Katie Pollard, PhD

Bio

Honors and Awards

Publications

• Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons. Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S. Mol Psychiatry. 2022 Apr 28.
• Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community. Lyalina S, Stepanauskas R, Wu F, Sanjabi S, Pollard KS. PLoS One. 2022; 17(4):e0261795.
• Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. Sci Rep. 2022 Apr 01; 12(1):5517.
• CellWalkR: An R Package for integrating and visualizing single-cell and bulk data to resolve regulatory elements. Przytycki PF, Pollard KS. Bioinformatics. 2022 Mar 11.
• Transcription factor protein interactomes reveal genetic determinants in heart disease. 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. Cell. 2022 03 03; 185(5):794-814.e30.
• Fast and accurate metagenotyping of the human gut microbiome with GT-Pro. Shi ZJ, Dimitrov B, Zhao C, Nayfach S, Pollard KS. Nat Biotechnol. 2021 Dec 23.
• Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes. 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. Cell Rep. 2021 12 07; 37(10):110089.
• Navigating the pitfalls of applying machine learning in genomics. Whalen S, Schreiber J, Noble WS, Pollard KS. Nat Rev Genet. 2022 03; 23(3):169-181.
• Human gut bacterial metabolism drives Th17 activation and colitis. Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. Cell Host Microbe. 2022 01 12; 30(1):17-30.e9.
• Publisher Correction: Accelerated RNA detection using tandem CRISPR nucleases. 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. Nat Chem Biol. 2021 Nov; 17(11):1210.
• Single-cell epigenomics reveals mechanisms of human cortical development. 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. Nature. 2021 10; 598(7879):205-213.
• Systematic identification of non-canonical transcription factor motifs. Chumpitaz-Diaz L, Samee MAH, Pollard KS. BMC Mol Cell Biol. 2021 Aug 31; 22(1):44.
• Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science. Smith BJ, Pollard KS. Cell Syst. 2021 09 22; 12(9):839-841.
• Accelerated RNA detection using tandem CRISPR nucleases. 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. Nat Chem Biol. 2021 09; 17(9):982-988.
• Genome-wide variability in recombination activity is associated with meiotic chromatin organization. Jin X, Fudenberg G, Pollard KS. Genome Res. 2021 09; 31(9):1561-1572.
• Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP. Genome Res. 2021 08; 31(8):1433-1446.
• Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. 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. Nat Protoc. 2021 Jul; 16(7):3736.
• A transcriptional switch governs fibroblast activation in heart disease. 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. Nature. 2021 07; 595(7867):438-443.
• Caloric restriction disrupts the microbiota and colonization resistance. 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. Nature. 2021 07; 595(7866):272-277.
• The gut microbiomes of 180 species. Lind AL, Pollard KS. Science. 2021 04 16; 372(6539):238-239.
• Ultraconservation of enhancers is not ultranecessary. Pittman M, Pollard KS. Nat Genet. 2021 04; 53(4):429-430.
• Accelerated RNA detection using tandem CRISPR nucleases. Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, 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 SE, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. medRxiv. 2021 Mar 24.
• Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing. Lind AL, Pollard KS. Microbiome. 2021 03 03; 9(1):58.
• CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues. Przytycki PF, Pollard KS. Genome Biol. 2021 02 14; 22(1):61.
• Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. 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. Cell. 2021 01 21; 184(2):323-333.e9.
• Building a chemical blueprint for human blood. Bradley PH, Pollard KS. Nature. 2020 12; 588(7836):36-37.
• Molecular basis of CTCF binding polarity in genome folding. 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. Nat Commun. 2020 11 05; 11(1):5612.
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. 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, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Science. 2020 12 04; 370(6521).
• Predicting 3D genome folding from DNA sequence with Akita. Fudenberg G, Kelley DR, Pollard KS. Nat Methods. 2020 11; 17(11):1111-1117.
• Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. 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. Proc Natl Acad Sci U S A. 2020 09 08; 117(36):22311-22322.
• A unified catalog of 204,938 reference genomes from the human gut microbiome. 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. Nat Biotechnol. 2021 01; 39(1):105-114.
• lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. 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. Nat Protoc. 2020 08; 15(8):2387-2412.
• A Chromatin Accessibility Atlas of the Developing Human Telencephalon. Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL. Cell. 2020 08 06; 182(3):754-769.e18.
• Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates. 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. bioRxiv. 2020 Apr 18.
• Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M. Front Microbiol. 2020; 11:476.
• phylogenize: correcting for phylogeny reveals genes associated with microbial distributions. Bradley PH, Pollard KS. Bioinformatics. 2020 02 15; 36(4):1289-1290.
• Early Palliative Care Consultation in the Medical ICU: A Cluster Randomized Crossover Trial. Ma J, Chi S, Buettner B, Pollard K, Muir M, Kolekar C, Al-Hammadi N, Chen L, Kollef M, Dans M. Crit Care Med. 2019 12; 47(12):1707-1715.
• Population Genetics in the Human Microbiome. Garud NR, Pollard KS. Trends Genet. 2020 01; 36(1):53-67.
• Principles of meiotic chromosome assembly revealed in S. cerevisiae. Schalbetter SA, Fudenberg G, Baxter J, Pollard KS, Neale MJ. Nat Commun. 2019 10 22; 10(1):4795.
• Global ecotypes in the ubiquitous marine clade SAR86. Hoarfrost A, Nayfach S, Ladau J, Yooseph S, Arnosti C, Dupont CL, Pollard KS. ISME J. 2020 01; 14(1):178-188.
• Cooking shapes the structure and function of the gut microbiome. 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. Nat Microbiol. 2019 12; 4(12):2052-2063.
• AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design. Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS. Genome Biol. 2019 08 15; 20(1):167.
• Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'. Whalen S, Pollard KS. Nat Genet. 2019 08; 51(8):1198-1200.
• Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. 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. Nat Ecol Evol. 2019 08; 3(8):1241-1252.
• Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming. 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. Cell Stem Cell. 2019 07 03; 25(1):87-102.e9.
• The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice. 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. Science. 2019 06 21; 364(6446):1156-1162.
• Empowering statistical methods for cellular and molecular biologists. Pollard DA, Pollard TD, Pollard KS. Mol Biol Cell. 2019 06 01; 30(12):1359-1368.
• Evolution of Mechanisms that Control Mating in Drosophila Males. Ahmed OM, Avila-Herrera A, Tun KM, Serpa PH, Peng J, Parthasarathy S, Knapp JM, Stern DL, Davis GW, Pollard KS, Shah NM. Cell Rep. 2019 05 28; 27(9):2527-2536.e4.
• A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. Armour CR, Nayfach S, Pollard KS, Sharpton TJ. mSystems. 2019 Jul-Aug; 4(4).
• Early-Career Scientists Shaping the World. Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. mSystems. 2019 May 07; 4(3).
• Consent insufficient for data release-Response. 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. Science. 2019 05 03; 364(6439):446.
• New insights from uncultivated genomes of the global human gut microbiome. Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. Nature. 2019 04; 568(7753):505-510.
• Toward unrestricted use of public genomic data. 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. Science. 2019 01 25; 363(6425):350-352.
• Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. Garud NR, Good BH, Hallatschek O, Pollard KS. PLoS Biol. 2019 01; 17(1):e3000102.
• Chromatin features constrain structural variation across evolutionary timescales. Fudenberg G, Pollard KS. Proc Natl Acad Sci U S A. 2019 02 05; 116(6):2175-2180.
• A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. Samee MAH, Bruneau BG, Pollard KS. Cell Syst. 2019 01 23; 8(1):27-42.e6.
• Most chromatin interactions are not in linkage disequilibrium. Whalen S, Pollard KS. Genome Res. 2019 03; 29(3):334-343.
• Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. 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. Cell. 2018 12 13; 175(7):1931-1945.e18.
• Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. 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. Proc Natl Acad Sci U S A. 2018 12 26; 115(52):E12353-E12362.
• Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes. Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H. mSystems. 2018 Sep-Oct; 3(5).
• A most wanted list of conserved microbial protein families with no known domains. Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS. PLoS One. 2018; 13(10):e0205749.
• Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. Bradley PH, Nayfach S, Pollard KS. PLoS Comput Biol. 2018 08; 14(8):e1006242.
• Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages. Kostka D, Holloway AK, Pollard KS. Mol Biol Evol. 2018 08 01; 35(8):2034-2045.
• American Gut: an Open Platform for Citizen Science Microbiome Research. 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, American Gut Consortium , Knight R. mSystems. 2018 May-Jun; 3(3).
• The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation. Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JL. J Virol. 2018 02 01; 92(3).
• A communal catalogue reveals Earth's multiscale microbial diversity. 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, Earth Microbiome Project Consortium. Nature. 2017 11 23; 551(7681):457-463.
• Human evolution: the non-coding revolution. Franchini LF, Pollard KS. BMC Biol. 2017 10 02; 15(1):89.
• Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice. Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS. mSystems. 2017 Sep-Oct; 2(5).
• Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression. Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L. J Dent. 2018 01; 68:72-78.
• Features that define the best ChIP-seq peak calling algorithms. Thomas R, Thomas S, Holloway AK, Pollard KS. Brief Bioinform. 2017 05 01; 18(3):441-450.
• Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. 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, LifeLines Cohort Study, InterAct Consortium, kConFab/AOCS Investigators, Endometrial Cancer Association Consortium, Ovarian Cancer Association Consortium, PRACTICAL consortium, 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. Nat Genet. 2017 Jun; 49(6):834-841.
• Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites. 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. Development. 2017 04 01; 144(7):1235-1241.
• Proteobacteria explain significant functional variability in the human gut microbiome. Bradley PH, Pollard KS. Microbiome. 2017 03 23; 5(1):36.
• Unboxing cluster heatmaps. Engle S, Whalen S, Joshi A, Pollard KS. BMC Bioinformatics. 2017 Feb 15; 18(Suppl 2):63.
• Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. 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. Cell. 2017 01 26; 168(3):517-526.e18.
• Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA. Cell Host Microbe. 2016 Dec 14; 20(6):709-715.
• An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. Genome Res. 2016 11; 26(11):1612-1625.
• Toward Accurate and Quantitative Comparative Metagenomics. Nayfach S, Pollard KS. Cell. 2016 Aug 25; 166(5):1103-1116.
• Urban greenness influences airborne bacterial community composition. Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL. Sci Total Environ. 2016 Nov 15; 571:680-7.
• Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. mBio. 2016 05 13; 7(3).
• Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Whalen S, Truty RM, Pollard KS. Nat Genet. 2016 05; 48(5):488-96.
• Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. PLoS Genet. 2016 Mar; 12(3):e1005738.
• Transcriptomic and epigenomic characterization of the developing bat wing. 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. Nat Genet. 2016 05; 48(5):528-36.
• SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. 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. Elife. 2016 Mar 07; 5:e10647.
• Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. 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. Cell. 2016 Feb 25; 164(5):999-1014.
• Joint mouse-human phenome-wide association to test gene function and disease risk. 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. Nat Commun. 2016 Feb 02; 7:10464.
• Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor. Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. Mol Biol Evol. 2016 Apr; 33(4):1008-18.
• Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. PLoS Comput Biol. 2015 Nov; 11(11):e1004573.
• MICROBIOME. A unified initiative to harness Earth's microbiomes. 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, Unified Microbiome Initiative Consortium. Science. 2015 Oct 30; 350(6260):507-8.
• Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. Haliburton GD, McKinsey GL, Pollard KS. Neurogenetics. 2016 Jan; 17(1):1-9.
• Genomic approaches to studying human-specific developmental traits. Franchini LF, Pollard KS. Development. 2015 Sep 15; 142(18):3100-12.
• Can a few non-coding mutations make a human brain? Franchini LF, Pollard KS. Bioessays. 2015 Oct; 37(10):1054-61.
• Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. Avila-Herrera A, Pollard KS. BMC Bioinformatics. 2015 Aug 25; 16:268.
• MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Nayfach S, Fischbach MA, Pollard KS. Bioinformatics. 2015 Oct 15; 31(20):3368-70.
• Marked seasonal variation in the wild mouse gut microbiota. Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. ISME J. 2015 Nov; 9(11):2423-34.
• Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Nucleic Acids Res. 2015 Jun 23; 43(11):5307-17.
• Continental-scale distributions of dust-associated bacteria and fungi. Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Proc Natl Acad Sci U S A. 2015 May 05; 112(18):5756-61.
• Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Nayfach S, Pollard KS. Genome Biol. 2015 Mar 25; 16:51.
• Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D. Cell. 2015 Mar 12; 160(6):1072-86.
• Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. BMC Evol Biol. 2015 Mar 10; 15:35.
• Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Mol Biol Evol. 2015 May; 32(5):1148-60.
• motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. Kostka D, Friedrich T, Holloway AK, Pollard KS. Stat Interface. 2015; 8(4):463-476.
• Gibbon genome and the fast karyotype evolution of small apes. 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. Nature. 2014 Sep 11; 513(7517):195-201.
• Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. Transl Psychiatry. 2014 Sep 02; 4:e431.
• Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution. Hubisz MJ, Pollard KS. Curr Opin Genet Dev. 2014 Dec; 29:15-21.
• Profile hidden Markov models for the detection of viruses within metagenomic sequence data. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. PLoS One. 2014; 9(8):e105067.
• Integrating diverse datasets improves developmental enhancer prediction. Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. PLoS Comput Biol. 2014 Jun; 10(6):e1003677.
• Protective role of HO-1 and carbon monoxide in ethanol-induced hepatocyte cell death and liver injury in mice. Bakhautdin B, Das D, Mandal P, Roychowdhury S, Danner J, Bush K, Pollard K, Kaspar JW, Li W, Salomon RG, McMullen MR, Nagy LE. J Hepatol. 2014 Nov; 61(5):1029-37.
• Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection. 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. J Virol. 2014 Jul; 88(13):7221-34.
• Exome capture from saliva produces high quality genomic and metagenomic data. 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. BMC Genomics. 2014 Apr 04; 15:262.
• A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. PLoS One. 2014; 9(1):e84689.
• Many human accelerated regions are developmental enhancers. Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. Philos Trans R Soc Lond B Biol Sci. 2013 Dec 19; 368(1632):20130025.
• Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. 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. Mol Cell. 2013 Nov 07; 52(3):314-24.
• Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Science. 2013 Nov 01; 342(6158):621-4.
• From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. PLoS One. 2013; 8(9):e75030.
• A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. PLoS Genet. 2013; 9(8):e1003684.
• How old is my gene? Capra JA, Stolzer M, Durand D, Pollard KS. Trends Genet. 2013 Nov; 29(11):659-68.
• A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. Genome Biol. 2013 Jul 18; 14(7):R72.
• Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis. Riesenfeld SJ, Pollard KS. BMC Genomics. 2013 Jun 22; 14:419.
• Global marine bacterial diversity peaks at high latitudes in winter. Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. ISME J. 2013 Sep; 7(9):1669-77.
• Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. BMC Bioinformatics. 2012 Oct 13; 13:264.
• G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. BMC Bioinformatics. 2012 Sep 28; 13:253.
• Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. 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. Cell. 2012 Sep 28; 151(1):206-20.
• ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. Capra JA, Williams AG, Pollard KS. PLoS Comput Biol. 2012; 8(6):e1002567.
• Novel bacterial taxa in the human microbiome. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. PLoS One. 2012; 7(6):e35294.
• Analysis of human accelerated DNA regions using archaic hominin genomes. Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S. PLoS One. 2012; 7(3):e32877.
• The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Kostka D, Hubisz MJ, Siepel A, Pollard KS. Mol Biol Evol. 2012 Mar; 29(3):1047-57.
• A high-resolution map of human evolutionary constraint using 29 mammals. 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, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, 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, Genome Institute at Washington University, 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. Nature. 2011 Oct 12; 478(7370):476-82.
• Chromosomal haplotypes by genetic phasing of human families. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF. Am J Hum Genet. 2011 Sep 09; 89(3):382-97.
• The phylogenetic diversity of metagenomes. Kembel SW, Eisen JA, Pollard KS, Green JL. PLoS One. 2011; 6(8):e23214.
• Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Katzman S, Capra JA, Haussler D, Pollard KS. Genome Biol Evol. 2011; 3:614-26.
• Substitution patterns are GC-biased in divergent sequences across the metazoans. Capra JA, Pollard KS. Genome Biol Evol. 2011; 3:516-27.
• SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. Aging (Albany NY). 2011 Jun; 3(6):635-42.
• Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P. PLoS One. 2011 Mar 18; 6(3):e17753.
• Chromatin remodelling complex dosage modulates transcription factor function in heart development. 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. Nat Commun. 2011 Feb 08; 2:187.
• PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PLoS Comput Biol. 2011 Jan 20; 7(1):e1001061.
• Novel genes exhibit distinct patterns of function acquisition and network integration. Capra JA, Pollard KS, Singh M. Genome Biol. 2010; 11(12):R127.
• PHAST and RPHAST: phylogenetic analysis with space/time models. Hubisz MJ, Pollard KS, Siepel A. Brief Bioinform. 2011 Jan; 12(1):41-51.
• Noncoding sequences near duplicated genes evolve rapidly. Kostka D, Hahn MW, Pollard KS. Genome Biol Evol. 2010; 2:518-33.
• The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. Mol Biol Evol. 2010 Oct; 27(10):2322-32.
• GC-biased evolution near human accelerated regions. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. PLoS Genet. 2010 May 20; 6(5):e1000960.
• Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes. Taylor SL, Pollard KS. Genet Res (Camb). 2010 Feb; 92(1):39-53.
• Detection of nonneutral substitution rates on mammalian phylogenies. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Genome Res. 2010 Jan; 20(1):110-21.
• A nearly exhaustive search for CpG islands on whole chromosomes. Hsieh F, Chen SC, Pollard K. Int J Biostat. 2009; 5(1).
• What makes us human? Pollard KS. Sci Am. 2009 May; 300(5):44-9.
• The bovine lactation genome: insights into the evolution of mammalian milk. 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. Genome Biol. 2009; 10(4):R43.
• Student engagement in interprofessional working in practice placement settings. Pollard K. J Clin Nurs. 2009 Oct; 18(20):2846-56.
• Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values. Taylor S, Pollard K. Stat Appl Genet Mol Biol. 2009; 8:Article 8.
• Hotspots of biased nucleotide substitutions in human genes. Berglund J, Pollard KS, Webster MT. PLoS Biol. 2009 Jan 27; 7(1):e26.
• Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. J Bacteriol. 2009 Feb; 191(3):782-94.
• Supervised distance matrices. Pollard KS, van der Laan MJ. Stat Appl Genet Mol Biol. 2008; 7(1):Article 33.
• Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. Walker WL, Liao IH, Gilbert DL, Wong B, Pollard KS, McCulloch CE, Lit L, Sharp FR. BMC Genomics. 2008 Oct 20; 9:494.
• Evaluation of two methods to estimate and monitor bird populations. Taylor SL, Pollard KS. PLoS One. 2008 Aug 27; 3(8):e3047.
• Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Holloway AK, Begun DJ, Siepel A, Pollard KS. Genome Res. 2008 Oct; 18(10):1592-601.
• Gene regulatory networks in lactation: identification of global principles using bioinformatics. Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. BMC Syst Biol. 2007 Nov 27; 1:56.
• A genome-wide approach to identifying novel-imprinted genes. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K. Hum Genet. 2008 Jan; 122(6):625-34.
• Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Dreszer TR, Wall GD, Haussler D, Pollard KS. Genome Res. 2007 Oct; 17(10):1420-30.
• Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. Magalhães TR, Palmer J, Tomancak P, Pollard KS. BMC Neurosci. 2007 Jul 31; 8:59.
• Forces shaping the fastest evolving regions in the human genome. 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. PLoS Genet. 2006 Oct 13; 2(10):e168.
• An RNA gene expressed during cortical development evolved rapidly in humans. 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. Nature. 2006 Sep 14; 443(7108):167-72.
• Discovery of a cool planet of 5.5 Earth masses through gravitational microlensing. 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. Nature. 2006 Jan 26; 439(7075):437-40.
• The UCSC Archaeal Genome Browser. Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D407-10.
• Identifying genetic networks underlying myometrial transition to labor. Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Genome Biol. 2005; 6(2):R12.
• Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. van der Laan MJ, Dudoit S, Pollard KS. Stat Appl Genet Mol Biol. 2004; 3:Article15.
• Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. van der Laan MJ, Dudoit S, Pollard KS. Stat Appl Genet Mol Biol. 2004; 3:Article14.
• Multiple testing. Part I. Single-step procedures for control of general type I error rates. Dudoit S, van der Laan MJ, Pollard KS. Stat Appl Genet Mol Biol. 2004; 3:Article13.
• Statistical inference for simultaneous clustering of gene expression data. Pollard KS, van der Laan MJ. Math Biosci. 2002 Mar; 176(1):99-121.

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