Katie Pollard, PhD

Professor in Residence
Epidemiology & Biostatistics
+1 415 734-2711

The Pollard lab develops statistical and computational methods for the analysis of massive biomedical datasets. Our research focuses on emerging technologies for genomics, mass spectrometry, and imaging. We specialize in evolutionary and comparative approaches, including machine-learning integration of diverse types of data and longitudinal models of dynamics in disease and development. Examples of current projects are massively parallel dissection of regulatory networks and decoding cryptic variation in the human microbiome.

Publications: 

Correction to: Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.

Molecular psychiatry

Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S

Differential Etv2 threshold requirement for endothelial and erythropoietic development.

Cell reports

Sinha T, Lammerts van Bueren K, Dickel DE, Zlatanova I, Thomas R, Lizama CO, Xu SM, Zovein AC, Ikegami K, Moskowitz IP, Pollard KS, Pennacchio LA, Black BL

Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.

Molecular psychiatry

Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis.

Scientific reports

Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N

Transcription factor protein interactomes reveal genetic determinants in heart disease.

Cell

Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.

Nature biotechnology

Shi ZJ, Dimitrov B, Zhao C, Nayfach S, Pollard KS

Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes.

Cell reports

Markenscoff-Papadimitriou E, Binyameen F, Whalen S, Price J, Lim K, Ypsilanti AR, Catta-Preta R, Pai EL, Mu X, Xu D, Pollard KS, Nord AS, State MW, Rubenstein JL

Navigating the pitfalls of applying machine learning in genomics.

Nature reviews. Genetics

Whalen S, Schreiber J, Noble WS, Pollard KS

Human gut bacterial metabolism drives Th17 activation and colitis.

Cell host & microbe

Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ

Publisher Correction: Accelerated RNA detection using tandem CRISPR nucleases.

Nature chemical biology

Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA

Single-cell epigenomics reveals mechanisms of human cortical development.

Nature

Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ

Systematic identification of non-canonical transcription factor motifs.

BMC molecular and cell biology

Chumpitaz-Diaz L, Samee MAH, Pollard KS

Accelerated RNA detection using tandem CRISPR nucleases.

Nature chemical biology

Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, IGI Testing Consortium , Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.

Genome research

Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP

Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.

Nature protocols

Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N

A transcriptional switch governs fibroblast activation in heart disease.

Nature

Alexanian M, Przytycki PF, Micheletti R, Padmanabhan A, Ye L, Travers JG, Gonzalez-Teran B, Silva AC, Duan Q, Ranade SS, Felix F, Linares-Saldana R, Li L, Lee CY, Sadagopan N, Pelonero A, Huang Y, Andreoletti G, Jain R, McKinsey TA, Rosenfeld MG, Gifford CA, Pollard KS, Haldar SM, Srivastava D

Caloric restriction disrupts the microbiota and colonization resistance.

Nature

von Schwartzenberg RJ, Bisanz JE, Lyalina S, Spanogiannopoulos P, Ang QY, Cai J, Dickmann S, Friedrich M, Liu SY, Collins SL, Ingebrigtsen D, Miller S, Turnbaugh JA, Patterson AD, Pollard KS, Mai K, Spranger J, Turnbaugh PJ

The gut microbiomes of 180 species.

Science (New York, N.Y.)

Accelerated RNA detection using tandem CRISPR nucleases.

medRxiv : the preprint server for health sciences

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.

Cell

Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M

Building a chemical blueprint for human blood.

Nature

Bradley PH, Pollard KS

Molecular basis of CTCF binding polarity in genome folding.

Nature communications

Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau BG

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

Science (New York, N.Y.)

Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D

Predicting 3D genome folding from DNA sequence with Akita.

Nature methods

Fudenberg G, Kelley DR, Pollard KS

Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.

Proceedings of the National Academy of Sciences of the United States of America

Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA

A unified catalog of 204,938 reference genomes from the human gut microbiome.

Nature biotechnology

Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.

Nature protocols

Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulous-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N

A Chromatin Accessibility Atlas of the Developing Human Telencephalon.

Cell

Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates.

bioRxiv : the preprint server for biology

Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth.

Frontiers in microbiology

Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M

Early Palliative Care Consultation in the Medical ICU: A Cluster Randomized Crossover Trial.

Critical care medicine

Ma J, Chi S, Buettner B, Pollard K, Muir M, Kolekar C, Al-Hammadi N, Chen L, Kollef M, Dans M

Population Genetics in the Human Microbiome.

Trends in genetics : TIG

Garud NR, Pollard KS

Principles of meiotic chromosome assembly revealed in S. cerevisiae.

Nature communications

Schalbetter SA, Fudenberg G, Baxter J, Pollard KS, Neale MJ

Global ecotypes in the ubiquitous marine clade SAR86.

The ISME journal

Hoarfrost A, Nayfach S, Ladau J, Yooseph S, Arnosti C, Dupont CL, Pollard KS

Cooking shapes the structure and function of the gut microbiome.

Nature microbiology

Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design.

Genome biology

Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards.

Nature ecology & evolution

Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR, Ciofi C, Kwok PY, Pollard KS, Bruneau BG

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming.

Cell stem cell

Stone NR, Gifford CA, Thomas R, Pratt KJB, Samse-Knapp K, Mohamed TMA, Radzinsky EM, Schricker A, Ye L, Yu P, van Bemmel JG, Ivey KN, Pollard KS, Srivastava D

The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice.

Science (New York, N.Y.)

Engle DD, Tiriac H, Rivera KD, Pommier A, Whalen S, Oni TE, Alagesan B, Lee EJ, Yao MA, Lucito MS, Spielman B, Da Silva B, Schoepfer C, Wright K, Creighton B, Afinowicz L, Yu KH, Grützmann R, Aust D, Gimotty PA, Pollard KS, Hruban RH, Goggins MG, Pilarsky C, Park Y, Pappin DJ, Hollingsworth MA, Tuveson DA

Empowering statistical methods for cellular and molecular biologists.

Molecular biology of the cell

Pollard DA, Pollard TD, Pollard KS

Evolution of Mechanisms that Control Mating in Drosophila Males.

Cell reports

Ahmed OM, Avila-Herrera A, Tun KM, Serpa PH, Peng J, Parthasarathy S, Knapp JM, Stern DL, Davis GW, Pollard KS, Shah NM

Early-Career Scientists Shaping the World.

mSystems

Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J

Consent insufficient for data release-Response.

Science (New York, N.Y.)

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I

Novel insights from uncultivated genomes of the global human gut microbiome.

Nature

Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides N

Toward unrestricted use of public genomic data.

Science (New York, N.Y.)

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.

PLoS biology

Garud NR, Good BH, Hallatschek O, Pollard KS

Chromatin features constrain structural variation across evolutionary timescales.

Proceedings of the National Academy of Sciences of the United States of America

Fudenberg G, Pollard KS

Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.

Cell

Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.

Proceedings of the National Academy of Sciences of the United States of America

Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes.

mSystems

Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H

A most wanted list of conserved microbial protein families with no known domains.

PloS one

Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS

American Gut: an Open Platform for Citizen Science Microbiome Research.

mSystems

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R

The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation.

Journal of virology

Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JJL

A communal catalogue reveals Earth's multiscale microbial diversity.

Nature

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R

Human evolution: the non-coding revolution.

BMC biology

Franchini LF, Pollard KS

Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice.

mSystems

Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS

Features that define the best ChIP-seq peak calling algorithms.

Briefings in bioinformatics

Thomas R, Thomas S, Holloway AK, Pollard KS

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

Nature genetics

Day FR, Thompson DJ, Helgason H, Chasman DI, Finucane H, Sulem P, Ruth KS, Whalen S, Sarkar AK, Albrecht E, Altmaier E, Amini M, Barbieri CM, Boutin T, Campbell A, Demerath E, Giri A, He C, Hottenga JJ, Karlsson R, Kolcic I, Loh PR, Lunetta KL, Mangino M, Marco B, McMahon G, Medland SE, Nolte IM, Noordam R, Nutile T, Paternoster L, Perjakova N, Porcu E, Rose LM, Schraut KE, Segrè AV, Smith AV, Stolk L, Teumer A, Andrulis IL, Bandinelli S, Beckmann MW, Benitez J, Bergmann S, Bochud M, Boerwinkle E, Bojesen SE, Bolla MK, Brand JS, Brauch H, Brenner H, Broer L, Brüning T, Buring JE, Campbell H, Catamo E, Chanock S, Chenevix-Trench G, Corre T, Couch FJ, Cousminer DL, Cox A, Crisponi L, Czene K, Davey Smith G, de Geus EJCN, de Mutsert R, De Vivo I, Dennis J, Devilee P, Dos-Santos-Silva I, Dunning AM, Eriksson JG, Fasching PA, Fernández-Rhodes L, Ferrucci L, Flesch-Janys D, Franke L, Gabrielson M, Gandin I, Giles GG, Grallert H, Gudbjartsson DF, Guénel P, Hall P, Hallberg E, Hamann U, Harris TB, Hartman CA, Heiss G, Hooning MJ, Hopper JL, Hu F, Hunter DJ, Ikram MA, Im HK, Järvelin MR, Joshi PK, Karasik D, Kellis M, Kutalik Z, LaChance G, Lambrechts D, Langenberg C, Launer LJ, Laven JSE, Lenarduzzi S, Li J, Lind PA, Lindstrom S, Liu Y, Luan J, Mägi R, Mannermaa A, Mbarek H, McCarthy MI, Meisinger C, Meitinger T, Menni C, Metspalu A, Michailidou K, Milani L, Milne RL, Montgomery GW, Mulligan AM, Nalls MA, Navarro P, Nevanlinna H, Nyholt DR, Oldehinkel AJ, O'Mara TA, Padmanabhan S, Palotie A, Pedersen N, Peters A, Peto J, Pharoah PDP, Pouta A, Radice P, Rahman I, Ring SM, Robino A, Rosendaal FR, Rudan I, Rueedi R, Ruggiero D, Sala CF, Schmidt MK, Scott RA, Shah M, Sorice R, Southey MC, Sovio U, Stampfer M, Steri M, Strauch K, Tanaka T, Tikkanen E, Timpson NJ, Traglia M, Truong T, Tyrer JP, Uitterlinden AG, Edwards DRV, Vitart V, Völker U, Vollenweider P, Wang Q, Widen E, van Dijk KW, Willemsen G, Winqvist R, Wolffenbuttel BHR, Zhao JH, Zoledziewska M, Zygmunt M, Alizadeh BZ, Boomsma DI, Ciullo M, Cucca F, Esko T, Franceschini N, Gieger C, Gudnason V, Hayward C, Kraft P, Lawlor DA, Magnusson PKE, Martin NG, Mook-Kanamori DO, Nohr EA, Polasek O, Porteous D, Price AL, Ridker PM, Snieder H, Spector TD, Stöckl D, Toniolo D, Ulivi S, Visser JA, Völzke H, Wareham NJ, Wilson JF, Spurdle AB, Thorsteindottir U, Pollard KS, Easton DF, Tung JY, Chang-Claude J, Hinds D, Murray A, Murabito JM, Stefansson K, Ong KK, Perry JRB

Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites.

Development (Cambridge, England)

Anderson CM, Hu J, Thomas R, Gainous TB, Celona B, Sinha T, Dickel DE, Heidt AB, Xu SM, Bruneau BG, Pollard KS, Pennacchio LA, Black BL

Unboxing cluster heatmaps.

BMC bioinformatics

Engle S, Whalen S, Joshi A, Pollard KS

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.

Cell

Guo CJ, Chang FY, Wyche TP, Backus KM, Acker TM, Funabashi M, Taketani M, Donia MS, Nayfach S, Pollard KS, Craik CS, Cravatt BF, Clardy J, Voigt CA, Fischbach MA

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.

Cell host & microbe

Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA

Urban greenness influences airborne bacterial community composition.

The Science of the total environment

Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.

mBio

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.

PLoS genetics

Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N

Transcriptomic and epigenomic characterization of the developing bat wing.

Nature genetics

Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N

SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells.

eLife

Myers SA, Peddada S, Chatterjee N, Friedrich T, Tomoda K, Krings G, Thomas S, Maynard J, Broeker M, Thomson M, Pollard K, Yamanaka S, Burlingame AL, Panning B

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

Cell

Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MA, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Müller CW, Bruneau BG

Joint mouse-human phenome-wide association to test gene function and disease risk.

Nature communications

Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW

Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.

Molecular biology and evolution

Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.

PLoS computational biology

Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ

MICROBIOME. A unified initiative to harness Earth's microbiomes.

Science (New York, N.Y.)

Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA

Genomic approaches to studying human-specific developmental traits.

Development (Cambridge, England)

Franchini LF, Pollard KS

Can a few non-coding mutations make a human brain?

BioEssays : news and reviews in molecular, cellular and developmental biology

Franchini LF, Pollard KS

Marked seasonal variation in the wild mouse gut microbiota.

The ISME journal

Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.

Nucleic acids research

Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S

Continental-scale distributions of dust-associated bacteria and fungi.

Proceedings of the National Academy of Sciences of the United States of America

Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N

Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency.

Cell

Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.

BMC evolutionary biology

Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA

Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.

Molecular biology and evolution

Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT

Gibbon genome and the fast karyotype evolution of small apes.

Nature

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA

Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.

Translational psychiatry

Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N

Integrating diverse datasets improves developmental enhancer prediction.

PLoS computational biology

Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA

Protective role of HO-1 and carbon monoxide in ethanol-induced hepatocyte cell death and liver injury in mice.

Journal of hepatology

Bakhautdin B, Das D, Mandal P, Roychowdhury S, Danner J, Bush K, Pollard K, Kaspar JW, Li W, Salomon RG, McMullen MR, Nagy LE

Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection.

Journal of virology

Roan NR, Liu H, Usmani SM, Neidleman J, Müller JA, Avila-Herrera A, Gawanbacht A, Zirafi O, Chu S, Dong M, Kumar ST, Smith JF, Pollard KS, Fändrich M, Kirchhoff F, Münch J, Witkowska HE, Greene WC

Exome capture from saliva produces high quality genomic and metagenomic data.

BMC genomics

Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM

A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter.

PloS one

Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS

Many human accelerated regions are developmental enhancers.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS

Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.

Molecular cell

Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.

Science (New York, N.Y.)

Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL

From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.

PloS one

Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.

PLoS genetics

Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A

How old is my gene?

Trends in genetics : TIG

Capra JA, Stolzer M, Durand D, Pollard KS

A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.

Genome biology

Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N

Global marine bacterial diversity peaks at high latitudes in winter.

The ISME journal

Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.

BMC bioinformatics

Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Cell

Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

PLoS computational biology

Capra JA, Williams AG, Pollard KS

Novel bacterial taxa in the human microbiome.

PloS one

Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS

Analysis of human accelerated DNA regions using archaic hominin genomes.

PloS one

Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.

Molecular biology and evolution

Kostka D, Hubisz MJ, Siepel A, Pollard KS

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M

Chromosomal haplotypes by genetic phasing of human families.

American journal of human genetics

Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF

The phylogenetic diversity of metagenomes.

PloS one

Kembel SW, Eisen JA, Pollard KS, Green JL

Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.

Genome biology and evolution

Katzman S, Capra JA, Haussler D, Pollard KS

SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.

Aging

Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E

Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.

PloS one

Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P

Chromatin remodelling complex dosage modulates transcription factor function in heart development.

Nature communications

Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y, Zhou YQ, Yeh RF, Henkelman RM, Harvey RP, Metzger D, Chambon P, Stainier DY, Pollard KS, Scott IC, Bruneau BG

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

PLoS computational biology

Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS

PHAST and RPHAST: phylogenetic analysis with space/time models.

Briefings in bioinformatics

Hubisz MJ, Pollard KS, Siepel A

Noncoding sequences near duplicated genes evolve rapidly.

Genome biology and evolution

Kostka D, Hahn MW, Pollard KS

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.

Molecular biology and evolution

Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH

GC-biased evolution near human accelerated regions.

PLoS genetics

Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D

Detection of nonneutral substitution rates on mammalian phylogenies.

Genome research

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A

A nearly exhaustive search for CpG islands on whole chromosomes.

The international journal of biostatistics

Hsieh F, Chen SC, Pollard K

What makes us human?

Scientific American

Pollard KS

The bovine lactation genome: insights into the evolution of mammalian milk.

Genome biology

Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, Rijnkels M

Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values.

Statistical applications in genetics and molecular biology

Taylor S, Pollard K

Hotspots of biased nucleotide substitutions in human genes.

PLoS biology

Berglund J, Pollard KS, Webster MT

Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.

Journal of bacteriology

Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM

Supervised distance matrices.

Statistical applications in genetics and molecular biology

Pollard KS, van der Laan MJ

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.

Genome research

Holloway AK, Begun DJ, Siepel A, Pollard KS

Gene regulatory networks in lactation: identification of global principles using bioinformatics.

BMC systems biology

Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB

A genome-wide approach to identifying novel-imprinted genes.

Human genetics

Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K

Forces shaping the fastest evolving regions in the human genome.

PLoS genetics

Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D

An RNA gene expressed during cortical development evolved rapidly in humans.

Nature

Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, Haussler D

Discovery of a cool planet of 5.5 Earth masses through gravitational microlensing.

Nature

Beaulieu JP, Bennett DP, Fouqué P, Williams A, Dominik M, Jørgensen UG, Kubas D, Cassan A, Coutures C, Greenhill J, Hill K, Menzies J, Sackett PD, Albrow M, Brillant S, Caldwell JA, Calitz JJ, Cook KH, Corrales E, Desort M, Dieters S, Dominis D, Donatowicz J, Hoffman M, Kane S, Marquette JB, Martin R, Meintjes P, Pollard K, Sahu K, Vinter C, Wambsganss J, Woller K, Horne K, Steele I, Bramich DM, Burgdorf M, Snodgrass C, Bode M, Udalski A, Szymanski MK, Kubiak M, Wieckowski T, Pietrzynski G, Soszynski I, Szewczyk O, Wyrzykowski L, Paczynski B, Abe F, Bond IA, Britton TR, Gilmore AC, Hearnshaw JB, Itow Y, Kamiya K, Kilmartin PM, Korpela AV, Masuda K, Matsubara Y, Motomura M, Muraki Y, Nakamura S, Okada C, Ohnishi K, Rattenbury NJ, Sako T, Sato S, Sasaki M, Sekiguchi T, Sullivan DJ, Tristram PJ, Yock PC, Yoshioka T

The UCSC Archaeal Genome Browser.

Nucleic acids research

Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM

Identifying genetic networks underlying myometrial transition to labor.

Genome biology

Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR

Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives.

Statistical applications in genetics and molecular biology

van der Laan MJ, Dudoit S, Pollard KS

Multiple testing. Part II. Step-down procedures for control of the family-wise error rate.

Statistical applications in genetics and molecular biology

van der Laan MJ, Dudoit S, Pollard KS

Multiple testing. Part I. Single-step procedures for control of general type I error rates.

Statistical applications in genetics and molecular biology

Dudoit S, van der Laan MJ, Pollard KS

Statistical inference for simultaneous clustering of gene expression data.

Mathematical biosciences

Pollard KS, van der Laan MJ