
MSUHEP-18-011;
ori:oai:arXiv.org:1806.09006 [hep-lat]Physical ReviewD98:03
(2018)
034503;
ori:doi:10.1103/PhysRevD.98.034503Published 17August2018.
[inspire].
Quark contribution to the proton spin from 2+1+1-flavor lattice QCD
(Huey-WenLin,
RajanGupta,
BoramYoon,
Yong-ChullJang, and
TanmoyBhattacharya
(Precision Neutron Decay Matrix Element (PNDME) Collaboration))
Los Alamos report
LA-UR-18-25337;
MSU publication
MSUHEP-18-010;
ori:oai:arXiv.org:1806.10604 [hep-lat]Physical ReviewD98:9
(2018)
094512;
ori:doi:10.1103/PhysRevD.98.094512Published November30, 2018.
[inspire].
Accumulated mutations by 6 months of infection collectively render transmitted/founder HIV-1 significantly less fit
or Accumulated mutations cause significant fitness losses and are associated with decreased viral loads during early HIV-1 infection.
(ChuWang,
DonglaiLiu,
TaoZuo,
BhavnaHora,
FangpingCai,
HaitaoDing,
JohnKappes,
ChristinaOchsenbauer,
WeiKong,
XianghuiYu,
TanmoyBhattacharya,
Alan S.
Perelson, and
FengGao)
Los Alamos report
LA-UR-19-30331October 2019.
Journal of Infection80:2
(2020)
210–218;
ori:doi:10.2139/ssrn.3318932;
ori:doi:10.1016/j.jinf.2019.12.001;
pmid:31812703;
PMC7010540.
Published online Dec5,
2019.
Superinfection and Cure of Infected Cells as Novel Mechanisms
for Hepatitis C Virus Adaptation and Persistence
(RuianKe,
HuiLi,
ShuyiWang,
WengeDing,
Ruy M.
Ribeiro,
Elena E.
Giorgi,
TanmoyBhattacharya,
Richard J.O.
Barnard,
Beatrice H.
Hahn,
George M.
Shaw, and
Alan S.
Perelson)
Los Alamos report
LA-UR-17-26176Jul 2017.
Proceedings of National Academy of Sciences115:30
(July24, 2018)
E7139–E7148;
ori:doi:10.1073/pnas.1805267115;
pmid:29987026;
PMC6065014.
Published ahead of print on 9July2018
Kinship structures create persistent channels for language transmission
(J. StephenLansing,
Cheryl Delos Santos
Abundo,
Guy S.
Jacobs,
Elsa G.
Guillot,
StefanThurner,
Sean S.
Downey,
LockYue Chew,
TanmoyBhattacharya,
Ning NingChung,
HerawatiSudoyo, and
Murray P.
Cox)
Los Alamos report
LA-UR-17-23693May 2017.
Proceedings of the National Academy of Sciences114:49
(2017)
12910–12915;
ori:doi:10.1073/pnas.1706416114;
Published ahead of print November20, 2017.pmid: 29158378;
PMC5724253.
A strongly selected mutation in the HIV-1 genome is independent of adaptive immune responses.
(DonglaiLiu,
ChuWang,
BhavnaHora,
TaoZuo,
NiluGoonetilleke,
Michael K.P.
Liu,
MarkBerrong,
GuidoFerrari,
Andrew J.
McMichael,
TanmoyBhattacharya,
Alan S.
Perelson, and
FengGao)
Los Alamos report
LA-UR-17-21998March 2017.
Retrovirology14:1
(2017)
46;
ori:doi:10.1186/s12977-017-0371-4;
pmid: 29017536;
PMC5634943.
Published
Oct10,
2017.
Axial-vector Form Factors of the Nucleon from Lattice QCD
(RajanGupta,
Yong-ChullJang,
Huey-WenLin,
BoramYoon, and
TanmoyBhattacharya
(Precision Neutron Decay Matrix Element (PNDME) Collaboration))
Los Alamos report
LA-UR-17-23678;
ori:oai:arXiv.org:1705.06834 [hep-lat]Physical ReviewD96:11
(2017)
114503;
ori:doi:10.1103/PhysRevD.96.114503Published December4, 2017.
[inspire].
Nucleon transverse momentum-dependent parton distributions in lattice
QCD: Renormalization patterns and discretization effects
(BoramYoon,
MichaelEngelhardt,
RajanGupta,
TanmoyBhattacharya,
Jeremy R.
Green,
Bernard U.
Munsch,
John W.
Negele,
Andrew V.
Pochinsky,
AndreasSchäfer, and
Sergey N.
Syritsin)
Los Alamos report
LA-UR-17-24472.
ori:oai:arXiv.org:1706.03406 [hep-lat]Physical ReviewD96:09
(2017)
094508;
ori:doi:10.1103/PhysRevD.96.094508Published Nov21, 2017.
[inspire].
Transmission of multiple HIV-1 transmitted/founder
viruses into the same recipients was not determined by
modest phenotypic differences. or
Disparate phenotypic properties of multiple
transmitted/founder viruses
in the same HIV-1-infected individuals
(HongshuoSong,
BhavnaHora,
Elena E.
Giorgi,
AmitKumar,
FangpingCai,
TanmoyBhattacharya,
AlanPerelson, and
FengGao)
Scientific Reports6
(2016)
38130;
ori:doi:10.1038/srep38130pmid: 27909304;
PMC5133561.
Published online Dec02, 2016.
Worldline approach for numerical computation of
electromagnetic Casimir energies.
I. Scalar field coupled to magnetodielectric media
(Jonathan B.
Mackory,
TanmoyBhattacharya and
Daniel A.
Steck)Los Alamos report
LA-UR-16-24039,
June2016.
ori:oai:arXiv.org:1606.00150 [quant-ph]Physical ReviewA94:4
(2016)
042508;
ori:doi:10.1103/PhysRevA.94.042508Published October12, 2016.
[inspire].
Isovector charges of the nucleon from 2+1-flavor QCD with clover fermions
(BoramYoon,
Yong-ChullJang,
RajanGupta,
TanmoyBhattacharya,
JeremyGreen,
BálintJoó,
Huey-WenLin,
KostasOrginos,
DavidRichards,
SergeySyritsyn, and
FrankWinter
(Nucleon Matrix Element (NME) Collaboration))
Los Alamos report
LA-UR-16-20523.
ori:oai:arXiv.org:1611.07452 [hep-lat]Physical ReviewD95:7
(2017)
074508;
ori:doi:10.1103/PhysRevD.95.074508Published Apr13, 2017.
[inspire].
Controlling Excited State Contamination in Nucleon Matrix Elements
(BoramYoon,
RajanGupta,
TanmoyBhattacharya,
MichaelEngelhardt,
JeremyGreen,
BálintJoó,
Huey-WenLin,
JohnNegele,
KostasOrginos,
AndrewPochinsky,
DavidRichards,
SergeySyritsyn, and
FrankWinter
(Nucleon Matrix Element (NME) Collaboration))
Los Alamos report
LA-UR-16-20524.
ori:oai:arXiv.org:1602.07737 [hep-lat]Physical ReviewD93:11
(2016)
114506;
ori:doi:10.1103/PhysRevD.93.114506Published June8, 2016.
[inspire].
Axial, Scalar and Tensor Charges of the Nucleon from 2+1+1-flavor Lattice QCD
(TanmoyBhattacharya,
VincenzoCirigliano,
Saul D.
Cohen,
RajanGupta,
Huey-WenLin, and
BoramYoon
(Precision Neutron Decay Matrix Element (PNDME) Collaboration))
Los Alamos report
LA-UR-16-20522,
LA-UR-15-28922;
Institute for Nuclear Theory report
INT-PUB-16-008,
ori:oai:arXiv.org:1606.07049 [hep-lat]Physical ReviewD94:5
(2016)
054508;
ori:doi:10.1103/PhysRevD.94.054508Published September19, 2016.
[inspire].
Tracking HIV-1 recombination to resolve its contribution to
HIV-1 evolution in natural infection
(HongshuoSong,
Elena E.
Giorgi,
Vitaly V.
Ganusov,
FangpingCai,
GayathriAthreya,
HyejinYoon,
OanaCarja,
BhavnaHora,
PeterHraber,
EthanRomero-Severson,
ChunlaiJiang,
XiaojunLi,
ShuyiWang,
HuiLi,
Jesus F.
Salazar-Gonzalez,
Maria G.
Salazar,
NiluGoonetilleke,
Brandon F.
Keele,
David C.
Montefiori,
Myron S.
Cohen,
George M.
Shaw,
Beatrice H.
Hahn,
Andrew J.
McMichael,
Barton F.
Haynes,
BetteKorber,
TanmoyBhattacharya, and
FengGao)
subsumes
Role of Recombination in HIV-1 infection.
(HongshuoSong,
Vitaly V.
Ganusov,
FangpingCai,
BhavnaHora,
PeterHraber,
ChunlaiJiang,
ShuyiWang,
HuiLi,
Jesus F.
Salazar-Gonzalez,
Maria G.
Salazar,
NiluGoonetilleke,
TanmoyBhattacharya,
Elena E.
Giorgi,
BrandonKeele,
David C.
Montefiori,
Myron S.
Cohen,
Bette T.
Korber,
George M.
Shaw,
Beatrice H.
Hahn,
Andrew J.
McMahon,
Barton F.
Haynes,
FengGao)
and
RAP: a new tool to detect recombination in longitudinal low-diversity HIV-1 samples
(E.E. Giorgi,
T. Bhattacharya,
H. Song,
F. Gao,
G. Athreya,
H. Yoon,
O. Carja,
B. Korber)
Nature Communications9:1
(2018)
1928;
ori:doi:10.1038/s41467-018-04217-5.
pmid: 29765018;
PMC5954121.
Published 15May, 2018.
Optimal Combination of Broadly Neutralizing
Antibodies for Prevention and Treatment of
HIV-1 Clade C Infection.
(KsitijWagh,
TanmoyBhattacharya,
CarolynWilliamson,
AlexRobles,
MadeleineBayne,
JettaGarrity,
MichaelRist,
CeciliaRademeyer,
HyejinYoon,
AlanLapedes,
HongmeiGao,
KelliGreene,
Mark K.
Louder,
RuiKong,
Salim Abdool
Karim,
Dennis R.
Burton,
Dan H.
Barouch,
Michael C.
Nussenzweig,
John R.
Mascola,
LynnMorris,
David C.
Montefiori,
BetteKorber,
Michael S.
Seaman)
Public Library of Science Pathogens12:3
(2016)
e1005520;
ori:doi:10.1371/journal.ppat.1005520.
pmid: 27028935;
PMC4814126.
Published March30, 2016.
Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs
Distinguishes Modes and Models of Virus Transmission
and Early Diversification.
(HuiLi,
Mark B. Stoddard,
ShuyiWang,
Elena E. Giorgi,
Lily M. Blair,
Gerald H. Learn,
Beatrice H. Hahn,
Harvey J. Alter,
Michael P. Busch,
Daniel S. Fierer,
Ruy M. Ribeiro,
Alan S. Perelson,
TanmoyBhattacharya, and
George M. Shaw)
Journal of Virology90:1
(January2016)
152–166.
ori:doi:10.1128/JVI.02156-15;
pmid: 26468546;
PMC4702571.
Published ahead of print October14, 2015.
Longitudinal Antigenic Sequences and Sites
from Intra-Host Evolution (LASSIE) Identifies
Immune-Selected HIV Variants.
(PeterHraber,
BetteKorber,
KsitijWagh,
Elena E.
Giorgi,
TanmoyBhattacharya,
S. Gnanakaran,
Alan S.
Lapedes,
Gerald H.
Learn,
Edward F.
Kreider,
YingyingLi,
George M.
Shaw,
Beatrice H.
Hahn,
David C.
Montefiori,
S. MunirAlam,
MattiaBonsignori,
M. AnthonyMoody,
Hua-XianLiao,
FengGao, and
Barton F.
Haynes)
ori:oai:arXiv.org:1508.00463 [q-bio.PE]Viruses7:10
(2015)
5443–5475;
pmid: 26506369;
PMC4632389.
ori:doi:10.3390/v7102881Published October21, 2015.
Isovector and Isoscalar Tensor Charges of the Nucleon from Lattice QCD
(TanmoyBhattacharya,
VincenzoCirigliano,
Saul D.
Cohen,
RajanGupta,
AnoshJoseph,
Huey-WenLin, and
BoramYoon
(Precision Neutron Decay Matrix Elements (PNDME) Collaboration))
Los Alamos report
LA-UR-15-23801.
ori:oai:arXiv.org:1506.06411 [hep-lat]Physical ReviewD92:09
(2015)
094511;
ori:doi:10.1103/PhysRevD.92.094511Published November10, 2015.
[inspire].
Studying Language Evolution in the Age of Big Data
(TanmoyBhattacharya,
NancyRetzlaff,
Damián E. Blasi,
WilliamCroft,
MichaelCysouw,
DanielHruschka,
IanMaddieson,
LydiaMüller,
EricSmith,
Peter F. Stadler,
GeorgeStarostin, and
HyejinYoun)
Los Alamos report
LA-UR-18-24872.
Journal of Language Evolution3:2
(1July2018)
94–129;
ori:doi:10.1093/jole/lzy004Published ahead of print June8, 2018.
A Likelihood Ratio Anomaly Detector for Identifying Within-Perimeter Computer Network Attacks.
(JustinGrana,
DavidWolpert,
JoshuaNeil,
DongpingXie,
TanmoyBhattacharya,
RusselBent)
Los Alamos report
LA-UR-16-22440,
Apr 2016.
Journal of Network and Computer Applications66
(May2016)
166–179;
ori:doi:10.1016/j.jnca.2016.03.008;
Available online Mar11, 2016. subsumes HMMs for Optimal Detection of Computer Network Attacks.
(JustinGrana,
DavidWolpert,
JoshuaNeil,
DongpingXie,
TanmoyBhattacharya)
Los Alamos report
LA-UR-14-24747,
Jul 2014.
Santa Fe working paper
2014-06-022,
Jun 26 2014.
Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutations.
(DonglaiLiu,
TaoZuo,
BhavnaHora,
HongshuoSong,
WeiKong,
XianghuiYu,
NiluGoonetilleke,
TanmoyBhattacharya,
Alan S.
Perelson,
Barton F.
Haynes,
AndrewMcMichael, and
FengGao)
Los Alamos report
LA-UR-14-24449July 2013.
Retrovirology11:1
(2014)
101;
ori:doi:10.1186/s12977-014-0101-0;
pmid: 25407514;
PMC4264250.
Published
Nov19,
2014.
Impact of clade, geography and age of epidemic on HIV-1 neutralization
by antibodies
(PeterHraber,
Bette T.
Korber,
Alan S.
Lapedes,
Robert T.
Bailer,
Michael S.
Seaman,
HongmeiGao,
Kelli M.
Greene,
FrancineMcCutchan,
CarolynWilliamson,
Jerome H.
Kim,
SodsaiTovanabutra,
Beatrice H.
Hahn,
RonaldSwanstrom,
Michael M.
Thompson,
FengGao,
LindaHarris,
ElenaGiorgi,
NicholasHengartner,
TanmoyBhattacharya,
John R.
Mascola,
David C.
Montefiori)
Journal of Virology88:21
(Nov2014).
12623–12643ori:doi:10.1128/JVI.01705-14;
pmid: 25142591;
PMC4248897.
Published ahead of print August20, 2014.
Equation of state in (2+1)-flavor QCD.
(A. Bazavov,
TanmoyBhattacharya,
C. DeTar,
H.-T. Ding,
StevenGottlieb,
RajanGupta,
P. Hegde,
U.M. Heller,
F. Karsch,
E. Laermann,
L. Levkova,
SwagatoMukherjee,
P. Petreczky,
C. Schmidt,
C. Schroeder,
R.A. Soltz,
W. Soeldner,
R. Sugar,
M. Wagner, and
P. Vranas
(HotQCD Collaboration))
Los Alamos report
LA-UR-14-25672.
ori:oai:arXiv.org:1407.6387 [hep-lat]Physical ReviewD90:09
(2014)
094503;
ori:doi:10.1103/PhysRevD.90.094503Published Nov4, 2014.
[inspire].
The QCD phase transition with physical-mass, chiral quarks.
(TanmoyBhattacharya,
Michael I.
Buchoff,
Norman H.
Christ,
H.-T. Ding,
RajanGupta,
ChulwooJung,
F. Karsch,
ZhongjieLin,
R.D. Mawhinney,
GregMcGlynn,
SwagatoMukherjee,
DavidMurphy,
P. Petreczky,
DwightRenfrew,
ChrisSchroeder,
R.A. Soltz,
P.M. Vranas, and
HantaoYin
(HotQCD Collaboration))
Brookhaven preprint
BNL-103837-2014-JA,
Columbia University preprint
CU-TP-1205,
INT preprint
INT-PUB-14-003,
Los Alamos report
LA-UR-14-21066, and
Livermore preprint
LLNL-JRNL-650194.
ori:oai:arXiv.org:1402.5175 [hep-lat]Physical Review Letters113:08
(2014)
082001;
ori:doi:10.1103/PhysRevLett.113.082001;
pmid:25192088;
Published Aug18, 2014.
[inspire].
Reversion and T cell escape mutations compensate the fitness loss of
a CD8+T cell escape mutant in their cognate transmitted/founder virus.
(HongshuoSong,
BhavnaHora,
TanmoyBhattacharya,
NiluGoonetilleke,
Michael K.P.
Liu,
KevinWiehe,
HuiLi,
Shilpa S.
Iyer,
Andrew J.
McMichael,
Alan S.
Perelson,
FengGao)
Public Library of Science One9:7
(2014)
e102734;
ori:doi:10.1371/journal.pone.0102734;
pmid: 25028937;
PMC4100905.
Published online Jul16, 2014.
Evolutionary dynamics and information hierarchies in biological systems.
(SaraImari Walker,
Benjamin J.
Callahan,
GauravArya,
J. DavidBarry,
TanmoyBhattacharya,
SergeiGrigoryev,
MatteoPellegrini,
KarstenRippe,
Susan M.
Rosenberg)
Annals of the New York Academy of Sciences,
1305:Annals Reports
(December2013)
1–17;
ori:doi:10.1111/nyas.12140;
pmid: 23691975.
First published online May20, 2013.
Nucleon Charges and Electromagnetic Form Factors from 2+1+1-Flavor Lattice QCD.
(TanmoyBhattacharya,
Saul D.
Cohen,
RajanGupta,
AnoshJoseph,
Huey-WenLin, and
BoramYoon)
Los Alamos report
LA-UR-13-24606,
University of Washington preprint
NT@UW-13-23,
ori:oai:arXiv.org:1306.5435 [hep-lat]Physical ReviewD89:9
(2014)
094502;
ori:doi:10.1103/PhysRevD.89.094502Published May6, 2014.
[inspire].
Detecting regular sound changes in linguistics as an example of concerted
evolution.
(Daniel J.
Hruschka,
SimonBranford,
Eric D.
Smith,
JonWilkins,
AndrewMeade,
MarkPagel, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-14-29463,
Dec 2014.
Current Biology25:1
(2015)
1–9;
ori:doi:10.1016/j.cub.2014.10.064;
pmid: 25532895;
PMC4291143Published online Dec18, 2014.
Molecular Mechanisms of HIV Type 1 Prophylaxis Failure Revealed by Single-Genome Sequencing.
(HuiLi,
LilyBlair,
YaluChen,
GeraldLearn,
KatjaPfafferott,
MinaJohn,
TanmoyBhattacharya,
Beatrice H
Hahn,
SimonMallal,
George M
Shaw, and
Katherine J
Bar)
The Journal of Infectious Diseases208:10
(2013)
1598–1603;
ori:doi:10.1093/infdis/jit485;
pmid: 24023257.
PMC3805246;
Published online Sep9, 2013.
Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation
and Evolution in Natural Infection.
(Eun-YoungKim,
RamonLorenzo-Redondo,
Susan J.
Little,
Yoon-SeokChung,
Prabhjeet K.
Phalora,
Irina Maliijkovic
Berry,
John P.
Archer,
SudhirPenugonda,
WillFischer,
Douglas D.
Richman,
TanmoyBhattacharya,
Michael H.
Malim, and
Steven M.
Wolinsky)
Los Alamos report
LA-UR-14-25673Public Library of Science Pathogens10:7
(2014)
e1004281;
ori:doi:10.1371/journal.ppat.1004281.
pmid:25080100;
PMC4117599Published online Jul31, 2014.
Modeling sequence evolution in HIV-1 infection with recombination.
(Elena E.
Giorgi,
Bette T.
Korber,
Alan S.
Perelson, and
TanmoyBhattacharya),
Los Alamos report
LA-UR-12-24298,
Sep 2012.
Journal of Theoretical Biology329
(21July2013)
82–93;
ori:doi:10.1016/j.jtbi.2013.03.026;
pmid: 23567647;
PMC3667750;
NIHMS465784.
Published online Apr6, 2013.
Quantifying the Diversification of Hepatitis C Virus (HCV)
During Primary Infection: Estimates of the In Vivo Mutation Rate.
(Ruy M.
Ribeiro,
HuiLi,
ShuyiWang,
Mark B.
Stoddard,
Gerald H.
Learn,
Bette T.
Korber,
TanmoyBhattacharya,
JeremieGuedj,
Erica H.
Parrish,
Beatrice H.
Hahn,
George M.
Shaw, and
Alan S.
Perelson),
Los Alamos report
LA-UR-12-20157,
22 Mar 2012.
Public Library of Science Pathogens8:8
(2012)
e1002881;
ori:doi:10.1371/journal.ppat.1002881;
pmid: 22927817;
PMC3426522.
Published online Aug23, 2012.
Elucidation of Hepatitis C Virus Transmission and Early
Diversification by Single Genome Sequencing.
(HuiLi,
Mark B.
Stoddard,
ShuyiWang,
Lily M.
Blair,
Elena E.
Giorgi,
Erica H.
Parrish,
Gerald H.
Learn,
PeterHraber,
Paul A.
Goepfert,
Michael S.
Saag,
Thomas N.
Denny,
Barton F.
Haynes,
Beatrice H.
Hahn,
Ruy M.
Ribeiro,
Alan S.
Perelson,
Bette T.
Korber,
TanmoyBhattacharya, and
George M.
Shaw),
Los Alamos report
LA-UR-12-20288,
Mar 2012.
Public Library of Science Pathogens8:8
(2012)
e1002880;
ori:doi:10.1371/journal.ppat.1002880;
pmid: 22927816;
PMC3426529.
Published online Aug23, 2012.
Impact of immune escape mutations on HIV-1 fitness in
the context of the cognate transmitted/founder genome.
(HongshuoSong,
Jeffrey W. Pavlichek,
FangpingCai,
TanmoyBhattacharya,
HuiLi,
Shilpa S. Iyer,
Katharine J. Bar,
Julie M. Decker,
NiluGoonetilleke,
Michael K.P. Liu,
AnnaBerg,
BhavnaHora,
Mark S. Drinker,
JoshEudailey,
JoyPickeral,
M. Anthony Moody,
GuidoFerrari,
AndrewMcMichael,
Alan S. Perelson,
George M. Shaw,
Beatrice H. Hahn,
Barton F. Haynes, and
FengGao),
Retrovirology9:10
(2012)
89;
ori:doi:10.1186/1742-4690-9-89;
pmid: 23110705;
PMC3496648.
Published online
Oct30,
2012.
Chiral transition and U(1)A symmetry restoration from
lattice QCD using Domain Wall Fermions.
(A. Bazavov,
TanmoyBhattacharya,
Michael I.
Buchoff,
MichaelCheng,
N.H. Christ,
H.-T. Ding,
RajanGupta,
PrasadHegde,
ChulwooJung,
F. Karsch,
ZhongjieLin,
R.D. Mawhinney,
SwagatoMukherjee,
P. Petreczky,
R.A. Soltz,
P.M. Vranas, and
HantaoYin
(HotQCD Collaboration))
Columbia University preprint
CU-TP-1200,
Brookhaven preprint
BNL-97301-2012-JA,
Los Alamos report
LA-UR-12-21329,
Livermore preprint
LLNL-JRNL-557574.
ori:oai:arXiv.org:1205.3535 [hep-lat]Physical ReviewD86:9
(2012)
094503;
ori:doi:10.1103/PhysRevD.86.094503Published Nov6, 2012.
[inspire].
Fluctuations and Correlations of net baryon number, electric charge,
and strangeness: A comparison of lattice QCD results with the hadron resonance
gas model.
(A. Bazavov,
TanmoyBhattacharya,
C.E. DeTar,
H.-T. Ding,
StevenGottlieb,
RajanGupta,
P. Hegde,
Urs M.
Heller,
F. Karsch,
E. Laermann,
L. Levkova,
SwagatoMukherjee,
P. Petreczky,
ChristianSchmidt,
R.A. Soltz,
W. Soeldner,
R. Sugar, and
Pavlos M.
Vranas
(HotQCD Collaboration))
ori:oai:arXiv.org:1203.0784 [hep-lat]Physical ReviewD86:3
(2012)
034509;
ori:doi:10.1103/PhysRevD.86.034509Published Aug31, 2012
[inspire].
Probing Novel Scalar and Tensor Interactions from (Ultra)Cold Neutrons to the LHC.
(TanmoyBhattacharya,
VincenzoCirigliano,
Saul D.
Cohen,
AlbertoFilipuzzi,
MartínGonzález-Alonso,
Michael L.
Graesser,
RajanGupta,
Huey-WenLin)
Los Alamos report
LA-UR-11-11460,
Septemper 2011.
University of Washington preprint
NT@UW-11-16,
Universitat de València preprint
IFIC/11-57 and
FTUV/11-1007,
University of Wisconsin-Madison preprint
NPAC-11-14,
ori:oai:arXiv.org:1110.6448 [hep-ph]Physical ReviewD85:5
(2012)
054512;
ori:doi:10.1103/PhysRevD.85.054512.
Published
Mar30,
2012.
[inspire].
Chiral and deconfinement aspects of the QCD transition
(A. Bazavov,
T. Bhattacharya,
M. Cheng,
C. DeTar,
H.-T. Ding,
StevenGottlieb,
R. Gupta,
P. Hegde,
U.M. Heller,
F. Karsch,
E. Laermann,
L. Levkova,
S. Mukherjee,
P. Petreczky,
C. Schmidt,
R.A. Soltz,
W. Soeldner,
R. Sugar,
D. Toussaint,
W. Unger, and
P. Vranas
(HotQCD Collaboration))
BNL report
BNL-96539-2011-JA,
LANL report
LA-UR-11928.
ori:oai:arXiv.org:1111.1710 [hep-lat]Physical ReviewD85:5
(2012)
054503;
ori:doi:10.1103/PhysRevD.85.054503.
Published
Mar5,
2012.
[inspire].
Greenbergian universals, diachrony and statistical
analysis
(WilliamCroft,
TanmoyBhattacharya,
DaveKleinschmidt,
D. EricSmith,
T. FlorianJaeger),
Los Alamos report
LA-UR-11-03658,
June 2011.
Linguistic Typology15:2
(2011)
433–453ori:doi:10.1515/LITY.2011.029.
Published online Nov22, 2011.
Geographical distribution of phonological complexity
(IanMaddieson,
TanmoyBhattacharya,
EricSmith,
WilliamCroft),
Los Alamos report
LA-UR-11-03659,
June 2011.
Linguistic Typology15:2
(2011)
267–269ori:doi:10.1515/LITY.2011.020.
Published online Nov22, 2011.
Role of Donor Genital Tract HIV-1 Diversity in the
Transmission Bottleneck
(Debrah I.
Boeras,
Peter T.
Hraber,
MackenzieHurlston,
TammyEvans-Strickfaden,
TanmoyBhattacharya,
Elena E.
Giorgi,
JosephMulenga,
EtienneKarita,
Bette T.
Korber,
SusanAllen,
Clyde E.
Hart,
Cynthia A.
Derdeyn and
EricHunter)
Los Alamos report
LA-UR-11-11256.
Proceedings of the National Academy of Sciences108:46
(2011)
E1156–E1163ori:doi:10.1073/pnas.1103764108;
pmid: 22065783;
PMC3219102.
Published online Nov7, 2011.
Recurrent Signature Patterns in HIV-1 B Clade Envelope
Glycoproteins Associated with either Early or Chronic Infection
(S.
Gnanakaran,
TanmoyBhattacharya,
MarcusDaniels,
Brandon F.
Keele,
Peter T.
Hraber,
Alan S.
Lapedes,
TongyeShen,
BrianGaschen,
MohanKrishnamoorthy,
HuiLi,
Julie M.
Decker,
Jesus F.
Salazar-Gonzalez,
ShuyiWang,
ChunlaiJiang,
FengGao,
RonaldSwanstrom,
Jeffrey A.
Anderson,
Li-HuaPing,
Myron S.
Cohen,
MartinMarkowitz,
Paul A.
Goepfert,
Michael S.
Saag,
Joseph J.
Eron,
Charles B.
Hicks,
William A.
Blattner,
Georgia D.
Tomaras,
MohammedAshmal,
Norman L.
Letvin,
Peter B.
Gilbert,
Allan C.
DeCamp,
Craig A.
Magaret,
William R.
Schief,
Yih-En Andrew
Ban,
MingZhang,
Kelly A.
Soderberg,
Joseph G.
Sodorsky,
Barton F.
Haynes,
George M.
Shaw,
Beatrice H.
Hahn and
BetteKorber)
Public Library of Science Pathogens7:9
(2011)
e1002209ori:doi:10.1371/journal.ppat.1002209;
pmid: 21980282;
PMC3182927.
Published online September29, 2011.
A Signature in HIV-1 Envelope Leader Peptide Associated with
Transition from Acute to Chronic Infection Impacts Envelope Processing and
Infectivity
(MohammedAsmal,
InaHellmann,
WeiminLiu,
Brandon F.
Keele,
Alan S.
Perelson,
TanmoyBhattacharya,
S. Gnanakaran,
MarcusDaniels,
Barton F.
Haynes,
Bette T.
Korber,
Beatrice H.
Hahn,
George M.
Shaw and
Norman L.
Letvin)
Public Library of Science One6:8
(2011)
e23673ori:doi:10.1371/journal.pone.0023673;
pmid: 21876761;
PMC3158090.
Published online August18, 2011.
Epitope-specific CD8+ T Lymphocytes Cross-recognize Mutant SIV Sequences but Fail to Contain Very Early Evolution and Eventual Fixation of Epitope Escape Mutations During SIV Infection.
(Evan M.
Cale,
PeterHraber,
Elena E.
Giorgi,
WillFisher,
TanmoyBhattacharya,
ThomasLeitner,
Wendy W.
Yeh,
CherylGleasner,
Lance D.
Green,
Cliff S.
Han,
BetteKorber, and
Norman L.
Letvin)
Journal of Virology85:8
(2011)
3746–3757.
ori:doi:10.1128/JVI.02420-10;
pmid: 21307185;
PMC3126128.
Published ahead of print February9, 2011.
Genital tract sequestration of SIV following acute infection
(James B.
Whitney,
Peter T.
Hraber,
CorinneLuedemann,
Elena E.
Giorgi,
Marcus G.
Daniels,
TanmoyBhattacharya,
Srinivas S.
Rao,
John R.
Mascola,
Gary J.
Nabel,
Bette T.
Korber, and
Norman L.
Letvin)
Public Library of Science Pathogens7:2
(2011)
e1001293ori:doi:10.1371/journal.ppat.1001293;
pmid: 21379569;
PMC3040679.
Published online February17, 2011.
Tiered Categorization of a Diverse Panel of HIV-1
Env Pseudoviruses for Neutralizing Antibody
Assessment
(Michael S.
Seaman,
HollyJanes,
NatalieHawkins,
Lauren E.
Grandpre,
ColleenDevoy,
AyushGiri,
Rory T.
Coffey,
LindaHarris,
BlakeWood,
Marcus G.
Daniels,
TanmoyBhattacharya,
AlanLapedes,
Victoria R.
Polonis,
Francine E.
McCutchan,
Peter B.
Gilbert,
Steve G.
Self,
Bette T.
Korber,
David C.
Montefiori, and
John R.
Mascola)
Journal of Virology84:3
(2010)
1439–1452ori:doi:10.1128/JVI.02108-09;
pmid: 19939925;
PMC2812321.
Published online November25, 2009.14 citations as of Apr13, 2011.
Breadth of HIV-specific Neutralizing Activity in Sera:
Clustering Analysis and Association with Clinical
Variables
(Nicole A.
Doria-Rose,
Rachel M.
Klein,
Marcus G.
Daniels,
SijyO'Dell,
MarthaNason,
AlanLapedes,
TanmoyBhattacharya,
Stephen A.
Migueles,
Richard T.
Wyatt,
Bette T.
Korber,
John R.
Mascola, and
MarkConnors),
Journal of Virology84:3
(2010)
1631–1636ori:doi:10.1128/JVI.01482-09;
pmid: 19923174;
PMC2812355.
Published online November18, 2009..
12 citations as of Apr13, 2011
Equation of state and QCD transition at finite
temperature
(A. Bazavov,
T. Bhattacharya,
M. Cheng,
N.H. Christ,
C. DeTar,
S. Ejiri,
StevenGottlieb,
R. Gupta,
U.M. Heller,
K. Huebner,
C. Jung,
F. Karsch,
E. Laermann,
L. Levkova,
C. Miao,
R.D. Mawhinney,
P. Petreczky,
C. Schmidt,
R.A. Soltz,
W. Soeldner,
R. Sugar,
D. Toussaint,
P. Vranas)
ori:oai:arXiv.org:0903.4379 [hep-lat]Physical ReviewD80:1
(2009)
014504;
ori:doi:10.1103/PhysRevD.80.014504.
Published
Jul17,
2009.
[inspire].
The First T Cell Response to Transmitted/Founder
Virus Contributes to the Control of Acute Viremia in HIV-1 Infection
(NiluGoonetilleke,
Michael K.P.
Liu,
Jesus F.
Salazar-Gonzalez,
GuidoFerrari,
ElenaGiorgi,
Vitaly V.
Ganusov,
Brandon F.
Keele,
Gerald H.
Learn,
Emma L.
Turnbull,
Maria G.
Salazar,
Kent J.
Weinhold,
StephenMoore,
CHAVI Clinical
Core B,
NormanLetvin,
Barton F.
Haynes,
Myron S.
Cohen,
PeterHraber,
TanmoyBhattacharya,
PersephoneBorrow,
Alan S.
Perelson,
Beatrice H.
Hahn,
George M.
Shaw,
Bette T.
Korber and
Andrew J.
McMichael)
Journal of Experimental Medicine206:6
(2009)
1253–1272ori:doi:10.1084/jem.20090365;
pmid: 19487423;
PMC2715063.
Published online June1, 2009.66 citations as of Apr13, 2011.
Human APOBEC3G-mediated Editing can Promote HIV-1 Sequence Diversification
and Accelerate Adaptation to Selective Pressure.
(Eun-YoungKim,
TanmoyBhattacharya,
KevinKunstman,
PeterSwantek,
Fransje A. Koning,
Michael H. Malim and
Steven M. Wolinsky)
Los Alamos report
LA-UR 08-07876,
December 2008.
Journal of Virology84:19
(2010)
10402–10405.
ori:doi:10.1128/JVI.01223-10;
pmid: 20660203;
PMC2937764.
Published ahead of print July21, 20101 citation as of Apr13, 2011.
CCL3L1 and HIV/AIDS susceptibility
(TanmoyBhattacharya,
JenniferStanton,
Eun-YoungKim,
Kevin J. Kunstman,
John P. Phair,
Lisa P. Jacobson and
Steven M. Wolinsky)
Los Alamos report
LA-UR-08-07711,
December 2008.
Nature Medicine15:10
(October2009)
1112–1115ori:doi:10.1038/nm1009-1112;
pmid: 19812561.
Corrected online Nov3, 2009.11 citations as of Apr13, 2011.
Highly Complex Neutralization Determinants on a Monophyletic Lineage of Newly Transmitted Subtype C
Human Immunodeficiency Virus Type 1 Env Clones from India
(Smita S. Julkarni,
AlanLapedes,
HailiTang,
S. Gnanakaran,
Marcus G. Daniels,
MingZhang,
TanmoyBhattacharya,
MingLi,
Victoria R. Polonis,
Francine E. McCutchan,
LynnMorris,
DennisEllenberger,
Salvatore T. Butera,
Robert C. Bollinger,
Bette T. Korber,
Ramesh S. Paranjape, and
David Charles Montefiori)
Los Alamos report
LA-UR-07-08163,
December 2007.
Virology385:2
(2009)
505–520ori:doi:10.1016/j.virol.2008.12.032;
pmid: 19167740;
PMC2677301;
NIHMS103344.
Published ahead of print January23, 200918 citations as of Apr13, 2011.
Quantitating the multiplicity of infection with HIV subtype C reveals a non-Poisson distribution of variants
(M-R Abrahams,
JA Anderson,
EE Giorgi,
C Seoighe,
K Milsana,
L-H Ping,
GS Athreya,
FK Treurnicht,
BF Keele,
N Wood,
JF Gonzalez-Salazar,
T Bhattacharya,
H Chu,
I Hoffman,
S Galvin,
C Mapanje,
P Kazembe,
R Thebus,
S Fiscus,
W Hide,
MS Cohen,
S Abdool Karim,
BF Haynes,
GM Shaw,
BH Hahn,
BT Korber,
R Swanstrom,
C Williamson,
for the CAPRISA Acute Infection Study Team and
the Center for HIV-AIDS Vaccine Immunology Consortium)
Los Alamos report
LA-UR-08-06483,
October 2008.
Journal of Virology83:8
(2009)
3556–3567.
ori:doi:10.1128/JVI.02132-08;
pmid: 19193811;
PMC2663249.
Published ahead of print February4, 2009
(Corrigendum:
Journal of Virology83:13
(2009)
6974–6974.
ori:doi:10.1128/JVI.00832-09)
33 citations as of Apr13, 2011.
Genetic Identity, Biological Phenotype, and
Evolutionary Pathways of Transmitted/Founder Viruses
in Acute and Early HIV-1 Infection
(Jesus F. Salazar-Gonzalez,
Maria G. Salazar,
Brandon F. Keele,
Gerald H. Learn,
Elena E. Giorgi,
HuiLi,
Julie M. Decker,
ShuyiWang,
JoshuaBaalwa,
Matthias H. Kraus,
Nicholas F. Parrish,
Katharina S. Shaw,
M. BradGuffey,
Katharine J. Bar,
Katie L. Davis,
ChristinaOchsenbauer-Jambor,
John C. Kappes,
Michael S. Saag,
Myron S. Cohen,
JoesphMulenga,
Cynthia A. Derdeyn,
SusanAllen,
EricHunter,
MartinMarkowitz,
PeterHraber,
Alan S. Perelson,
TanmoyBhattacharya,
Barton F. Haynes,
Bette T. Korber,
Beatrice H. Hahn, and
George M. Shaw)
Journal of Experimental Medicine206:6
(2009)
1273–1289ori:doi:10.1084/jem.20090378;
pmid: 19487424;
PMC2715054.
Published online June1, 2009.73 citations as of Apr13, 2011.
Human Leukocyte Antigen-Associated Sequence Polymorphisms in Hepatitis C Virus Reveal
Reproducible Immune Responses and Constraints on Viral
Evolution
(JoergTimm,
BinLi,
Marcus G.
Daniels,
TanmoyBhattacharya,
Laura L.
Reyor,
RachelAllgaier,
ThomasKuntzen,
WillFischer,
Brian E.
Nolan,
JaredDuncan,
JulianSchulze zur Wiesch,
Arthur Y.
Kim,
NicoleFrahm,
ChristianBrander,
Raymond T.
Chung,
George M.
Lauer,
Bette T.
Korber, and
Todd M.
Allen),
Los Alamos report
LA-UR-06-8196,
November 2006.
Hepatology,
46:2
(2007)
339–349ori:doi:10.1002/hep.21702;
pmid: 17559151.
Published online June8, 200734 citations as of Apr13, 2011.
Successive dominance of human immunodeficiency virus type 1
sequences in patients receiving combination antiretroviral therapy or
Evolution of human immunodeficiency virus type 1 sequences in patients
receiving combination antiretroviral therapy.
(CarlaKuiken,
KevinKunstman,
TanmoyBhattacharya,
JenniferKunstman,
KristinaKommander,
JohnPhair,
BenjaminGood,
SatishPillai, and
StevenWolinsky),
Los Alamos report
LA-UR-04-5456.
Timing of the HIV-1 subtype C epidemic in Ethiopia: An improved
estimate using maximum likelihood methods. or
Molecular Paleontology of HIV-1 M Subtype C in Ethiopia.
(Una R. Smith,
TanmoyBhattacharya, and
Carla L. Kuiken)
Los Alamos report
LA-UR-02-7315,
November 2002 and
LA-UR-03-0468,
2003HIV Dynamics and Evolution: 10th International Workshop,
Lake Arrowhead, California, USA13–16April, 2003.
Abstract number 22
Reanalysis of HIV-1A putative recombinant sequences.
(Una R. Smith,
TanmoyBhattacharya, and
Carla L. Kuiken)
HIV Dynamics and Evolution: 9th International Workshop,
2002.
Abstract number 21
Duality and the Extraction of Light Quark Masses From Finite Energy
and QCD Sum Rules. or
Extraction of Light Quark Masses from Sum Rule Analyses of Axial Vector and
Vector Current Ward IDentities.
(TanmoyBhattacharya,
RajanGupta, and
KimMaltman)
Los Alamos report
LA-UR-96-2698,
March 1997.
ori:oai:arXiv.org:hep-ph/9703455Physical ReviewD57:9
(1998)
5455–5467;
ori:doi:10.1103/PhysRevD.57.5455.
[inspire].
31 citations as of Apr13, 2011.
This section contains a bunch of talk abstracts that appeared in published lists of abstracts,
unrefereed talks that were written up, and certain miscellaneous kinds of unreferreed publications
(e.g., prefaces, articles for internal publication). If it is refereed and
appeared as a full paper (e.g., in computer science), it is included in the
first section, not here. Proceedings in which only a collaboration I am part of, but not me personally, is
listed as an author are listed separately in the next section.
Rise of Complexity Sciences in a Reductionist World(TanmoyBhattacharya)Los Alamos report
LA-UR-22-31342,
In Foundational Papers in Complexity Science,
Edited by
David C. Krakauer,
Volume 2,
Santa Fe, NM,
SFI Press,
2024,
1191–1203;
ori:doi:10.37911/9781947864535.39.
Electroweak box diagram contribution for pion and kaon decay from lattice QCD(Jun-SikYoo,
TanmoyBhattacharya,
RajanGupta,
SantanuMondal, and
BoramYoon)Proceedings of the
40th
annual International Symposium on Lattice Field Theory,
30July–5August2023,
Fermilab, Batavia, IL, United States.
Eds.
IanCloet,
Aida X.
El-Khadra,
GeorgeFleming,
AndreasKronfeld,
HenryLamm,
JamesOsborn,
James N.
Simone,
MikhailStephanov,
RuthVan de Water,
MichaelWagman, and
YongZhao.
Proceedings of ScienceLATTICE2023
(2024)
257;
ori:doi:10.22323/1.453.0257.
[inspire]
Progress report on testing robustness of the Newton method in data analysis on 2-point correlation
function using a MILC HISQ ensemble or
Progress report on data analysis of 2 point correlation functions for semileptonic decay
B(s)→D(*)(s)ℓν
form factors
(TanmoyBhattacharya,
Benjamin J.
Choi,
RajanGupta,
Yong-ChullJang,
SungyeobJwa,
SungheeKim,
SunkyuLee,
WeonjongLee,
JaehoonLeem,
JeongwhanPak, and
SungwooPark)
Los Alamos report
LA-UR-23-34205,
ori:oai:arXiv.org:2401.01584 [hep-lat]Proceedings of the
40th
annual International Symposium on Lattice Field Theory,
30July–5August2023,
Fermilab, Batavia, IL, United States.
Eds.
IanCloet,
Aida X.
El-Khadra,
GeorgeFleming,
AndreasKronfeld,
HenryLamm,
JamesOsborn,
James N.
Simone,
MikhailStephanov,
RuthVan de Water,
MichaelWagman, and
YongZhao.
Proceedings of ScienceLATTICE2023
(2024)
155;
ori:doi:10.22323/1.453.0155.
[inspire]
Neutron electric dipole moment from isovector quark chromo-electric dipole moment
(TanmoyBhattacharya,
VincenzoCirigliano,
RajanGupta,
EmanueleMereghetti,
Jun-SikYoo, and
BoramYoon)
Los Alamos report
LA-UR-23-29484,
ori:oai:arXiv.org:2404.13516 [hep-lat]Proceedings of the
40th
annual International Symposium on Lattice Field Theory,
30July–5August2023,
Fermilab, Batavia, IL, United States.
Eds.
IanCloet,
Aida X.
El-Khadra,
GeorgeFleming,
AndreasKronfeld,
HenryLamm,
JamesOsborn,
James N.
Simone,
MikhailStephanov,
RuthVan de Water,
MichaelWagman, and
YongZhao.
Proceedings of ScienceLATTICE2023
(2024)
339;
ori:doi:10.22323/1.453.0339.
[inspire]
Update on flavor diagonal nucleon charges from clover fermions or
Flavor diagonal nucleon charges from clover fermions on MILC HISQ ensembles(SungwooPark,
TanmoyBhattacharya,
RajanGupta,
Huey-WenLin, and
SantanuMondal,
BoramYoon)Livermore report
LLNL-PROC-858664,
Los Alamos report
LA-UR-24-20016,
ori:oai:arXiv.org:2401.00721 [hep-lat]Proceedings of the
40th
annual International Symposium on Lattice Field Theory,
30July–5August2023,
Fermilab, Batavia, IL, United States.
Eds.
IanCloet,
Aida X.
El-Khadra,
GeorgeFleming,
AndreasKronfeld,
HenryLamm,
JamesOsborn,
James N.
Simone,
MikhailStephanov,
RuthVan de Water,
MichaelWagman, and
YongZhao.
Proceedings of ScienceLATTICE2023
(2024)
328;
ori:doi:10.22323/1.453.0328.
[inspire]
Current progress on the semileptonic form factors for 𝑩̅→𝑫∗lν̅ decay using the Oktay-Kronfeld action
(TanmoyBhattacharya,
Benjamin J.
Choi,
RajanGupta,
Yong-ChullJang,
SungyeobJwa,
SungheeKim,
SunkyuLee,
WeonjongLee,
JaehoonLeem,
JeongwhanPak, and
SungwooPark)
Los Alamos report
LA-UR-23-34204,
ori:oai:arXiv.org:2401.01561 [hep-lat]Proceedings of the
40th
annual International Symposium on Lattice Field Theory,
30July–5August2023,
Fermilab, Batavia, IL, United States.
Eds.
IanCloet,
Aida X.
El-Khadra,
GeorgeFleming,
AndreasKronfeld,
HenryLamm,
JamesOsborn,
James N.
Simone,
MikhailStephanov,
RuthVan de Water,
MichaelWagman, and
YongZhao.
Proceedings of ScienceLATTICE2023
(2024)
245;
ori:doi:10.22323/1.453.0245.
[inspire]
Electroweak box diagrams on the lattice for pion and neutron decay(Jun-SikYoo,
TanmoyBhattacharya,
RajanGupta,
SantanuMondal, and
BoramYoon)Los Alamos report
LA-UR-22-26124,
LA-UR-22-28091, and
LA-UR-22-33079,
ori:oai:arXiv.org:2212.12830 [hep-lat]Proceedings of the
39th
annual International Symposium on Lattice Field Theory,
8–13August2022,
Bonn, Germany.
Eds.
SzabolcsBorsanyi,
StephanDurr,
ZoltanFodor,
AndreasFrommer,
Jana N.
Günther,
ChristianHoelbling,
FrancescoKnechtli,
StephanKrieg,
ThomasLippert,
ThomasLuu,
Uri-GerritMeißner,
DirkPleiter,
AkakiRusetsky,
FernandaSteffens,
EstelaSuarez,
Kálmán K.
Szabó, and
CarstenUrbach.
Proceedings of ScienceLATTICE2022
(2023)
360;
ori:doi:10.22323/1.430.0360.
[inspire]
nEDM from the theta-term and chromoEDM operators(TanmoyBhattacharya,
VincenzoCirigliano,
RajanGupta,
EmanueleMereghetti, and
BoramYoon)Los Alamos report
LA-UR-22-33051,
ori:oai:arXiv.org:2301.08161 [hep-lat]Proceedings of the
40th
annual International Symposium on Lattice Field Theory,
8–13August2022,
Bonn, Germany.
Eds.
SzabolcsBorsanyi,
StephanDurr,
ZoltanFodor,
AndreasFrommer,
Jana N.
Günther,
ChristianHoelbling,
FrancescoKnechtli,
StephanKrieg,
ThomasLippert,
ThomasLuu,
Uri-GerritMeißner,
DirkPleiter,
AkakiRusetsky,
FernandaSteffens,
EstelaSuarez,
Kálmán K.
Szabó, and
CarstenUrbach.
Proceedings of ScienceLATTICE2022
(2023)
304;
ori:doi:10.22323/1.430.0304.
[inspire]
Nucleon form factors and pion-nucleon sigma term(RajanGupta,
TanmoyBhattacharya,
VincenzoCirigliano,
MartinHoferichter,
Yong-ChullJang,
BalintJoo,
EmanueleMereghetti,
SantanuMondal,
SungwooPark,
FrankWinter, and
BoramYoon)Los Alamos report
LA-UR-22-33201,
ori:oai:arXiv.org:2301.07885 [hep-lat]Proceedings of the
39th
annual International Symposium on Lattice Field Theory,
8–13August2022,
Bonn, Germany.
Eds.
SzabolcsBorsanyi,
StephanDurr,
ZoltanFodor,
AndreasFrommer,
Jana N.
Günther,
ChristianHoelbling,
FrancescoKnechtli,
StephanKrieg,
ThomasLippert,
ThomasLuu,
Uri-GerritMeißner,
DirkPleiter,
AkakiRusetsky,
FernandaSteffens,
EstelaSuarez,
Kálmán K.
Szabó, and
CarstenUrbach.
Proceedings of ScienceLATTICE2022
(2023)
427;
ori:doi:10.22323/1.430.0427.
[inspire]
Update on Flavor Diagonal Nucleon Charges(SungwooPark,
TanmoyBhattacharya,
RajanGupta,
Huey-WenLin,
SantanuMondal, and
BoramYoon)ori:oai:arXiv.org:2301.07890 [hep-lat]Proceedings of the
39th
annual International Symposium on Lattice Field Theory,
8–13August2022,
Bonn, Germany.
Eds.
SzabolcsBorsanyi,
StephanDurr,
ZoltanFodor,
AndreasFrommer,
Jana N.
Günther,
ChristianHoelbling,
FrancescoKnechtli,
StephanKrieg,
ThomasLippert,
ThomasLuu,
Uri-GerritMeißner,
DirkPleiter,
AkakiRusetsky,
FernandaSteffens,
EstelaSuarez,
Kálmán K.
Szabó, and
CarstenUrbach.
Proceedings of ScienceLATTICE2022
(2023)
106;
ori:doi:10.22323/1.430.0118.
[inspire]
Abstention in Regression
(CristinaGarcia Cardona,
JamaludinMohd-Yusof, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-22-32066;
Los Alamos report
LA-UR-23-22064;
Proceedings of the
5th International Conference on Uncertainty Quantification in Computational Sciences and Engineering (UNCECOMP 2023),
Athens, Greece12–14June, 2023,
In Review.
Exascale Deep Learning Enabled Precision Medicine for Cancer (CANDLE)
(ThomasBrettin,
RickStevens,
JamalMohd-Yusof,
CristinaGarcia Cardona,
JohnGounley,
GeorgiaTourassi,
AdamMoody,
BrianVan Essen,
FrankAlexander,
JustinWozniak,
FredStreitz, and
TanmoyBhattacharya)
Proceedings of the
2023 Exascale Computing Project Annual Meeting,
17–20January2023,
Houston, TX, USA.
UQ in AI for Science
(TanmoyBhattacharya, and
CristinaGarcia Cardona,
JamaludinMohd-Yusof)
Los Alamos report
LA-UR-22-21448;
In Artificial Intelligence for Science, by
AlokChoudhary,
GeoffreyFox, and
TonyHey,
World Scientific,
2023,
ISBN: 978-981-126-566-2,
doi:10.1142/13123.
AI and Theoretical Particle Physics
(RajanGupta,
TanmoyBhattacharya, and
BoramYoon)
Los Alamos report
LA-UR-22-22125;
ori:oai:arXiv.org:2205.05803 [hep-lat]
In Artificial Intelligence for Science, by
AlokChoudhary,
GeoffreyFox, and
TonyHey,
World Scientific,
2023,
ISBN: 978-981-126-566-2,
doi:10.1142/13123.
[inspire].
Report of the Snowmass 2021 Topical Group on Lattice Gauge Theory
(ZohrehDavoudi,
Ethan T.
Neil,
Christian W.
Bauer,
TanmoyBhattacharya,
ThomasBlum,
PeterBoyle,
Richard C.
Brower,
SimonCatterall,
Norman H.
Christ,
VincenzoCirigliano,
GilbertoColangelo,
CarletonDeTar,
WilliamDetmold,
Robert G.
Edwards,
Aida X.
El-Khadra,
StevenGottlieb,
RajanGupta,
Daniel C.
Hackett,
AnnaHasenfratz,
TakuIzubuchi,
William I.
Jay,
LuchangJin,
ChristopherKelly,
Andreas S.
Kronfeld,
ChristophLehner,
Huey-WenLin,
MeifengLin,
Andrew T.
Lytle,
StefanMeinel,
YannickMeurice,
SwagatoMukherjee,
AmyNicholson,
SasaPrelovsek,
Martin J.
Savage,
Phiala E.
Shanahan,
Ruth S.
Van de Water,
Michael L.
Wagman, and
OliverWitzel)
University of Maryland report
UMD-PP-022-08,
Los Alamos National Laboratory report
LA-UR-22-2931,
Fermilab report
FERMILAB-CONF-22-703-T,
ori:oai:arXiv.org:2209.10758 [hep-lat]
[inspire].
Fundamental Physics in Small Experiments
(T.
Blum,
P.
Winter,
T.
Bhattacharya,
T.Y.
Chen,
V.
Cirigliano,
D.
DeMille,
A.
Gerarchi,
N.R.
Hutzler,
T.M.
Ito,
O.
Kim,
R.
Lehnert,
W.M.
Morse, and
Y.K.
Semertzidis)
Los Alamos report
LA-UR-22-29372.
ori:oai:arXiv.org:2209.08041 [hep-ex]
[inspire].
Lattice QCD and Particle Physics
(Andreas S.
Kronfeld,
TanmoyBhattacharya,
ThomasBlum,
Norman H.
Christ,
CarletonDeTar,
WilliamDetmold,
RobertEdwards,
AnnaHasenfratz,
Huey-WenLin,
SwagatoMukherjee,
KonstantinosOrginos,
RichardBrower,
VincenzoCirigliano,
ZohrehDavoudi,
BálintJóo,
ChulwooJung,
ChristophLehner,
StefanMeinel,
Ethan T.
Neil,
PeterPetreczky,
David G.
Richards,
AlexeiBazavov,
SimonCatterall,
Jozef J.
Dudek,
Aida X.
El-Khadra,
MichaelEngelhardt,
George T.
Fleming,
JoelGiedt,
RajanGupta,
Maxwell T.
Hansen,
TakuIzubuchi,
FritzofKarsch,
JackLaiho,
Keh-FeiLiu,
Aaron S.
Meyer,
EnricoRinaldi,
MartinSavage,
DavidShaich,
Phiala E.
Shanahan,
Stephen R.
Sharpe,
RazaSufian,
SergeySyritsyn,
Ruth S.
Van de Water,
Michael L.
Wagman,
EvanWeinberg,
OliverWitzel,
ChristopherAubin,
PeterBoyle,
ShaileshChandrasekharan,
Ian C.
Clöet,
MarthaConstantinou,
KimmyKushman,
ThomasDeGrand,
ZoltanFodor,
SamForeman,
StevenGottlieb,
DanielHoying,
Yong-ChullJang,
William I.
Jay,
Xiao-YongJin,
ChristopherKelly,
JuliusKuti,
HenryLamm,
MeifengLin,
YinLin,
Andrew T.
Lytle,
PaulMackenzie,
JeffreyMandula,
YannickMeurice,
ChristopherMonahan,
ColinMorningstar,
James C.
Osborn,
SungwooPark,
James N.
Simone,
AlexeiStrelchenko,
MasaakiTomii,
AlejandroVaquero,
PavlosVranas,
BigengWang,
WalterWilcox,
BoramYoon, and
YongZhao)
ori:oai:arXiv.org:2207.07641 [hep-lat]
[inspire].
Learning Not to Answer: Training a Multi-Task Abstaiing Classifier Using PID Control
(JamaludinMohd-Yusof,
SunilThulasidasan,
SayeraDhaubhadel,
CristinaGarcia Cardona, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-21-30329 and
LA-UR-22-23372;
Proceedings of the
SIAM Conference on Uncertainty Quantification (UQ22),
Atlanta, GA, USA12–15April, 2022,
When Abstention Is Really the Best Policy
(SayeraDhaubhadel,
JamaludinMohd-Yusof,
SunilThulasidasan,
KumkumGanguly,
CristinaGarcia Cardona,
BenjaminMcMahon, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-21-30330 and
LA-UR-22-23355;
Proceedings of the
SIAM Conference on Uncertainty Quantification (UQ22),
Atlanta, GA, USA12–15April, 2022,
Qubit Regularization of Asymptotic Freedom(HershSingh,
ShaileshChandrasekharan,
TanmoyBhattacharya,
RajanGupta, and
AlexBuser)Proceedings of the
38th
annual International Symposium on Lattice Field Theory,
26–30July2021,
Ed.
MeifengLin.
Nucleon Form Factors in the Continuum Limit from Clover-on-HISQ Formulation(Yong-ChullJang,
RajanGupta,
TanmoyBhattacharya, and
BoramYoon)Proceedings of the
38th
annual International Symposium on Lattice Field Theory,
26–30July2021,
Ed.
MeifengLin.
Electric dipole moments and the search for new physics
(RicardoAlarcon,
JimAlexander,
VassilisAnastassopoulos,
TakatoshiAoki,
RickBaartman,
StefanBaeßler,
LarryBartoszek,
Douglas H.
Beck,
FrancoBedeschi,
RobertBerger,
MartinBerz,
Hendrick L.
Bethlem,
TanmoyBhattacharya,
MichaelBlaskiewicz,
ThomasBlum,
ThemisBowcock,
AnastasiaBorschevsky,
KevinBrown,
DmitryBudker,
SergeyBurdin,
Brendan C.
Casey,
GianluigiCasse,
GiovanniCantatore,
LanCheng,
TimothyChupp,
VinceCianciolo,
VincenzoCirigliano,
Steven M.
Clayton,
ChrisCrawford,
B. P.
Das,
HoomanDavoudiasl,
Jordy de
Vries,
DavidDeMille,
DmitriDenisov,
Milind V.
Diwan,
John M.
Doyle,
JonathanEngel,
GeorgeFanourakis,
ReneeFatemi,
Bradley W.
Filippone,
Victor V.
Flambaum,
TimoFleig,
NadiaFomin,
WolframFischer,
GeraldGabrielse,
R. F.
Garcia Ruiz,
AntoniosGardikiotis,
ClaudioGatti,
AndrewGeraci,
JamesGooding,
BobGolub,
PeterGraham,
FrederickGray,
W. ClarkGriffith,
SelcukHaciomeroglu,
GeraldGwinner,
StevenHoekstra,
Georg H.
Hoffstaetter,
HaixinHuang,
Nicholas R.
Hutzler,
MarcoIncagli,
Takeyasu M.
Ito,
TakuIzubuchi,
Andrew M.
Jayich,
HoyongJeong,
DavidKaplan,
MarinKaruza,
DavidKawall,
OnKim,
IvanKoop,
WolfgangKorsch,
EkaterinaKorobkina,
ValeriLebedev,
JonathanLee,
SoohyungLee,
RalfLehnert,
Kent K. H.
Leung,
Chen-YuLiu,
JoshuaLong,
AlbertoLusiani,
William J.
Marciano,
MariosMaroudas,
AndreiMatlashov,
NobuyukiMatsumoto,
RichardMawhorter,
FrancoisMeot,
EmanueleMereghetti,
James P.
Miller,
William M.
Morse,
JamesMott,
ZhanibekOmarov,
Luis A.
Orozco,
Christopher M.
O'Shaughnessy,
CenapOzben,
SeongTaePark,
Robert W.
Pattie Jr.Alexander N.
Petrov,
GiovanniMaria Piacentino,
Bradley R.
Plaster,
BorisPodobedov,
MatthewPoelker,
DinkoPocanic,
V. S.
Prasannaa,
JoePrice,
Michael J.
Ramsey-Musolf,
DeepakRaparia,
SurjeetRajendran,
MatthewReece,
AustinReid,
SergioRescia,
AdamRitz,
B. LeeRoberts,
Marianna S.
Safronova,
YasuhiroSakemi,
PhilippSchmidt-Wellenburg,
AndreaShindler,
Yannis K.
Semertzidis,
AlexanderSilenko,
Jaideep T.
Singh,
Leonid V.
Skripnikov,
AmarjitSoni,
EdwardStephenson,
RiadSuleiman,
AyakiSunaga,
MichaelSyphers,
SergeySyritsyn,
M. R.
Tarbutt,
PiaThoerngren,
Rob G. E.
Timmermans,
VolodyaTishchenko,
Anatoly V.
Titov,
NikolaosTsoupas,
SpyrosTzamarias,
AlessandroVariola,
GrazianoVenanzoni,
EvaVilella,
JoostVossebeld,
PeterWinter,
EunilWon,
AnatoliZelenski,
TanyaZelevinsky,
YanZhou, and
KonstantinZioutas)
Los Alamos report
LA-UR-22-22083;
ori:oai:arXiv.org:2203.08103 [hep-ph]
[inspire].
Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-COV-2 mutations on viral transmissinility or
Matters Arising. Response to “No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2”
by Van Dorp et al. Nature Communication 11:5986 (Nov 25, 2020)
(Elena E.
Giorgi,
TanmoyBhattacharya,
WillFischer,
HyejinYoon,
WernerAbfalterer, and
BetteKorber)
Los Alamos report
LA-UR-21-20393.
bioRxiv 2021.01.29.428535 ori:doi:10.1101/2021.01.29.428535Rejected.
Quantum Simulation of Quantum Field Theory with Qubit Models(AlexBuser,
TanmoyBhattacharya,
ShaileshChandraskharan,
HershdeepSingh,
RajanGupta)Bulletin of the American Physical Society,65:1
(2020)
Abstract F90.00002;
APS March Meeting 2020,
Denver, Colorado, USA,
2–6March2020.
Knows When it Doesn't Know: Deep Abstaining Classifiers
(SunilThulasidasan,
TanmoyBhattacharya,
JeffreyBilmes,
GopinathChennupati, and
JamalMohd-Yusof)
7th International Conference on Learning Representations,
New Orleans, Lousiana, USA6–9May, 2019.
Conference Paper 1381.Rejected.
Uncertainty Quantification Analysis of Data-Driven Models of Cancer Cell Line Response
(Jonathan E.
Allen,
MarianAnghel,
TanmoyBhattacharya,
ThomasBrettin,
Jason D.
Gans,
CristinaGarcia-Cardona,
Nicolas W.
Hengartner,
SergeiMaslov,
Rick L.
Stevens, and
FangfangXia)
30th Anniversary American Association for Cancer Research Special Conference—Convergence:
Artificial Intelligence, Big Data and Prediction in Cancer,
Newport, Rhode Island, USA14–17October, 2018.
Poster B40.
Do not measure correlated observables, but train an artificial intelligence to predict them(BoramYoon and
TanmoyBhattacharya)Proceedings of the
36th
annual International Symposium on Lattice Field Theory,
Michigan State University, East Lansing, Michigan, USA,
22–28July2018.
Proceedings of ScienceLATTICE2018
(2019)
Unpublished
Uncertainty Quantification: Characterizing the Sources of Error in
Automated Information Extraction from Pathology Reports
(BenjaminMcMahon,
KumkumGanguly,
NicolasHengartner,
Xiao-ChengWu,
LynnePenberthy,
BlairChristian, and
TanmoyBhattacharya)
North American Association for Central Cancer Registries Annual Conference 2018,
Pittsburgh, Pennsylvania, USA9–14June, 2018.
Presentation 1C1.
Using SEER Data to Develop Synthetic Cancer Trajectories that Enable
Cancer Research
(SarahMichalak,
NicolasHengartner,
KumkumGanguly,
BenMcMahon,
TanmoyBhattacharya,
BlairChristian,
PaulFearn,
DonnaRivera,
Xiao-ChengWu, and
LynnePenberthy)
North American Association for Central Cancer Registries Annual Conference 2018,
Pittsburgh, Pennsylvania, USA9–14June, 2018.
Presentation 4B1.
Extracting Breast Cancer Genetic Markers in Pathology Reports using Natural
Language Processing
(GopinathChennupati,
KumkumGanguly,
BenjaminMcMahon,
SunilThulasidasan,
JessicaBoten,
ValentinaPetkov,
LynnePenberthy,
Xiao-ChengWu,
PaulFearn, and
TanmoyBhattacharya)
North American Association for Central Cancer Registries Annual Conference 2018,
Pittsburgh, Pennsylvania, USA9–14June, 2018.
Presentation 4E4.
Quantifying uncertainty in the inference of generalized coalescents
(Timothy C.
Wallstrom,
TanmoyBhattacharya, and
Jon F.
Wilkins)
Los Alamos report
LA-UR-16-27366.
bioRxiv 150342 ori:doi:10.1101/150342
Surveillance in an Era of Emerging Technology and Precision Medicine
(TanmoyBhattacharya)
North American Association for Central Cancer Registries Annual Conference 2018,
Albuquerque, New Mexico, USA16–23June, 2017.
Plenary Presentation 4PL2.
Lattice QCD calculations of transverse momentum-dependent parton
distributions (TMDs).(M. Engelhardt,
B. Musch,
T. Bhattacharya,
J.R. Green,
R. Gupta,
P. Hägler,
S. Krieg,
J. Negele,
A. Pochinsky,
A. Schäfer,
S. Syritsyn,
B. Yoon)Proceedings of the
6th
International Conference on Physics Opportunities at an ElecTron-Ion Collider,
Palaiseau, France,
7–11September2015.
European Physics Journal Web of Conferences112
(2016)
01008;
ori:doi:10.1051/epjconf/201611201008Published 21Mar2016.
[inspire]
Aspects of Lattice QCD Calculations of Transverse
Momentum-Dependent Parton Distributions.
(M. Engelhardt,
B. Musch,
T. Bhattacharya,
J.R. Green,
R. Gupta,
P. Hägler,
S. Krieg,
J. Negele,
A. Polchinsky,
A. Schäfer,
S. Syritsyn, and
B. Yoon)
Proceedings of the
QCD
Evolution 2015,
Jefferson Lab, Newport News, Virgina, USA,
26–30May2015.
Proceedings of ScienceQCDEV2015
(2016)
18;
ori:doi:10.22323/1.249.0018
[inspire]
Lattice QCD calculations of nucleon transverse
momentum-dependent parton distributions (TMDs) at 170 MeV pion
mass.
(M. Engelhardt,
B. Musch,
T. Bhattacharya,
R. Gupta,
P. Hägler,
S. Krieg,
J. Negele,
A. Polchinsky,
A. Schäfer,
S. Syritsyn, and
B. Yoon)
Proceedings of the
33rd
International Symposium on Lattice Field Theory,
Kobe, Japan,
14–18July2015.
Proceedings of ScienceLATTICE 2015
(2016)
117;
ori:doi:10.22323/1.251.0117
[inspire]
Nucleon transverse momentum-dependent parton
distributions from domain wall fermion calculations
at 297 MeV pion mass.
(MichaelEngelhardt,
BernhardMusch,
TanmoyBhattacharya,
RajanGupta,
PhillipHägler,
JohnNegele,
AndrewPolchinsky,
AndreasSchäfer,
SergeySyritsyn, and
BoramYoon)
Los Alamos report
LA-UR-14-29420,
Jefferson Lab report
JLAB-THY-14-1971.
Proceedings of the
32nd
International Symposium on Lattice Field Theory,
New York, New York, USA,
23–28June2014.
Proceedings of ScienceLATTICE2014
(2015)
167;
ori:doi:10.22323/1.214.0167
[inspire]
Complex Impact of Reversion Mutations and CD8+ T Cell Escape Mutations on HIV-1 Fitness
(HongshuoSong,
TanmoyBhattacharya,
NiluGoonetilleke,
KevinWiehe,
AndrewMcMichael,
GeorgeShaw,
BeatriceHahn,
AlanPerelson,
BartonHaynes, and
FengGao)
Abstract 369 at the
Conference on Retroviruses and
Opportunistic Infections (CROI),
Boston, Massachusetts, USA,
3–6March2014.
The Chiral Transition, Deconfinement, and the Equation of State of QCD
(FrithjofKarsch,
WolfgangSöldner,
A. Bazavov,
T. Bhattacharya,
M. Cheng,
C. DeTar,
H.-T. Ding,
StevenGottlieb,
R. Gupta,
P. Hegde,
U.M. Heller,
E. Laermann,
L. Levkova,
S. Mukherjee,
P. Petreczky,
C. Schmidt,
R.A. Soltz,
R. Sugar,
D. Toussaint,
W. Unger, and
P. Vranas)
Proceedings of the
NIC Symposium,
2012.
18,
15.
Worldline Method for Electromagnetic Casimir Energies.
(JonathanMackrory,
TanmoyBhattacharya, and
DanielSteck)
43rd Annual Meeting of the APS
Division of Atomic, Molecular and Optical Physics,
Orange County, California,
June4–82012.
Bulletin of the American Physical Society57:5
(2012)
BAPS.2012.DAMOP.D1.153.
Genital tract sequestration of SIV during acute infection
(James B.
Whitney,
PeterHraber,
CorinneLuedemann,
TanmoyBhattacharya,
Srinivas S.
Rao,
John R.
Mascola,
Bette T.
Korber,
Gary J.
Nabel, and
Norman L.
Letvin)
Journal of Medical Primatology40:4
(2011)
283.
in ori:doi:10.1111/j.1600-0684.2011.00491.x
Computationally identified mutations suspected to cause gp120 charge inversion and gp41-mediated allosteric effects
impact IgG1b12 suspectibility.
(A.R. Geonnotti,
S. Gnanakaran,
M.G. Daniels,
T. Bhattacharya,
A.S. Lapedes,
B. Korber, and
D.C. Montefiori)
Abstracts from
AIDS Vaccine 2010, Atlanta, Georgia, USA28September–1October, 2010.
Published in
AIDS Research and Human Retroviruses26:10
(Oct15, 2010)
A-1-A-184ori:doi:10.1089/aid.2010.9998
The HotQCD Collaboration
(A. Bazavov,
T. Bhattacharya,
M. Cheng,
N.H. Christ,
C. DeTar,
S. Ejiri,
StevenGottlieb,
R. Gupta,
U.M. Heller,
K. Huebner,
C. JungF. KarschE. LaermannL. LevkovaC. MiaoR.D. MawhinneyP. PetreczkyC. SchmidtR.A. SoltzW. SoeldnerR. SugarD. ToussaintP. Vranas)
Proceeding of
Quark Matter 2009—21st International Conference on
Ultrarelativistic Nucleus-Nucleus Collision,
Nuclear PhysicsA830:1–4
(2009)
958c;
ori:doi:10.1016/j.nuclphysa.2009.10.149.
Available online 10November2009
Quantifying semantic shift for reconstructing language families
(W. Croft,
C. Beckner,
L. Sutton,
J. Wilkins,
T. Bhattacharya, and
D. Hruschka)
Poster presented at the
83rd Annual meeting of the Lingustics Society of America,
San Francisco, California, USA,
2009.
Unpublished
Age-structured Stochastic Model of Intrapatient HIV Evolution
(Elena E Giorgi,
Alan S Perelson, and
(TanmoyBhattacharya)
3rd q-bio Conferencec2.016
P09-21. Deep sequencing of HIV-1 from acute infection: low initial diversity, and rapid but variable CTL escape.
(W. Fischer,
B. Keele,
T. Bhattacharya,
C. Lo,
E. Giorgi,
P. Hraber,
T. Leitner,
C. Han,
C. Gleasner,
L. Green,
B. Hahn,
G. Shaw,
B. Haynes, and
B. Korber)
Abstracts from
AIDS Vaccine 2009,
19–22October, 2009.
Retrovirology6:Suppl 3
(2009)
P401ori:doi:10.1186/1742-4690-6-S3-P401
P04-54. Genetic signature analysis identifies the CD4i region of gp120
as a determinant of broadly NAb responses in HIV-1-infected individuals.
(S. Gnanakaran,
T. Bhattacharya,
M. Daniels,
A. Lapedes,
F. Gao,
A. Kumar,
M. Li,
H. Tang,
K. Greene,
H. Gao,
M. Seaman,
B.F. Haynes,
D.C. Montefiori,
B.T. Korber)
Abstracts from
AIDS Vaccine 2009,
19–22October, 2009.
Retrovirology6:Suppl 3
(2009)
P394ori:doi:10.1186/1742-4690-6-S3-P394
The Petaflops Router: Harnessing FPGAs and Accelerators for
High Performance Computing
(Zachary K.
Baker,
TanmoyBhattacharya,
MarkDunham,
Paul S.
Graham,
RajanGupta,
JeffInman,
AndreasKlein,
Gerd J.
Kunde,
AlMcPherson,
MattStettler, and
Justin L.
Tripp)
Proceedings of the
Thirteenth
Annual Workshop of High Performance Embedded Computing (HPEC 2009),
Lexington, Massachusetts, USA,
22September2009.
Poster A.4.
Computational Approaches to Viral Evolution and Rational Vaccine Design
(TanmoyBhattacharya)
American Physical Society, Four Corners Section of the APS Fall Meeting,
October6–72006Abstract number #B1.001
Rational design of HCV vaccine cocktails that maximize coverage of potential CTL epitopes
(K Yusim,
W Fischer,
S Perkins,
T Bhattacharya,
J Theiler,
T Allen,
G Lauer,
B Korber, and
C Kuiken)
Abstracts from the
12th International Symposium on Viral Hepatitis and Liver Disease,
Paris, France,
July1–5,
2006.
Journal of Clinical Virology36:suppl.2 (Jul2006)
S164—S165.
ori:doi:10.1016/S1386-6532(06)80511-1
HLA-associated sequence polymorphisms in HCV
reveal the reproducibility of immune responses and constraints on
viral evolution.
(J Timm,
B Li,
T Bhattacharya,
MG Daniels,
LL Reyor,
R Allgaier,
T Kuntzen,
W Fischer,
J Duncan,
J Schulzezur Wiesch,
A Kim,
N Frahm,
C Brander,
RT Chung,
GM Lauer,
BT Korber,
BD Walker, and
TM Allen)
Abstracts from the
12th International Symposium on Viral Hepatitis and Liver Disease,
Paris, France,
July1–5,
2006.
Journal of Clinical Virology36:suppl.2 (Jul2006)
S119—S120.
ori:doi:10.1016/S1386-6532(06)80371-9
Recovering classical chaotic dynamics from coupled quantum systems through continuous measurements
(Paul M Alsing,
ShohiniGhose,
IvanDeutsch,
SalmanHabib,
TanmoyBhattacharya, and
KurtJacobs)
34th Meeting of the Division of Atomic, Molecular and Optical Physics,
Boulder, Colorado, USA,
May20–242003Abstract number #H5.009
Recovering the Classical Limit of a System with Spin via Continuous Measurement.
(ShohiniGhose,
IvanDeutsch,
PaulAlsing,
KurtJacobs,
TanmoyBhattacharya, and
SalmanHabib)
Proceedings of
American Physical Society, 2002 Division of Atomic,
Molecular, and Optical,
Abstract #L4.004
Tracking the Worldwide Subtype C Epidemic
(C Kuiken,
UR Smith,
D Lang,
T Bhattacharya)
9th Conference on Retroviruses and Opportunistic Infections,
Seattle, Washington, USA,
February24–282002Abstract number 18 (N45e)
The Evolutionary and Biogeographic History of HIV-1 Subtype C
(UR Smith,
CL Kuiken,
T Bhattacharya)
Los Alamos report
LA-UR-01-4292,
2001.
AIDS vaccine 2001,
Philadelphia, Pennsylvania, USA,
September5–82001Abstract number 264 (Page 112)
Continuous measurement and the classical limit of the motion of an atom in a magneto-optical double-well potential.
(S. Ghose,
P.M. Alsing,
I.H. Deutsch,
K. Jacobs,
T. Bhattacharya,
S. Habib)
Proceedings of the
Quantum Electronics and Laser Science Conference.
May11, 2001,
Baltimore, MD, USA
Conference Edition-6 91–92.
ori:doi:10.1109/QELS.2001.961897.
Detailed analysis of the evolution of HIV-1 subtype C
(C Kuiken,
BT Korber,
B Foley, and
T Bhattacharya)
Proceedings of the
2000 International Meeting of Institute of Human Virology,
Baltimore, Maryland, USA,
2000.
Journal of Human Virology3:5
(Sep–Oct2000)
272.
Timing the origin of the HIV-1 pandemic
(B Korber,
M Muldoon,
J Theiler,
F Gao,
R Gupta,
A Lapedes,
BH Hahn,
S Wolinsky, and
T Bhattacharya)
7th Annual Conference on Retroviruses and Opportunisitic Infections,
San Francisco, California, USA,
June2000.
Light Fermion Masses from Lattice QCD.
(T. Bhattacharya)
Proceedings of
American Physical Society, APS/AAPT Joint April Meeting,
Columbus, Ohio, USA,
18–21April1998,
Abstract #3WK.06
Hadron Spectroscopy with NRQCD b quarks.
(C. Davies,
A. Ali Khan,
J. Shigemitsu,
J. Sloan,
S. Collins,
T. Bhattacharya, and
R. Gupta)
Proceedings of
American Physical Society, APS/AAPT Joint April Meeting,
Columbus, Ohio, USA,
18–21April1998,
Abstract #M16.84
Semileptonic form factors from lattice QCD.
(T. Bhattacharya and
R. Gupta)
Los Alamos report
LA-UR-94-3079,
August 1994.ori:oai:arXiv.org:hep-ph/9409284
Proceedings of
1994
Meeting of the
American Physical Society, Division of Particles and FieldsDPF94,
Albuquerque, New Mexico,
1995,
World Scientific, Ed.
Sally Seidel
(pages 605–607).
[inspire].
3 citations as of Apr13, 2011.
Some work was meant for peer review, but never completed or published in such a forum, nor formally published in an unrefereed forum. Some of these may, however, be available as preprints and are listed here. Talks at unrefereed conferences that were not published in proceedings or elsewhere are in the previous section, not here, as are papers rejected from conferences that make such papers available on the web.
Identifying Sources of Mismatches in an Abstaining
Classifier for Text Reports on Cancer Pathology
(SayeraDhaubhadel,
JamaludinMohd-Yusof,
KumkumGanguly,
SunilThulasidasan,
NicolasHengartner,
Brent J.
Mumphrey,
Eric B.
Durban,
GeorgiaTourassi,
LindaCoyle,
LynnePenberthy,
BenjaminMcMahon, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-21-29019 and
LA-UR-21-31252.
Proceedings of the
Seventh
Computational Approaches for Cancer Workshop (CAFCW21),
14November2021,
2023Unpublished
A Two-Phase Classifier for Primary Site and Histological Type in Clinical Cancer Text
(GopinathChennupati,
SunilThulasidasan,
BenjaminMcMahon,
KumkumGanguly,
SayeraDhaubhadel,
JamaludinMohd-Yusof,
Nicolas W.
Hengartner,
LynnePenberthy, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-20-273862022Rejected.
A Control Theoretic Approach to Robust Learning in the Presence of Label Noise
(SunilThulasidasan,
AqueelJivan,
TanmoyBhattacharya,
GopinathChennupati, and
JeffreyBilmes)
2022Rejected from AISTATS22.
Feature Determinants for Tissue Classification with Transcriptomic Data
(SayeraDhaubhadel,
KumkumGanguly,
TanmoyBhattacharya,
Judith D.
Cohn,
BenjaminMcMahon)2021Incomplete
Towards a more realistic elementary model of language evolution or
Devising Null Models of Lexicostatistics and Glottochronology
(NancyRetzlaff,
MatteoMorini,
ArtemyKolchinsky,
HamzaGiaffar,
AnamariaBerea,
SinaTafazoli,
Peter F.
Stadler,
DavidWolpert,
WilliamCroft,
Richard A.
Blythe, and
TanmoyBhattacharya)
2021Incomplete.
Ensuring consistency of physical laws across scales in large multiscale simulations
(SumantraSarkar,
Yen TingLin,
Sandrasegaram
Gnanakaran,
TanmoyBhattacharya, and
Nicolas W.
Hengartner)
Los Alamos report
LA-UR-20-29949.
2020Incomplete.
Statistical properties of the λ measure of phylogenetic signal
(AnneKandler,
LauraFortunato,
MarkGalassi, and
TanmoyBhattacharya)
Los Alamos report
LA-UR-15-23517,
May11,
2014.
2018Incomplete.
A Theory of Adaptive Systems
(TanmoyBhattacharya and
John H.
Miller)
2017Incomplete.
Event-driven non-cooperative games.
(DavidWolpert,
JustinGrana,
TanmoyBhattacharya,
BrendanTracey and
JamesBono)
2016Rejected subsumes Event-driven non-cooperative games.
(David H.
Wolpert,
TanmoyBhattacharya,
RusselBent,
JoshuaNeil,
AlexanderKent and
AnnaritaGiani)
Los Alamos report
LA-UR-13-22238,
Mar 2013.
Rejected.
Automatic Estimation of Transmitted Founder Variants in
Acute HIV-1 Infection.
(LilyBlair,
Elena E.
Giorgi,
WillFischer,
RanjitWarrier,
SampaSantra,
GeorgeShaw,
BetteKorber, and
TanmoyBhattacharya)
2013Incomplete.
Universal replication and the origins of biological diversity.
(SaraImari Walker and
TanmoyBhattacharya)
Los Alamos report
LA-UR-13-25377July2013.
Rejected.
Computationally-Identified Mutations Suspected to
Cause gp120 Charge Inversion and gp41-Mediated Allosteric Effects
Impact HIV-1 Susceptibility to Neutralization.
(Anthony R.
Geonnotti,
S. Gnanakaran,
Marcus G.
Daniels,
TanmoyBhattacharya,
Alan S.
Lapedes,
BetteKorber, and
David C.
Montefiori),
2011Incomplete.
Maternal and paternal imprinted genes oppositely
influence risk-based decision making
(Claire L.
Dent,
TrevorHumby,
AntoniusPlagge,
TanmoyBhattacharya,
AndrewWard,
Lawrence S.
Wilkinson,
Jon F.
Wilkins, and
Anthony R.
Isles)
Los Alamos report
LA-UR-06-6156,
September2006.
Rejected.
Tapping the Cellular Telephone: processive vs random search
(TanmoyBhattacharya and
AnimeshRay)March1990Rejected.
Comment on “Anomalous weight reduction on a gyroscope's right
rotation around the vertical axis on the Earth”
(D.
Atwood,
T.
Bhattacharya,
M.
Goldhaber, and
A.D.
Jackson)
BNL preprint,
February1990.
Rejected.
Comment on the Claimed Non-observablity of Proton Decay(T.
Bhattacharya)BNL preprint.
February1990Rejected.
Papers by Collaborations
Papers by collaborations to which I belong sometimes include the collaboration, but not me explicitly, as an author. I list those publications here (some peer reviewed, some not). These are usually not considered my publications for bibliometric purposes.
Deep sequential neural network models improve stratification of suicide attempt risk among US veterans
(CarianneMartinez,
DrewLevin,
JessicaJones,
Patrick D.
Finley,
BenjaminMcMahon,
SayeraDhaubhadel,
JudithCohn,
Million Veteran Program,
Million Veteran Program Suicide Exemplar Workgroup
(KhushbuAgarwal,
Allison E Ashley-Koch,
MihaelaAslan,
Jean C Beckham,
EdmondBegoli,
TanmoyBhattacharya,
BenBrown,
Patrick S Calhoun,
Mikaels S Cashman McDevitt,
Kei-HoiCheung,
SutanayChoudhury,
Ashley M Cliff,
Judith D Cohn,
SilviaCrivelli,
LeticiaCuellar-Hengartner,
Haedi E Deangelis,
Michelle F Dennis,
SayeraDhaubhadel,
Patrick D Finley,
KumkumGanguly,
Michael R Garvin,
Joel E Gelernter,
Lauren P Hair,
Phillip D Harvey,
Elizabeth R Hauser,
Michael A Hauser,
Nick W Hengartner,
Daniel A Jacobson,
Piet C Jones,
DavidKainer,
Alan D Kaplan,
Ira R Katz,
Rachel L Kember,
Nathan A Kimbrel,
Angela C Kirby,
John C Ko,
BeautyKolade,
John H Lagergren,
Matthew J Lane,
Daniel F Levey,
DrewLevin,
Jennifer H Lindquist,
XianlianLiu,
Ravi K Madduri,
CarrieManore,
Susana B Martins,
John F McCarthy,
Benjamin H McMahon,
IzaakMiller,
DestineeMorrow,
David W Oslin,
MirkoPavicic-Venegas,
JohnPestian,
SaijuPyarajan,
Xue J Qin,
NallakkandiRajeevan,
Christine M Ramsey,
RuyRibeiro,
JonathanRomero,
AlexRodriguez,
DanielSantel,
NoahSchaefferkoetter,
YunlingShi,
Murray B Stein,
KyleSullivan,
NingSun,
Suzanne R Tamang,
AliceTownsend,
Jodie A Trafton,
AngelicaWalker,
XiangeWang,
VictoriaWangia-Anderson,
RenjiYang,
Hong-JunYoon,
ShinjaeYoo,
RafaelZamora-Resendiz,
HongyuZhao),
David W.
Oslin,
Nathan A.
Kimbrel,
Jean C.
Beckham)
Journal of the American Medical Informatics Association31:1
(Jan1, 2024)
220–230;
ori:doi:10.1093/jamia/ocad167.
Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans
(Nathan A
Kimbrel,
Allison E
Ashley-Koch,
Xue J
Qin,
Jennifer H
Lindquist,
Melanie E
Garrett,
Michelle F
Dennis,
Lauren P
Hair,
Jennifer E
Huffman,
Daniel A
Jacobson,
Ravi K
Madduri,
Jodie A
Trafton,
HilaryCoon,
Anna R
Docherty,
NiamhMullins,
Douglas M
Ruderfer,
Philip D
Harvey,
Benjamin H
McMahon,
David W
Oslin,
Jean C
Beckham,
Elizabeth R
Hauser, and
Michael A
Hauser;
Million Veteran Program Suicide Exemplar Workgroup
(KhushbuAgarwal,
Allison E Ashley-Koch,
MihaelaAslan,
Jean C Beckham,
EdmondBegoli,
TanmoyBhattacharya,
BenBrown,
Patrick S Calhoun,
Kei-HoiCheung,
SutanayChoudhury,
Ashley M Cliff,
Judith D Cohn,
SilviaCrivelli,
LeticiaCuellar-Hengartner,
Haedi E Deangelis,
Michelle F Dennis,
SayeraDhaubhadel,
Patrick D Finley,
KumkumGanguly,
Michael R Garvin,
Joel E Gelernter,
Lauren P Hair,
Phillip D Harvey,
Elizabeth R Hauser,
Michael A Hauser,
Nick W Hengartner,
Daniel A Jacobson,
Piet C Jones,
DavidKainer,
Alan D Kaplan,
Ira R Katz,
Rachel L Kember,
Nathan A Kimbrel,
Angela C Kirby,
John C Ko,
BeautyKolade,
John H Lagergren,
Matthew J Lane,
Daniel F Levey,
DrewLevin,
Jennifer H Lindquist,
XianlianLiu,
Ravi K Madduri,
CarrieManore,
Susana B Martins,
John F McCarthy,
MikaelaMcDevitt-Cashman,
Benjamin H McMahon,
IzaakMiller,
DestineeMorrow,
David W Oslin,
MirkoPavicic-Venegas,
JohnPestian,
SaijuPyarajan,
Xue J Qin,
NallakkandiRajeevan,
Christine M Ramsey,
RuyRibeiro,
AlexRodriguez,
JonathanRomero,
DanielSantel,
NoahSchaefferkoetter,
YunlingShi,
Murray B Stein,
KyleSullivan,
NingSun,
Suzanne R Tamang,
AliceTownsend,
Jodie A Trafton,
AngelicaWalker,
XiangeWang,
VictoriaWangia-Anderson,
RenjiYang,
Hong-JunYoon,
ShinjaeYoo,
RafaelZamora-Resendiz,
HongyuZhao),
the International Suicide Genetics Consortium
(Anna R Docherty,
NiamhMullins,
Jonathan R I Coleman,
AndreyShabalin,
JooEunKang,
BalaszMurnyak,
FrankWendt,
MarkAdams,
Adrian I Campos,
EmilyDiBlasi,
Janice M Fullerton,
Henry R Kranzler,
AmandaBakian,
Eric T Monson,
Miguel E Rentería,
Ole A Andreassen,
Cynthia M Bulik,
Howard J Edenberg,
Ronald C Kessler,
J JohnMann,
John I Nurnberger Jr,
GiorgioPistis,
FabianStreit,
Robert J Ursano,
SwapnilAwasthi,
Andrew W Bergen,
Wade H Berrettini,
MartinBohus,
HarryBrandt,
XiaoChang,
Hsi-ChungChen,
Wei J Chen,
Erik D Christensen,
StevenCrawford,
ScottCrow,
PhilibertDuriez,
Alexis C Edwards,
FernandoFern´ndez-Aranda,
Manfred M Fichter,
HangaGalfalvy,
StevenGallinger,
MichaelGandal,
PhilipGorwood,
YiranGuo,
Jonathan D Hafferty,
HakonHakonarson,
Katherine A Halmi,
AkitoyoHishimoto,
SoniaJain,
StéphaneJamain,
SusanaJiméez-Murcia,
CraigJohnson,
Allan S Kaplan,
Walter H Kaye,
Pamela K Keel,
James L Kennedy,
MinsooKim,
Kelly L Klump,
Daniel F Levey,
DongLi,
Shih-ChengLiao,
KlausLieb,
LisaLilenfeld,
AdrianaLori,
Pierre J Magistretti,
Christian R Marshall,
James E Mitchell,
Richard M Myers,
SatoshiOkazaki,
IkuoOtsuka,
DalilaPinto,
AbigailPowers,
NicolasRamoz,
StephanRipke,
StefanRoepke,
VsevolodRozanov,
Stephen W Scherer,
ChristianSchmahl,
MarcusSokolowski,
AnnaStarnawska,
MichaelStrober,
Mei-HsinSu,
Laura M Thornton,
JanetTreasure,
Erin B Ware,
Hunna J Watson,
Stephanie H Witt,
D BlakeWoodside,
ZeynepYilmaz,
LeaZillich,
EsbenAgerbo,
Anders D Børglum,
GeromeBreen,
DitteDemontis,
AnnetteErlangsen,
TõnuEsko,
JoelGelernter,
Stephen J Glatt,
David M Hougaard,
Hai-GwoHwu,
Po-HsiuKuo,
Cathryn M Lewis,
Qingqin S Li,
Chih-MinLiu,
Nicholas G Martin,
Andrew M McIntosh,
Sarah E Medland,
OleMors,
MereteNordentoft,
John I Nurnberger Jr,
CatherineOlsen,
DavidPorteous,
Daniel J Smith,
Eli A Stahl,
Murray B Stein,
DanutaWasserman,
ThomasWerge,
David C Whiteman,
VirginiaWillour,
HilaryCoon,
Douglas M Ruderfer),
the Veterans Affairs Mid-Atlantic Mental Illness Research, Education, and Clinical Center Workgroup
(EricDedert,
Eric B Elbogen,
John A Fairbank,
Robin A Hurley,
Jason D Kilts,
Sarah L Martindale,
Christine E Marx,
Scott D McDonald,
Scott D Moore,
Rajendra A Morey,
Jennifer C Naylor,
JaredRowland,
Robert D Shura,
CindySwinkels,
Larry A Tupler,
Elizabeth E Van Voorhees,
RuthYoash-Gantz), and
the Veterans Affairs Million Veteran Program
(J MichaelGaziano,
SumitraMuralidhar,
RachelRamoni,
Kyong-MiChang,
Christopher J O'Donnell,
Philip S Tsao,
JamesBreeling,
ElizabethHauser,
YanSun,
GrantHuang,
Juan P Casas,
JenniferMoser,
Stacey B Whitbourne,
Jessica V Brewer,
ToddConner,
Dean P Argyres,
BradyStephens,
Mary T Brophy,
Donald E Humphries,
Luis E Selva,
NhanDo,
Shahpoor AlexShayan,
KellyCho,
LoriChurby,
PeterWilson,
RachelMcArdle,
LouisDellitalia,
KristinMattocks,
JohnHarley,
JeffreyWhittle,
FrankJacono,
JohnWells,
SalvadorGutierrez,
GretchenGibson,
KimberlyHammer,
LaurenceKaminsky,
GerardoVillareal,
ScottKinlay,
JunzheXu,
MarkHamner,
RoyMathew,
SujataBhushan,
PranIruvanti,
MichaelGodschalk,
ZuhairBallas,
DouglasIvins,
StephenMastorides,
JonathanMoorman,
SaibGappy,
JonKlein,
NoraRatcliffe,
HermesFlorez,
OlaoluwaOkusaga,
MaureenMurdoch,
PeruvembaSriram,
Shing ShingYeh,
NeerajTandon,
DarshanaJhala,
SuthatLiangpunsakul,
Kris AnnOursler,
MaryWhooley,
SunilAhuja,
JosephConstans,
PaulMeyer,
JenniferGreco,
MichaelRauchman,
RichardServatius,
MelindaGaddy,
AgnesWallbom,
TimothyMorgan,
ToddStapley,
ScottSherman,
GeorgeRoss,
PatrickStrollo,
EdwardBoyko,
LaurenceMeyer,
SamirGupta,
MostaqulHuq,
JosephFayad,
AdrianaHung,
JackLichy,
RobinHurley,
BrooksRobey,
RobertStriker))
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135–145;
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pmid:36515925;
PMC9857322.
Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program
(Allison E
Ashley-Koch,
Nathan A
Kimbrel,
Xue J
Qin,
Jennifer H
Lindquist,
Melanie E
Garrett,
Michelle F
Dennis,
Lauren P
Hair,
Jennifer E
Huffman,
Daniel A
Jacobson,
Ravi K
Madduri,
HilaryCoon,
Anna R
Docherty,
JooeunKang,
NiamhMullins,
Douglas M
Ruderfer,
the Veterans Affairs Million Veteran Program,
Million Veteran Program Suicide Exemplar Workgroup
(KhushbuAgarwal,
Allison E Ashley-Koch,
MihaelaAslan,
Jean C Beckham,
EdmondBegoli,
TanmoyBhattacharya,
BenBrown,
Patrick S Calhoun,
MikaelaCashman McDevitt,
Kei-HoiCheung,
SutanayChoudhury,
Ashley M Cliff,
Judith D Cohn,
SilviaCrivelli,
LeticiaCuellar-Hengartner,
Haedi E Deangelis,
Michelle F Dennis,
SayeraDhaubhadel,
Patrick D Finley,
KumkumGanguly,
Michael R Garvin,
Joel E Gelernter,
Lauren P Hair,
Phillip D Harvey,
Elizabeth R Hauser,
Michael A Hauser,
Nick W Hengartner,
Daniel A Jacobson,
Piet C Jones,
DavidKainer,
Alan D Kaplan,
Ira R Katz,
Rachel L Kember,
Nathan A Kimbrel,
Angela C Kirby,
John C Ko,
BeautyKolade,
John H Lagergren,
Matthew J Lane,
Daniel F Levey,
DrewLevin,
Jennifer H Lindquist,
XianlianLiu,
Ravi K Madduri,
CarrieManore,
Susana B Martins,
John F McCarthy,
Benjamin H McMahon,
J. IzaakMiller,
DestineeMorrow,
David W Oslin,
MirkoPavicic-Venegas,
JohnPestian,
SaijuPyarajan,
Xue J Qin,
NallakkandiRajeevan,
Christine M Ramsey,
RuyRibeiro,
JonathanRomero,
AlexRodriguez,
DanielSantel,
NoahSchaefferkoetter,
YunlingShi,
Murray B Stein,
KyleSullivan,
NingSun,
Suzanne R Tamang,
AliceTownsend,
Jodie A Trafton,
AngelicaWalker,
XiangeWang,
VictoriaWangia-Anderson,
RenjiYang,
Hong-JunYoon,
ShinjaeYoo,
RafaelZamora-Resendiz,
HongyuZhao),
the International Suicide Genetics Consortium,
Philip D
Harvey,
Benjamin H
McMahon,
David W
Oslin,
Jean C
Beckham,
Elizabeth R
Hauser, and
Michael A
Hauser)Public Library of Science Genetics19:3
(2023)
e1010623;
ori:doi:10.1371/journal.pgen.1010623.
Using iterative random forest to find geospatial environmental and Sociodemographic predictors of suicide attempts
or Using Explainable-AI to Find Geospatial Environmental and Sociodemographic Predictors of Suicide Attempts
(MirkoPavicic,
Angelica M
Walker,
Kyle A
Sullivan,
JohnLagergren,
AshleyCliff,
JonathanRomero,
JaredStreich,
Michael R
Garvin for the
Million Veteran Program Suicide Exemplar Workgroup
(KhushbuAgarwal,
Allison E Ashley-Koch,
MihaelaAslan,
Jean C Beckham,
EdmondBegoli,
TanmoyBhattacharya,
BenBrown,
Patrick S Calhoun,
MikaelaCashman McDevitt,
Kei-HoiCheung,
SutanayChoudhury,
Ashley M Cliff,
Judith D Cohn,
SilviaCrivelli,
LeticiaCuellar-Hengartner,
Haedi E Deangelis,
Michelle F Dennis,
SayeraDhaubhadel,
Patrick D Finley,
KumkumGanguly,
Michael R Garvin,
Joel E Gelernter,
Lauren P Hair,
Phillip D Harvey,
Elizabeth R Hauser,
Michael A Hauser,
Nick W Hengartner,
Daniel A Jacobson,
Piet C Jones,
DavidKainer,
Alan D Kaplan,
Ira R Katz,
Rachel L Kember,
Nathan A Kimbrel,
Angela C Kirby,
John C Ko,
BeautyKolade,
John H Lagergren,
Matthew J Lane,
Daniel F Levey,
DrewLevin,
Jennifer H Lindquist,
XianlianLiu,
Ravi K Madduri,
CarrieManore,
Susana B Martins,
John F McCarthy,
Benjamin H McMahon,
J. IzaakMiller,
DestineeMorrow,
David W Oslin,
MirkoPavicic-Venegas,
JohnPestian,
SaijuPyarajan,
Xue J Qin,
NallakkandiRajeevan,
Christine M Ramsey,
RuyRibeiro,
JonathanRomero,
AlexRodriguez,
DanielSantel,
NoahSchaefferkoetter,
YunlingShi,
Murray B Stein,
KyleSullivan,
NingSun,
Suzanne R Tamang,
AliceTownsend,
Jodie A Trafton,
AngelicaWalker,
XiangeWang,
VictoriaWangia-Anderson,
RenjiYang,
ShinjaeYoo,
Hong-JunYoon,
RafaelZamora-Resendiz,
HongyuZhao),
the Veterans Affairs Million Veteran Program,
JohnPestian,
BenjaminMcMahon,
David W
Oslin,
Jean C
Beckham,
Nathan A
Kimbrel, and
Daniel A
Jacobson)
medRxiv 2022.04.26.22274333 ori:doi:2022.04.26.22274333Frontiers in Psychiatry14
(2023)
1178633;
ori:doi:10.3389/fpsyt.2023.1178633.
pmid:37599888;
PMC10433206.
An examination of the association between altitude and suicide deaths, suicide attempts, and suicidal ideation among veterans at both the patient and geospatial level
(XiangeWang,
RafaelZamora-Resendiz,
Courtney D
Shelley,
CarrieManore,
XinlianLiu,
David W
Oslin,
BenjaminMcMahon,
Jean C
Beckham,
Nathan A
Kimbrel,
Million Veteran Program Suicide Exemplar Workgroup, and
SilviaCrivelli)Journal of Psychiatric Research153
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ori:doi:10.1016/j.jpsychires.2022.07.017.
Continuous-time probabilistic models for longitudinal electronic health records
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Kaplan,
UttaraTipnis,
Jean C
Beckham,
Nathan A
Kimbrel,
David W
Oslin,
Benjamin H
McMahon, and
Million Veteran Program Suicide Exemplar Workgroup
(KhushbuAgarwal,
Allison E Ashley-Koch,
MihaelaAslan,
Jean C Beckham,
EdmondBegoli,
TanmoyBhattacharya,
BenBrown,
Patrick S Calhoun,
MikaelaCashman McDevitt,
Kei-HoiCheung,
SutanayChoudhury,
Ashley M Cliff,
Judith D Cohn,
SilviaCrivelli,
LeticiaCuellar-Hengartner,
Haedi E Deangelis,
Michelle F Dennis,
SayeraDhaubhadel,
Patrick D Finley,
KumkumGanguly,
Michael R Garvin,
Joel E Gelernter,
Lauren P Hair,
Phillip D Harvey,
Elizabeth R Hauser,
Michael A Hauser,
Nick W Hengartner,
Daniel A Jacobson,
Piet C Jones,
DavidKainer,
Alan D Kaplan,
Ira R Katz,
Rachel L Kember,
Nathan A Kimbrel,
Angela C Kirby,
John C Ko,
BeautyKolade,
John H Lagergren,
Matthew J Lane,
Daniel F Levey,
DrewLevin,
Jennifer H Lindquist,
XianlianLiu,
Ravi K Madduri,
CarrieManore,
Susana B Martins,
John F McCarthy,
Benjamin H McMahon,
J. IzaakMiller,
DestineeMorrow,
David W Oslin,
MirkoPavicic-Venegas,
JohnPestian,
SaijuPyarajan,
Xue J Qin,
NallakkandiRajeevan,
Christine M Ramsey,
RuyRibeiro,
JonathanRomero,
AlexRodriguez,
DanielSantel,
NoahSchaefferkoetter,
YunlingShi,
Murray B Stein,
KyleSullivan,
NingSun,
Suzanne R Tamang,
AliceTownsend,
Jodie A Trafton,
AngelicaWalker,
XiangeWang,
VictoriaWangia-Anderson,
RenjiYang,
ShinjaeYoo,
Hong-JunYoon,
RafaelZamora-Resendiz, and
HongyuZhao))
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The QCD equation of state with 2+1 flavors of Highly Improved Staggered Quarks (HISQ)
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The finite temperature phase transition from domain wall fermions
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Proceedings of the
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Fluctuations and Higher Moments of Conserved Charges from the Lattice
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Proceedings of the
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QCD thermodynamics at zero and non-zero density
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Quark Mass Dependence of the QCD Equation of State on N_tau=8 Lattices
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The QCD EoS from simulations on BlueGene L Supercomputers at LLNL and NYBlue
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