Publications
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Fundamental constraints to the logic of living systems
(2024)
Interface Focus 14 (5), 20240010
PDF
origin of life -
Assembly theory and its relationship with computational complexity
(2024)
arXiv preprint arXiv:2406.12176
PDF
origin of life -
Effectiveness of interventions to reduce COVID-19 transmission in schools
(2024)
Epidemics 47, 100762
COVID-19 -
Optimizing COVID-19 testing strategies on college campuses: evaluation of the health and economic costs
(2023)
PLoS computational biology 19 (12), e1011715
PDF
COVID-19 -
Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
(2023)
Nature communications 14 (1), 7260
PDF
COVID-19 -
Assembly theory explains and quantifies selection and evolution
(2023)
Nature 622 (7982), 321-328
PDF
origin of life -
Protocol for the automatic extraction of epidemiological information via a pre-trained language model
(2023)
STAR protocols 4 (3), 102392
PDF
COVID-19 , methods -
Informing pandemic response in the face of uncertainty. An evaluation of the US COVID-19 Scenario Modeling Hub
(2023)
medRxiv
COVID-19 -
Disproportionate impacts of COVID-19 in a large US city
(2023)
PLoS computational biology 19 (6), e1011149
PDF
COVID-19 -
COVID-19 test allocation strategy to mitigate SARS-CoV-2 infections across school districts
(2023)
Emerging infectious diseases 29 (3), 501
PDF
COVID-19 -
Scenario projections for the spread of SARS-CoV-2 Omicron BA. 4 and BA. 5 subvariants in the US and Texas
(2022)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
Omicron scenario projections for the Austin-Round Rock MSA
(2022)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
COVID-19 scenario projections: The emergence of Omicron in the US-January 2022
(2022)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
Detecting in-school transmission of SARS-CoV-2 from case ratios and documented clusters
(2021)
medRxiv
PDF
COVID-19 -
Early estimates of SARS-CoV-2 B. 1.1. 7 variant emergence in a university setting
(2021)
medRxiv, 2021.03. 05.21252541
PDF
COVID-19 -
The impacts of COVID-19 vaccine timing, number of doses, and risk prioritization on mortality in the US
(2021)
medRxiv
PDF
COVID-19 report -
Potential impacts of statewide relaxation of COVID-19 policies, the B. 1.1. 7 variant, and vaccination in Austin-March 2021
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
COVID-19 scenario projections: the emergence of Omicron in the US
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
Mitigating COVID-19 in schools with face masks and proactive testing
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
COVID-19 projections for the reopening of the University of Texas at Austin in fall of 2021
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
Projecting Need for a COVID-19 Alternative Care Site (ACS) Austin, TX
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
Heterogeneous burden of the COVID-19 pandemic in central Texas
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
COVID-19 alert stages, healthcare projections and mortality patterns in Austin, Texas, May 2021
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 -
Spatial distribution of COVID-19 infections and vaccinations in Austin, Texas
(2021)
UT Austin COVID-19 Modeling Consortium
PDF
COVID-19 report -
Emergence of the B. 1.1. 7 SARS-CoV-2 variant at the University of Texas at Austin-March 5, 2021
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
COVID-19 Campus Introduction Risks for Spring 2021 at the University of Texas at Austin
(2021)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
The COVID-19 herd immunity threshold is not low: a re-analysis of European data from spring of 2020
(2020)
medRxiv, 2020.12. 01.20242289
PDF
COVID-19 preprint -
Comparative cost-effectiveness of SARS-CoV-2 testing strategies
(2020)
medRxiv
COVID-19 -
The impact of asymptomatic COVID-19 infections on future pandemic waves
(2020)
MedRxiv, 2020.06. 22.20137489
PDF
COVID-19 -
Projections for first-wave COVID-19 deaths across the US using social-distancing measures derived from mobile phones
(2020)
Medrxiv, 2020.04. 16.20068163
PDF
COVID-19 -
Potential Impact of Holiday Gatherings on Covid-19 Hospitalizations in Austin
(2020)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
Houston Area COVID-19 School Introduction Risks
(2020)
UT Austin COVID-19 Modeling Consortium
PDF
COVID-19 report -
Texas Trauma Service Area (TSA) COVID-19 transmission estimates and healthcare projections: Oct. 20 update
(2020)
UT Austin COVID-19 Modeling Consortium
PDF
COVID-19 report -
Risks of COVID-19 introductions as schools reopen
(2020)
UT Austin COVID-19 Modeling Consortium
COVID-19 -
COVID-19 campus introduction risks for school reopenings
(2020)
UT Austin COVID-19 Modeling Consortium
PDF
COVID-19 report -
Austin COVID-19 transmission estimates and healthcare projections
(2020)
UT Austin COVID-19 Modeling Consortium
COVID-19 report -
Signalling architectures can prevent cancer evolution
(2020)
Scientific reports 10(1)
PDF
cancer , cooperative behavior -
Effects of COVID-19 vaccination timing and risk prioritization on mortality rates, United States
(2021)
Emerging Infectious Diseases 27(7)
PDF
COVID-19 -
Cost-effective proactive testing strategies during COVID-19 mass vaccination: A modelling study
(2022)
The Lancet Regional Health-Americas 8
PDF
COVID-19 -
Natural Selection beyond Life? A Workshop Report
(2021)
Life 11(10)
PDF
origin of life -
Real-Time Projections of SARS-CoV-2 B. 1.1. 7 Variant in a University Setting, Texas, USA
(2021)
Emerging infectious diseases 27(12)
PDF
COVID-19 -
Real-time pandemic surveillance using hospital admissions and mobility data
(2022)
Proceedings of the National Academy of Sciences 119(7)
PDF
COVID-19 -
Epidemiologic information discovery from open-access COVID-19 case reports via pretrained language model
(2022)
iScience 25(10)
PDF
COVID-19 -
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States
(2022)
Proceedings of the National Academy of Sciences 119(15)
PDF
COVID-19 -
The effectiveness of COVID-19 testing and contact tracing in a US city
(2022)
Proceedings of the National Academy of Sciences 119(34)
PDF
COVID-19 -
On the fitness of informative cues in complex environments
(2021)
Journal of Theoretical Biology 527
PDF
information -
The experience of 2 independent schools with in‐person learning during the COVID‐19 pandemic
(2021)
Journal of School Health 91(5)
PDF
COVID-19 -
Comparative cost-effectiveness of SARS-CoV-2 testing strategies in the USA: a modelling study
(2021)
The Lancet Public Health 6(3)
PDF
COVID-19 -
The complexity of understanding others as the evolutionary origin of empathy and emotional contagion
(2019)
Scientific Reports 9(1)
PDF -
What can Schrödinger’s cat say about 3D printers on Mars?
(2019)
Aeon
origin of life -
Epigenetic inheritance systems contribute to the evolution of a germline.
(2016)
Philos Trans R Soc Lond B Biol Sci 371(1701)
PDF
epigenetics , multicellularity -
Human adaptation and population differentiation in the light of ancient genomes.
(2016)
Nat Commun 7
PDF
ancient DNA -
Excess maternal transmission of variants in the THADA gene to offspring with type 2 diabetes.
(2016)
Diabetologia 59(8)
PDF
ancient DNA -
Selective Strolls: Fixation and Extinction in Diploids Are Slower for Weakly Selected Mutations Than for Neutral Ones.
(2015)
Genetics 201(4)
PDF
popgen -
The complete genome sequence of a Neanderthal from the Altai Mountains
(2014)
Nature 505(7481)
PDF
ancient DNA -
Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans
(2014)
Nature Communications 5(1)
PDF
ancient DNA -
When unreliable cues are good enough.
(2013)
Am Nat 182(3)
PDF
information -
The value of information in signals and cues
(2013)
Animal communication theory
PDF
information -
Great ape genetic diversity and population history
(2013)
Nature 499(7459)
PDF
popgen -
On the role of resonance in drug failure under HIV treatment interruption
(2013)
Theoretical Biology and Medical Modelling 10(1)
PDF -
The bonobo genome compared with the chimpanzee and human genomes
(2012)
Nature 486(7404)
PDF -
Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes
(2012)
PLOS ONE 7(3)
PDF -
'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences
(2012)
BMC Bioinformatics 13(1)
PDF
methods , evolution of differentiation -
Inferring the History of Population Size Change from Genome-Wide SNP Data
(2012)
Molecular Biology and Evolution 29(12)
PDF
popgen -
The adaptive value of developmental plasticity in response to individually variable cues
(2011)
PDF
information , plasticity -
Ant aggression and evolutionary stability in plant–ant and plant–pollinator mutualistic interactions
(2011)
Journal of Evolutionary Biology 24(3)
PDF
ants , cooperative behavior -
Targeted investigation of the Neandertal genome by array-based sequence capture.
(2010)
Science 328(5979)
PDF
ancient DNA, neandertal -
A draft sequence of the Neandertal genome.
(2010)
Science 328(5979)
PDF
neandertal , ancient DNA -
The fitness value of information.
(2010)
Oikos 119(2)
PDF
information -
MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain
(2010)
Genome Research 20(9)
PDF
heterochrony , evolution of differentiation -
The effects of probe binding affinity differences on gene expression measurements and how to deal with them.
(2009)
Bioinformatics (Oxford, England) 25(21)
PDF
methods , gene expression -
The Neandertal genome and ancient DNA authenticity.
(2009)
The EMBO journal 28(17)
PDF
neandertal , ancient DNA -
Transcriptional neoteny in the human brain.
(2009)
Proceedings of the National Academy of Sciences 106(14)
PDF
heterochrony , evolution of differentiation -
Linkage disequilibrium extends across putative selected sites in FOXP2.
(2009)
Molecular Biology and Evolution 26(10)
PDF
popgen -
The fitness value of information
(2009)
PDF
information -
Phenotypic diversity as an adaptation to environmental uncertainty
(2008)
Evolutionary Ecology Research 10(4)
PDF
information , plasticity -
Human and chimpanzee gene expression differences replicated in mice fed different diets.
(2008)
PLoS One 3(1)
PDF
evolution of differentiation -
PatMaN: rapid alignment of short sequences to large databases
(2008)
Bioinformatics 24(13)
PDF
ancient DNA , methods -
Building trust by wasting time
(2008)
Moral markets: The critical role of values in the economy
PDF
cooperative behavior -
The evolution of functionally referential meaning in a structured world.
(2007)
Journal of Theoretical Biology 246(2)
PDF
information -
Patterns of damage in genomic DNA sequences from a Neandertal
(2007)
Proceedings of the National Academy of Sciences 104(37)
PDF
ancient DNA, neandertal -
FUNC: a package for detecting significant associations between gene sets and ontological annotations
(2007)
BMC Bioinformatics 8(1)
PDF
methods , evolution of differentiation -
Evolution of primate gene expression
(2006)
Nature Reviews Genetics 7(9)
evolution of differentiation -
Gene expression becomes heterogeneous with age
(2006)
Current Biology 16(10)
PDF
heterochrony , evolution of differentiation -
Positive selection on gene expression in the human brain
(2006)
Current Biology 16(10)
PDF
evolution of differentiation -
Evolution of primate gene expression
(2006)
Nature Reviews Genetics 7(9)
PDF
evolution of differentiation -
Functionality of Intergenic Transcription: An Evolutionary Comparison
(2006)
PLOS Genetics 2(10)
PDF
evolution of differentiation -
Quasispecies made simple.
(2005)
PLoS Comput Biol 1(6)
PDF
information, popgen -
Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees
(2005)
Science 309(5742)
PDF
evolution of differentiation -
Evolution of Genetic Potential
(2005)
PLOS Computational Biology 1(3)
PDF
popgen -
Shannon information and biological fitness
(2004)
Information Theory Workshop, 2004. IEEE
PDF
information -
The disadvantage of combinatorial communication.
(2004)
Proceedings of the Royal Society of London. Series B: Biological Sciences 271(1555)
PDF
signalling -
The physical limits of communication or Why any sufficiently advanced technology is indistinguishable from noise
(2004)
Am. J. Phys. 72(10)
PDF
fun -
A neutral model of transcriptome evolution.
(2004)
PLoS Biol 2(5)
PDF
evolution of differentiation -
Regional Patterns of Gene Expression in Human and Chimpanzee Brains
(2004)
Genome Research 14(8)
PDF
evolution of differentiation -
Cooperation and Conflict in the evolution of genomes, cells, and multicellular organisms
(2003)
Genetic and cultural evolution of cooperation
PDF
cooperative behavior , multicellularity -
The Red King effect: When the slowest runner wins the coevolutionary race
(2003)
Proceedings of the National Academy of Sciences 100(2)
PDF
popgen -
On the evolution of polygyny: a theoretical examination of the polygyny threshold model
(2003)
Behavioral Ecology 14(2)
PDF
popgen -
Separating equilibria in continuous signalling games
(2002)
Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 357(1427)
PDF
signalling -
Cost and conflict in animal signals and human language
(2001)
Proceedings of the National Academy of Sciences 98(23)
PDF
signalling -
Alarm calls as costly signals of antipredator vigilance: the watchful babbler game
(2001)
Animal Behaviour 61(3)
PDF
signalling -
Role of begging and sibling competition in foraging strategies of nestlings
(2001)
Animal Behaviour 61(4)
PDF
signalling -
On the advantages of information sharing
(2000)
Proceedings of the Royal Society of London. Series B: Biological Sciences 267(1450)
PDF
information , multicellularity -
On the dynamic persistence of cooperation: how lower individual fitness induces higher survivability.
(2000)
J Theor Biol 206(4)
PDF
cooperative behavior , multicellularity -
Who Wins Domineering on Rectangular Boards?
(2000)
arXiv:math/0006066
PDF
fun -
Adopting adoption
(1998)
Animal Behaviour 55(6)
PDF
epigenetics -
Signaling among relatives. III. Talk is cheap
(1998)
Proceedings of the National Academy of Sciences 95(9)
PDF
signalling -
Signalling among Relatives: II. Beyond the Tower of Babel
(1998)
Theoretical Population Biology 54(2)
PDF
signalling -
Signalling among relatives. I. Is costly signalling too costly?
(1997)
Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 352(1353)
PDF
signalling -
The Inheritance of Phenotypes: an Adaptation to Fluctuating Environments
(1996)
Journal of Theoretical Biology 181(1)
PDF
information , epigenetics -
The computationally complete ant colony: Global coordination in a system with no hierarchy
(1995)
European Conference on Artificial Life
PDF
ants , cooperative behavior -
The alternative fitness sets which preserve allele trajectories: a general treatment.
(1994)
Genetics 138(4)
PDF
popgen -
Evidence, mechanisms and models for the inheritance of acquired characters
(1992)
Journal of Theoretical Biology 158(2)
PDF
epigenetics -
Origins of Evolution
(1991)
PDF
origin of life