Pre-prints
K. Gjoni, X. Ren, A. Everitt, Y. Shen, K.S. Pollard (2024). De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes, BioRxiv. (Link to BioRxiv)
R. Sharma, K.M. Berendzen, A. Everitt, B. Wang, G. Williams, S. Wang, K. Quine, R.D. Larios, K.L. P. Long, N. Hoglen, B.A. Sulaman, M.C. Heath, M. Sherman, M. Kinkel, A. Cai, D. Galo, L.C. Caamal, N.L. Goodwin, A. Beery, K.L. Bales, K.S. Pollard, A.J. Willsey, D.S. Manoli (2024). Oxytocin receptor controls distinct components of pair bonding and development in prairie voles, BioRxiv. (Link to BioRxiv)
4D Nucleome Consortium (2024). An integrated view of the structure and function of the human 4D nucleome, BioRxiv. (Link to BioRxiv)
S. Drusinsky, S. Whalen, K.S. Pollard (2024). Deep-learning prediction of gene expression from personal genomes, BioRxiv. (Link to BioRxiv)
M. Goldman, C. Zhao, K.S. Pollard (2024). Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM), BioRxiv. (Link to BioRxiv)
X. Jin, A.G. Cheng, R. Chanin, F.B. Yu, A. Dimas, M. Jasper, A. Weakley, J. Yan, A.S. Bhatt, K.S. Pollard (2024). Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion, BioRxiv. (Link to BioRxiv)
Z. Hu, P.F. Przytycki, K.S. Pollard (2024). CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations, BioRxiv. (Link to BioRxiv)
B.J. Smith, C. Zhao, V. Dubinkina, X. Jin, J. Moltzau-Anderson, K.S. Pollard (2024). Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC, BioRxiv. (Link to BioRxiv)
N. Sun, N. Teyssier, B. Wang, S. Drake, M. Seyler, Y. Zaltsman, A. Everitt, N. Teerikorpi, H.R. Willsey, H. Goodarzi, R. Tian, M. Kampmann, A.J. Willsey (2024). Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis, BioRxiv. (Link to BioRxiv)
L.M. Gunsalus, M.J. Keiser, K.S. Pollard (2023). ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization, BioRxiv. (Link to BioRxiv)
A. Lind, N.A. McDonald, E.R. Gerrick, A.S. Bhatt, K.S. Pollard (2023). Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology, BioRxiv. (Link to BioRxiv)
P.F. Przytycki, K.S. Pollard (2023). Hierarchical annotation of eQTLs enables identification of genes with cell-type divergent regulation, BioRxiv. (Link to BioRxiv)
C.M. Brand, S. Kuang, E.N. Gilbertson, E. McArthur, K.S. Pollard, T.H. Webster, J.A. Capra (2023). Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees, BioRxiv. (Link to BioRxiv)
IGVF Consortium (2023). The Impact of Genomic Variation on Function (IGVF) Consortium, Arxiv. (Link to Arxiv)
L.M. Gunsalus, E. McArthur, K. Gjoni, S. Kuang, M. Pittman, J.A. Capra, K.S. Pollard (2023). Comparing chromatin contact maps at scale: methods and insights, BioRxiv. (Link to BioRxiv)
S.S. Ranade, S. Whalen, I. Zlatanova, T. Nishino, B. van Soldt, L. Ye, A. Pelonero, L.G. Wallace, Y. Huang, M. Alexanian, A. Padmanabhan, B. Gonzalez-Teran, P. Przytycki, M.W. Costa, C.A. Gifford, B.L. Black, K.S. Pollard, D. Srivastava (2022). Single cell epigenetics reveal cell-cell communication networks in normal and abnormal cardiac morphogenesis, BioRxiv. (Link to BioRxiv)
M. Pittman, K. Lee, D. Srivastava, K.S. Pollard (2022). An oligogenic inheritance test detects risk genes and their interactions in congenital heart defects and developmental comorbidities, BioRxiv. (Link to BioRxiv)
E. McArthur, D.C. Rinker, E.N. Gilbertson, G. Fudenberg, M. Pittman, K. Keough, K.S. Pollard, J.A. Capra (2022). Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence, BioRxiv. (Link to BioRxiv)
A.R. Norman, A.H. Ryu, K. Jamieson, S. Thomas, Y. Shen, N. Ahituv, K.S. Pollard, J.F. Reiter (2021). A Human Accelerated Region is a Leydig cell GLI2 enhancer that affects male-typical behavior, BioRxiv. (Link to BioRxiv)
K.S. Smith, D. Ghosh, K.S. Pollard, S. De (2017). A computational framework for detecting signatures of accelerated somatic evolution in cancer genomes, BioRxiv. (Link to BioRxiv)
J. Ladau, J.L. Green, K.S. Pollard (2017). The geometry of the distance-decay of similarity in ecological communities, BioRxiv. (Link to BioRxiv)
2024
M. Alexanian, A. Padmanabhan, T. Nishino, J.G. Travers, L. Ye, A. Pelonero, C.Y. Lee, N. Sadagopan, Y. Huang, K. Auclair, A. Zhu, Y. An, C.A. Ekstrand, C. Martinez, B.G. Teran, W.R. Flanigan, C.K.S. Kim, K. Lumbao-Conradson, Z. Gardner, L. Li, M.W. Costa, R. Jain, I. Charo, A.J. Combes, S.M. Haldar, K.S. Pollard, R.J. Vagnozzi, T.A. McKinsey, P.F. Przytycki, D. Srivastava (2024). Chromatin remodelling drives immune cell–fibroblast communication in heart failure, Nature. (Link to journal) (Link to BioRxiv)
E.N. Gilbertson, C.M. Brand, E. McArthur, D.C. Rinker, S. Kuang, K.S. Pollard, J.A. Capra (2024). Machine Learning Reveals the Diversity of Human 3D Chromatin Contact Patterns, Molecular Biology and Evolution, 41(10): msae209. (Link to journal) (Link to BioRxiv)
D. Häcker, K. Siebert, B.J. Smith, N. Köhler, A. Riva, A. Mahapatra, H. Heimes, J. Nie, A. Metwaly, H. Hölz, Q. Manz, F.D. Zen, J. Heetmeyer, K. Socas, G.L. Thi, C. Meng, K. Kleigrewe, J.K. Pauling, K. Neuhaus, M. List, K.S. Pollard, T. Schwerd, D. Haller (2024). Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease, Cell Host and Microbe. (Link to journal) (Link to MedRxiv)
S. Shoer, L. Reicher, C. Zhao, K.S. Pollard, Y. Pilpel, E. Segal (2024). Pangenomes of human gut microbiota uncover links between genetic diversity and stress response, Cell Host and Microbe, 32(10): 1744-1757. (Link to journal)
F.W. Lindhout, F.M. Krienen, K.S. Pollard, M.A. Lancaster (2024). A molecular and cellular perspective on human brain evolution and tempo, Nature, 630: 596–608. (Link to journal)
B. Zhang, K.M. Magnaye, E. Stryker, J. Moltzau-Anderson, C.E. Porsche, S. Hertz, K.E. McCauley, B.J. Smith, M. Zydek, K.S. Pollard, A. Ma, N. El-Nachef, S.V. Lynch (2024). Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients, Scientific Reports, 14: 18558. (Link to journal)
L. Pasquini, F.L. Pereira, S. Seddighi, Y. Zeng, Y. Wei, I. Illán-Gala, S.C. Vatsavayai, A. Friedberg, A.J. Lee, J.A. Brown, S. Spina, L.T. Grinberg, D.W. Sirkis, L.W. Bonham, J.S. Yokoyama, A.L. Boxer, J.H. Kramer, H.J. Rosen, J. Humphrey, A.D. Gitler, B.L. Miller, K.S. Pollard, M.E. Ward, W.W. Seeley (2024). Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes, Brain, 147(9): 3032–3047. (Link to journal)
S. Kuang, K.S. Pollard (2024). Exploring the roles of RNAs in chromatin architecture using deep learning, Nature Communications. (Link to journal) (Link to BioRxiv)
K. Gjoni, K.S. Pollard (2024). SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models, Bioinformatics: btae340. (Link to journal) (Link to BioRxiv)
C.T. Mowery, J.W. Freimer, Z. Chen, S. Casaní-Galdón, J.M. Umhoefer, M.M. Arce, K. Gjoni, B. Daniel, K. Sandor, B.G. Gowen, V. Nguyen, D.R. Simeonov, C.M. Garrido, G.L. Curie, R. Schmidt, Z. Steinhart, A.T. Satpathy, K.S. Pollard, J.E. Corn, B.E. Bernstein, C.J. Ye, A. Marson (2024). Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells, Nature Genetics. (Link to journal)
C. Deng, S. Whalen, M. Steyert, R. Ziffra, P.F. Przytycki, F. Inoue, D.A. Pereira, D. Capauto, S. Norton, F.M. Vaccarino, A. Pollen, T.J. Nowakowski, N. Ahituv, K.S. Pollard (2024). Massively parallel characterization of regulatory elements in the developing human cortex, Science, 384: eadh0559. (Link to journal) (Link to BioRxiv)
C. Wen, M. Margolis, R. Dai, P. Zhang, P.F. Przytycki, D.D. Vo, A. Bhattacharya, N. Matoba, C. Jiao, M. Kim, E. Tsai, C. Hoh, N. Aygün, R.L. Walker, C. Chatzinakos, D. Clarke, H. Pratt, PsychENCODE Consortium, M.A. Peters, M. Gerstein, N.P. Daskalakis, Z. Weng, A.E. Jaffe, J.E. Kleinman, T.M. Hyde, D.R. Weinberger, N.J. Bray, N. Sestan, D.H. Geschwind, K. Roeder, A. Gusev, B. Pasaniuc, J.L. Stein, M.I. Love, K.S. Pollard, C. Liu, M.J. Gandal (2024). Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain, Science, 384: eadh0829. (Link to journal) . (Link to MedRxiv)
C. Martyn, B.M. Hayes, D. Lauko, E. Mithun, G. Castaneda, A. Bosco-Lauth, A. Kistler, K.S. Pollard, S. Chou (2024). Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements, mSystems.
(Link to journal) (Link to BioRxiv)
2023
L.M. Gunsalus, M.J. Keiser, K.S. Pollard (2023). In silico discovery of repetitive elements as key sequence determinants of 3D genome folding, Cell Genomics, 3(10): 100410. (Link to journal) (Link to BioRxiv)
Z.J. Shi, S. Nayfach, K.S. Pollard (2023). Maast: genotyping thousands of microbial strains efficiently, Genome Biology, 24: 186. (Link to journal) (Link to BioRxiv) (Earlier Version)
J. Dekker, F. Alber, S. Aufmkolk, B.J. Beliveau, B.G. Bruneau, A.S. Belmont, L. Bintu, A. Boettiger, R. Calandrelli, C.M. Disteche, D.M. Gilbert, T. Gregor, A.S. Hansen, B. Huang, D. Huangfu, R. Kalhor, C.S. Leslie, W. Li, Y. Li, J. Ma, W.S. Noble, P.J. Park, J.E. Phillips-Cremins, K.S. Pollard, S.M. Rafelski, B. Ren, Y. Ruan, Y. Shav-Tal, Y. Shen, J. Shendure, X. Shu, C. Strambio-De-Castillia, A. Vertii, H. Zhang, S. Zhong (2023). Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project, Molecular Cell, 83(15): 2624-2640. (Link to journal)
X. Jin, F.B. Yu, J. Yan, A. Weakley, K.S. Pollard (2023). Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization, Nature Communications, 14: 3510. (Link to journal) (Link to BioRxiv)
A. Bustion, A. Agrawal, P.J. Turnbaugh, K.S. Pollard (2023). SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations, ELife, 12: e82401. (Link to journal) (Link to BioRxiv)
K.C. Keough, S. Whalen, F. Inoue, P.F. Przytycki, T. Fair, C. Deng, M. Steyert, H. Ryu, K. Lindblad-Toh, E. Karlsson, Zoonomia Consortium, T.J. Nowakowski, N.J. Ahituv, A.A. Pollen, K.S. Pollard (2023). Three-dimensional genome re-wiring in loci with Human Accelerated Regions, Science, 380 (6643): abm1696. (Link to journal) (Link to BioRxiv)
P.F. Sullivan, J.R.S. Meadows, S. Gazal, B.D.N. Phan, X. Li, D.P. Genereux, M.X. Dong, M. Bianchi, G. Andrews, S. Sakthikumar, J. Nordin, A. Roy, M.J. Christmas, V.D. Marinescu, C. Wang, O. Wallerman, J.R. Xue, Y. Li, S. Yao, Q. Sun, J. Szatkiewicz, J. Wen, L.M. Huckins, A.J. Lawler, K.C. Keough, Z. Zheng, J. Zeng, N.R. Wray, J. Johnson, J. Chen, Zoonomia Consortium, B. Paten, S.K. Reilly, G.M. Hughes, Z. Weng, K.S. Pollard, A.R. Pfenning, K. Forsberg-Nilsson, E.K. Karlsson, K. Lindblad-Toh (2023). Leveraging base pair mammalian constraint to understand genetic variation and human disease, Science, 380 (6643): abn2937. (Link to journal) (Link to BioRxiv)
M.J. Christmas, I.M. Kaplow, D.P. Genereux, M.X. Dong, G.M. Hughes, X. Li, P.F. Sullivan, A.G. Hindle, G. Andrews, J.C. Armstrong, M. Bianchi, A.M. Breit, M. Diekhans, C. Fanter, N.M. Foley, D.B. Goodman, L. Goodman, K.C. Keough, B. Kirilenko, A. Kowalczyk, C. Lawless, A.L. Lind, J.R.S. Meadows, L.R. Moreira, R.W. Redlich, L. Ryan, R. Swofford, A. Valenzuela, F. Wagner, O. Wallerman, A.R. Brown, J. Damas, K. Fan, J. Gatesy, J. Grimshaw, J. Johnson, S.V. Kozyrev, A.J. Lawler, V.D. Marinescu, K.M. Morrill, A. Osmanski, N.S. Paulat, B.D.N. Phan, S.K. Reilly, D.E. Schäffer, C. Steiner, M.A. Supple, A.P. Wilder, M.E. Wirthlin, J.R. Xue, Zoonomia Consortium, B.W. Birren, S. Gazal, R.M. Hubley, K.-P. Koepfli, T. Marques-Bonet, W.K. Meyer, M. Nweeia, P.C. Sabeti, B. Shapiro, A.F.A. Smit, M. Springer, E. Teeling, Z. Weng, M. Hiller, D.L. Levesque, H.A. Lewin, W.J. Murphy, A. Navarro, B. Paten, K.S. Pollard, D.A. Ray, I. Ruf, O.A. Ryder, A.R. Pfenning, K. Lindblad-Toh, E.K. Karlsson (2023). Evolutionary constraint and innovation across hundreds of placental mammals, Science, 380 (6643): abn3943. (Link to journal) (Link to BioRxiv)
S. Whalen, F. Inoue, H. Ryu, T. Fair, E. Markenscoff-Papadimitriou, K. Keough, M. Kircher, B. Martin, B. Alvarado, O. Elor, D. Laboy Cintron, A. Williams, Md.A.H. Samee, S. Thomas, R. Krencik, E.M. Ullian, A. Kriegstein, J. Shendure, A.A. Pollen, N. Ahituv, K.S. Pollard (2023). Machine-learning dissection of Human Accelerated Regions in primate neurodevelopment, Neuron, 111 (6): 857-873. (Link to journal) (Link to BioRxiv) (Earlier version)
M. Yu, M. Aguirre, M. Jia, K. Gjoni, A. Cordova-Palomera, C. Munger, D. Amgalan, X. R. Ma, A. Pereira, C. Tcheandjieu, C. Seidman, J. Seidman, M. Tristani-Firouzi, W. Chung, E. Goldmuntz, D. Srivastava, R.J.F. Loos, N. Chami, H. Cordell, M. Dreßen, B. Mueller-Myhsok, H. Lahm, M. Krane, K.S. Pollard, J.M. Engreitz, S.A.G. Taliun, B.D. Gelb, J.R. Priest (2023). Oligogenic architecture of rare noncoding variants distinguishes four congenital heart disease phenotypes, Circulation: Genomic and Precision Medicine, 16(3): 258-266. (Link to journal)
M. Yu, A.R. Harper, M. Aguirre, M. Pittman, C. Tcheandjieu, D. Amgalan, C. Grace, A. Goel, M. Farrall, K. Xiao, J. Engreitz, K.S. Pollard, H. Watkins, J.R. Priest (2023). Genetic determinants of interventricular septal anatomy and the risk of ventricular septal defects and hypertrophic cardiomyopathy, Circulation: Genomic and Precision Medicine, 16(3): 207-215. (Link to journal) (Link to MedRxiv)
C. Zhao, Z.J.Shi, K.S. Pollard (2023). Pitfalls of genotyping microbial communities with rapidly growing genome collections, Cell Systems, 14(2): 160-175. (Link to journal) (Link to BioRxiv)
Z.J. Shi, S. Nayfach, K.S. Pollard (2023). Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro, STAR Protocols, 4(1): 101964. (Link to journal)
P.P. Shah, K.C. Keough, K. Gjoni, G.T. Santini, R.J. Abdill, N.M. Wickramasinghe, C.E. Dundes, A. Karnay, A. Chen, R.E.A. Salomon, P.J. Walsh, S.C. Nguyen, S. Whalen, E.F. Joyce, K.M. Loh, N. Dubois, K.S. Pollard, R. Jain (2023). An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype, Genome Biology, 24: 16. (Link to journal) (Link to BioRxiv)
2022
C. Zhao, B. Dimitrov, M. Goldman, S. Nayfach, K.S. Pollard (2022). MIDAS2: Metagenomic Intra-species Diversity Analysis System, Bioinformatics: btac713. (Link to journal) (Link to BioRxiv)
C. Zhao, M. Goldman, B.J. Smith, K.S. Pollard (2022). Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables, Current Protocols, 2: e604. (Link to journal)(Link to Protocols.io)
S. Whalen, K.S. Pollard (2022). Enhancer function and evolutionary roles of Human Accelerated Regions, Annual Review of Genetics, 56. (Link to journal)
P. Spanogiannopoulos, P.H. Bradley, J. Melamed, Y.N.A. Malig, K.N. Lam, R.R. Gerona, K.S. Pollard, P.J. Turnbaugh (2022). Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism, Nature Microbiology, 7: 1605–1620. (Link to journal) (Link to BioRxiv)
A.P. Blair, R.K. Hu, E.N. Farah, N.C. Chi, K.S. Pollard, P.F. Przytycki, I.S. Kathiriya, B.G. Bruneau (2022). Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis, Bioinformatics Advances, 2(1): vbac051. (Link to journal)(Link to BioRxiv)
B.J. Smith, X. Li, Z.J. Shi, A. Abate, K.S. Pollard (2022). Scalable microbial strain inference in metagenomic data using StrainFacts, Frontiers in Bioinformatics. (Link to journal) (Link to BioRxiv)
T. Sinha, K. Lammerts van Bueren, D.E. Dickel, I. Zlatanova, R. Thomas, C.O. Lizama. S.-M. Xu, A.C. Zovein, K. Ikegami, I.P. Moskowitz, K.S. Pollard, L.A. Pennacchio, B.L. Black (2022). Differential Etv2 threshold requirement for endothelial and erythropoietic development, Cell Reports, 39(9): 110881. (Link to journal)
M. Wagle, M. Zarei, M. Lovett-Barron, K.T. Poston, J. Xu, V. Ramey, K.S. Pollard, D.A. Prober, J. Schulkin, K. Deisseroth, S. Guo (2022). Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons, Molecular Psychiatry, 27: 3777-3793. (Link to journal)
S. Lyalina, R. Stepanauskas, F. Wu, S. Sanjabi, K.S. Pollard (2022). Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community, PLoS ONE, 17(4): e0261795. (Link to journal) (Link to BioRxiv)
B.J. Smith, Y. Piceno, M. Zydek, B. Zhang, L.A. Syriani, J.P. Terdiman, Z. Kassam, A. Ma, S.V. Lynch, K.S. Pollard, N. El-Nachef (2022). Clinical efficacy and increased donor strain engraftment after antibiotic pretreatment in a randomized trial of ulcerative colitis patients receiving fecal microbiota transplant, Scientific Reports, 12: 5517. (Link to journal) (Link to MedRxiv)
L. Zhu, K. Choudhary, B. Gonzalez-Teran, Y.-S. Ang, R. Thomas, N.R. Stone, L. Liu, P. Zhou, C. Zhu, H. Ruan, Y. Huang, S. Jin, A. Pelonero, F. Koback, A. Padmanabhan, N. Sadagopan, A. Hsu, M.W. Costa, C.A. Gifford, J.G. van Bemmel, R. Hüttenhain, V. Vedantham, B.R. Conklin, B.L. Black, B.G. Bruneau, L. Steinmetz, N.J. Krogan, K.S. Pollard, D. Srivastava (2022). Transcription Factor GATA4 Regulates Cell Type–Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell–Derived Cardiac Progenitors, Circulation, 146: 770–787. (Link to journal)
P.F. Przytycki, K.S. Pollard (2022). CellWalkR: An R Package for integrating single-cell and bulk data to resolve regulatory elements, Bioinformatics, 38(9): 2621–2623. (Link to journal) (Link to BioRxiv)
R. Pálovics, A. Keller, N. Schaum, W. Tan, T. Fehlmann, M. Borja, F. Kern, L. Bonanno, K. Calcuttawala, J. Webber, A. McGeever, The Tabula Muris Consortium, J. Luo, A.O. Pisco, J. Karkanias, N.F. Neff, S. Darmanis, S.R. Quake, T. Wyss-Coray (2022). Molecular hallmarks of heterochronic parabiosis at single-cell resolution, Nature, 603: 309–314. (Link to journal)
B. Gonzalez-Teran, M. Pittman, F. Felix, D. Richmond-Buccola, R. Thomas, K. Choudhary, E. Moroni, G. Colombo, M. Alexanian, B. Cole, K. Samse-Knapp, M. McGregor, C.A. Gifford, R. Huttenhain, B.D. Gelb, B. Conklin, B.L. Black, B.G. Bruneau, N.J. Krogan, K.S. Pollard, D. Srivastava (2022). Transcription factor protein interactomes reveal genetic determinants in heart disease, Cell, 185: 1–21. (Link to journal) (Link to SSRN) (Highlighted in Nature Reviews Cardiology) (Highlighted in Nature Cardiovascular Research)
S. Whalen, J. Schreiber, W.S. Noble, K.S. Pollard (2022). Navigating the pitfalls of applying machine learning in genomics, Nature Reviews Genetics, 23: 169-181. (Link to journal) (Cover Art)
M. Alexander, Q.Y. Ang, R.R. Nayak, A.E. Bustion, V. Upadhyay, K.S. Pollard, P.J. Turnbaugh (2022). Human gut bacterial metabolism drives Th17 activation and colitis, Cell Host and Microbe, 30(1): 17-30.e9. (Link to journal) (Link to BioRxiv)
Z.J. Shi, B. Dimitrov, C. Zhao, S. Nayfach, K.S. Pollard (2022). Fast and accurate metagenotyping of the human gut microbiome with GT-Pro, Nature Biotechnology, 40: 507–516. (Link to journal) (Link to BioRxiv)
2021
E. Markenscoff-Papadimitriou, F. Binyameen, S. Whalen, J. Price, K. Lim, R. Catta-Preta, E.L. Pai, X. Mu, D. Xu, K.S. Pollard, A. Nord, M.W. State, J.L. Rubenstein (2021). Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes, Cell Reports, 37(10): 110089. (Link to journal) (Link to BioRxiv)
R.S. Ziffra, C.N. Kim, A. Wilfert, T.N. Turner, M. Haeussler, A.M. Casella, P.F. Przytycki, A. Kreimer, K.S. Pollard, S.A. Ament, E.E. Eichler, N. Ahituv, T.J. Nowakowski (2021). Single cell epigenomic atlas of the developing human brain and organoids, Nature, 598: 205–213. (Link to journal) (Link to BioRxiv)
L. Chumpitaz-Diaz, Md.A.H. Samee, K.S. Pollard (2021). Systematic identification of non-canonical transcription factor motifs, BMC Molecular and Cell Biology, 22: 44. (Link to journal)
T.Y. Liu, G.J. Knott, D.C.J. Smock, J.J. Desmarais, S. Son, A. Bhuiya, S. Jakhanwal, N. Prywes, S. Agrawal, M. Díaz de León Derby, N.A. Switz, M. Armstrong, A.R. Harris, E.J. Charles, B.W. Thornton, P. Fozouni, J. Shu, S.I. Stephens, G.R. Kumar, C. Zhao, A. Mok, A.T. Iavarone, A.M. Escajeda, R. McIntosh, S.E. Kim, E.J. Dugan, IGI Testing Consortium, K.S. Pollard, M.X. Tan, M. Ott, D.A. Fletcher, L.F. Lareau, P.D. Hsu, D.F. Savage, J.A. Doudna (2021). Accelerated RNA detection using tandem CRISPR nucleases, Nature Chemical Biology, 17: 982–988. (Link to journal) (Link to MedRxiv)
X. Jin, G. Fudenberg, K.S. Pollard (2021). Genome-wide variability in recombination activity is associated with meiotic chromatin organization, Genome Research, 31: 1561-1572. (Link to journal) (Link to BioRxiv)
M. Roodgar, B.H. Good, N.R. Garud, S. Martis, M. Avula, W. Zhou, S. Lancaster, H. Lee, A. Babveyh, S. Nesamoney, K.S. Pollard, M.P. Snyder (2021). Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment, Genome Research, 31: 1433-1446. (Link to journal) (Link to BioRxiv) (Cover)
R.J. von Schwartzenberg, J.E. Bisanz, S. Lyalina, P. Spanogiannopoulos, Q.Y. Ang, J. Cai, S. Dickmann, M. Friedrich, S.-Y. Liu, S.L. Collins, D. Ingebrigtsen, S. Miller, J.A. Turnbaugh, A.D. Patterson, K.S. Pollard, K. Mai, J. Spranger, P.J. Turnbaugh (2021). Caloric restriction disrupts the microbiota and colonization resistance, Nature, 595: 272–277. (Link to journal)
M. Alexanian, P.F. Przytycki, R. Micheletti, A. Padmanabhan, L. Ye, J.G. Travers, B.G. Teran, Q. Duan, S.S. Ranade, F. Felix, R. Linares-Saldana, Y. Huang, G. Andreoletti, J. Yang, K.N. Ivey, R. Jain, T.A. McKinsey, M.G. Rosenfeld, C. Gifford, K.S. Pollard, S.M. Haldar, D. Srivastava (2021). A transcriptional switch governs fibroblast activation in heart disease, Nature, 595: 438–443. (Link to journal) (Link to BioRxiv)
P.B. Cooch, A. Watson, A. Olarte, E.D. Crawford, J.L. DeRisi, B. Greenhouse, J. Hakim, K. Turcios, K.S. Pollard, L.R. Atkinson-McEvoy, R. Hirsch, R.L. Keller, T.D. Ruel, A. Cohen-Ross, A. Leon, N.S. Bardach (2021). Supervised self-collected SARS-Cov-2 testing in classroom-based summer camps to inform safe in-person learning, Journal of Pediatrics, Perinatology and Child Health, 5: 75-93. (Link to journal)
M. Pittman, K.S. Pollard (2021). Ultraconservation of enhancers is not ultranecessary, Nature Genetics, 53: 29–430. (Link to journal)
A.L. Lind, K.S. Pollard (2021). The gut microbiomes of 180 species, Science, 372: 238-239. (Link to journal)
A.L. Lind, K.S. Pollard (2021). Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data, Microbiome, 9: 58. (Link to journal) (Link to BioRxiv)
P.F. Przytycki, K.S. Pollard (2021). CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues, Genome Biology, 22: 61. (Link to journal) (Link to BioRxiv)
P. Fozouni, S. Son, M.D.L. Derby, G.J. Knott, C.N. Gray, M.V. D’Ambrosio, C. Zhao, N.A. Switz, G.R. Kumar, S.I. Stephens, D. Boehm, C.-L. Tsou, J. Shu, A. Bhuiya, M. Armstrong, A.R. Harris, P.-Y. Chen, J.M. Osterloh, A. Meyer-Franke, B. Joehnk, K. Walcott, A. Sil, C. Langelier, K.S. Pollard, E.D. Crawford, A.S. Puschnik, M. Phelps, A. Kistler, J.L. DeRisi, J.A. Doudna, D.A. Fletcher, M. Ott (2021). Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy, Cell, 184(2): 323-333.e9. (Link to journal) (Link to MedRxiv)
2020
P.H. Bradley, K.S. Pollard (2020). Building a chemical blueprint for human blood, Nature, 588: 36-37. (Link to Nature)
The Tabula Muris Consortium (2020). A single-cell transcriptomic atlas characterizes ageing tissues in the mouse, Nature, 583: 590–595. (Link to Nature)
Zoonomia Consortium (2020). A comparative genomics multitool for scientific discovery and conservation, Nature, 587: 240-245. (Link to Nature) (Press Release)
E.P. Nora, L. Caccianini, G. Fudenberg, V. Kameswaran, A. Nagle, A. Uebersohn, K. So, B. Hajj, A.L. Saux, A. Coulon, L.A. Mirny, K.S. Pollard, M. Dahan, B.G. Bruneau (2020). Molecular basis of CTCF binding polarity in genome folding, Nature Communications, 11: 5612. (Link to Nature) (Link to BioRxiv)
D.E. Gordon, J. Hiatt, …, K.C. Keough, A.L. Lind, … K.S. Pollard, … N. Krogan (2020). Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms, Science, 370: eabe9403. (Link to Science)
G. Fudenberg, D.R. Kelley, K.S. Pollard (2020). Predicting 3D genome folding from DNA sequence with Akita, Nature Methods, 17: 1111–1117. (Link to Nature) (Link to BioRxiv)
J. Damas, G.M. Hughes, K.C. Keough, C.A. Painter, N.S. Persky, M. Corbo, M. Hiller, K.-P. Koepfli, A.R. Pfenning, H. Zhao, D.P. Genereux, R. Swofford, K.S. Pollard, O.A. Ryder, M.T. Nweeia, K. Lindblad-Toh, E.C. Teeling, E.K. Karlsson, H.A. Lewin (2020). Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates, Proceedings of the National Academy of Sciences, 117(36): 22311-22322. (Link to PNAS) (Link to BioRxiv)
M.G. Gordon, F. Inoue, B. Martin, M. Schubach, V. Agarwal, S. Whalen, S. Feng, J. Zhao, T. Ashuach, R. Ziffra, A. Kreimer, I. Georgakopoulous-Soares, N. Yosef, C.J. Ye, K.S. Pollard, J. Shendure, M. Kircher, N. Ahituv (2020). lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements, Nature Protocols, 15: 2387–2412. (Link to Nature)
E. Markenscoff-Papadimitriou, S. Whalen, P. Przytycki, R. Thomas, F. Binyameen, T.J. Nowakowski, S.J. Sanders, M.W. State, K.S. Pollard, J.L. Rubenstein (2020). A chromatin accessibility atlas of the developing human telencephalon, Cell, 182(3): 754-769.e18. (Link to Cell) (Link to BioRxiv)
A. Almeida, S. Nayfach, M. Boland, F. Strozzi, M. Beracochea, Z.J. Shi, K.S. Pollard, D.H. Parks, P. Hugenholtz, N. Segata, N.C. Kyrpides, R.D. Finn (2020). A unified catalog of 204,938 reference genomes from the human gut microbiome, Nature Biotechnology, 39: 105–114. (Link to Nature) (Link to BioRxiv)
I. Kosti, S. Lyalina, K.S. Pollard, A.J. Butte, M. Sirota (2020). Meta-Analysis of vaginal microbiome data provides new insights into preterm birth, Frontiers in Microbiology, 11:476. (Link to Frontiers)
P.H. Bradley, K.S. Pollard (2020). phylogenize: correcting for phylogeny reveals genes associated with microbial distributions, Bioinformatics, 36(4): 1289-1290. (Link to Bioinformatics) (Link to BioRxiv)
2019
N.G. Garud, K.S. Pollard (2019). Population Genetics in the Human Microbiome, Trends in Genetics, 36(1): 53-67. (Link to TIG)
S.A. Schalbetter, G. Fudenberg, J. Baxter, K.S. Pollard, M.J. Neale (2019). Principles of meiotic chromosome assembly revealed in S. cerevisiae, Nature Communications, 10: article 4795. (Link to Nature) (Link to BioRxiv) (Editor’s Highlight)
A. Hoarfrost, S. Nayfach, J. Ladau, S. Yooseph, C. Arnosti, C.L. Dupont, K.S. Pollard (2019). Global ecotypes in the ubiquitous marine clade SAR86, ISME Journal, 14: 178-188. (Link to ISME) (Link to BioRxiv)
R.N. Carmody, J.E. Bisanz, B.P. Bowen, C.F. Maurice, S. Lyalina, K.B. Louie, D. Treen, K.S. Chadaideh, V.M. Rekdal, E.N. Bess, P. Spanogiannopoulos, Q.Y. Ang, K.C. Bauer, T.W. Balon, K.S. Pollard, T.R. Northen, P.J. Turnbaugh (2019). Cooking shapes the structure and function of the gut microbiome, Nature Microbiology, 4: 2052–2063. (Link to Nature)
K.C. Keough, S. Lyalina, M.P. Olvera, S. Whalen, B.R. Conklin, K.S. Pollard (2019). AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design, Genome Biology, 20: article 167. (Link to Genome Biology) (Link to BioRxiv)
S. Whalen, K.S. Pollard (2019). Reply to ‘Inflated performance measures in enhancer–promoter interaction-prediction methods’, Nature Genetics, 51: 1198–1200. (Link to Nature)
A. Lind, Y.Y.Y. Lai, Y. Mostovoy, A.K. Holloway, A. Iannucci, A.C.Y. Mak, M. Fondi, V. Orlandini, W.L. Eckalbar, M. Milan, M. Rovatsos, I.G. Kichigin, A.I. Makunin, V. Trifonov, E. Schijlen, L. Kratochvil, R. Fani, T.S. Jessop, T. Patarnello, J.W. Hicks, O.A. Ryder, J.R. Mendelson III, C. Ciofi, P.-Y.A. Kwok, K. S. Pollard, B. Bruneau (2019). Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards, Nature Evolution and Ecology, 3: 1241–1252. (Link to Nature) (Link to BioRxiv)
N.R. Stone, C.A. Gifford, R. Thomas, K.J.B. Pratt, K. Samse-Knapp, T.M.A. Mohamed, E.M. Radzinsky, A. Schricker, P. Yu, K.N. Ivey, K.S. Pollard, D. Srivastava (2019). Unique transcription factor functions regulate epigenetic and transcriptional dynamics during cardiac reprogramming, Cell Stem Cell, 25(1): 87-102. (Link to Cell) (Link to BioRxiv)
D.A. Pollard, T.D. Pollard, K.S. Pollard (2019). Empowering statistical methods for cellular and molecular biologists, Molecular Biology of the Cell, 30(12). (Link to MBoC)
D.D. Engle, H. Tiriac, K.D. Rivera, A. Pommier, S. Whalen, T.E. Oni, B. Alagesan, E.J. Lee, M.A. Yao, M.S. Lucito, B. Spielman, B. Da Silva, C. Schoepfer, K. Wright, B. Creighton, L. Afinowicz, K.H. Yu, R. Grützmann, D. Aust, P.A. Gimotty, K.S. Pollard, R.H. Hruban, M.G. Goggins, C. Pilarsky, Y. Park, D.J. Pappin, M.A. Hollingsworth, D.A. Tuveson (2019). The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice, Science, 364(6446): 1156-1162. (Link to Science)
C.R. Armour, S. Nayfach, K.S. Pollard, T.J. Sharpton (2019). A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome, mSystems, 4:e00332-18. (Link to mSystems) (Link to BioRxiv)
O.M. Ahmed, A. Avila-Herrera, K.M. Tun, G.W. Davis, K.S. Pollard, N.M. Shah (2019). Evolution of mechanisms that control mating in Drosophila males, Cell Reports, 27(9): P2527-2536.E4. (Link to Cell)
I.M. Cristea, P.C. Dorrestein, J.A. Eisen, J.A. Gilbert, J.A. Huber, J.K. Jansson, R. Knight, K.S. Pollard, J. Raes, P.A. Silver, N.S. Webster, J. Xu (2019). Early-career scientists shaping the world, mSystems, 4:e00196-19. (Link to mSystems)
The 2017 NIH-wide microbiome workshop writing team (2019). The human microbiome: Emerging themes at the horizon of the 21st century, Microbiome, 7:32. (Link to Microbiome)
S. Nayfach, Z.J. Shi, R. Seshadri, K.S. Pollard, N. Kyrpides (2019). Novel insights from uncultivated genomes of the global human gut microbiome, Nature, 568: 505–510. (Link to Nature)
Md. A.H. Samee, B.G. Bruneau, K.S. Pollard (2019). A de novo shape motif discovery algorithm reveals preferences of transcription factors for DNA shape beyond sequence motifs, Cell Systems, 8(1): 27-42.e6. (Link to Cell) (Link to BioRxiv)
S. Whalen, K.S. Pollard (2019). Most regulatory interactions are not in linkage disequilibrium, Genome Research, 29: 334-343. (Link to Genome Research) (Link to BioRxiv)
R.I. Amann, S. Baichoo, B.J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P.S.G. Chain, R.R. Colwell, D.G. Daffonchio, A. Danchin, V. de Lorenzo, P.C. Dorrestein, R.D. Finn, C.M. Fraser, J.A. Gilbert, S.J. Hallam, P. Hugenholtz, J.P.A. Ioannidis, J.K. Jansson, J.F. Kim, H.-P. Klenk, M.G. Klotz, R. Knight, K.T. Konstantinidis, N.C. Kyrpides, C.E. Mason, A.C. McHardy, F. Meyer, C.A. Ouzounis, A.A.N. Patrinos, M. Podar, K.S. Pollard, J. Ravel, A. Reyes Muñoz, R.J. Roberts, R. Rosselló-Móra, S.-A. Sansone, P.D. Schloss, L.M. Schriml, J.C. Setubal, R. Sorek, R.L. Stevens, J.M. Tiedje, A. Turjanski, G.W. Tyson, D.W. Ussery, G.M. Weinstock, O. White, W.B. Whitman, I. Xenarios (2019). Toward unrestricted use of public data, Science, 363(6425): 350-352. (Link to Science) (Response to Letter in Science) (NOAA Oceanic and Atmospheric Research Outstanding Scientific Paper)
G. Fudenberg, K.S. Pollard (2019). Chromatin features constrain structural variation across evolutionary timescales, Proceedings of the National Academy of Sciences, 116(6): 2175-2180. (Link to PNAS) (Link to BioRxiv)
N.R. Garud, B.H. Good, O. Hallatschek, K.S. Pollard (2019). Evolutionary dynamics of bacteria in the gut microbiome within and across hosts, PLoS Biology, 17(1): e3000102. (Link to PLoS) (Link to BioRxiv)
2018
C. Langelier, K.L. Kalantar, F. Moazed, M.R. Wilson, E.D. Crawford, T. Deiss, A. Belzer, S. Bolourchi, S. Caldera, M. Fung, A. Jauregui, K. Malcolm, A. Lyden, L. Khan, K. Vessel, J. Quan, M. Zinter, C.Y. Chiu, E.D. Chow, J. Wilson, S. Miller, M.A. Matthay, K.S. Pollard, S. Christenson, C.S. Calfee, J.L. DeRisi (2018). Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults, Proceedings of the National Academy of Sciences, 115(52): E12353-E12362. (Link to PNAS) (Commentary)
P.S. Shah, N. Link, G.M. Jang, P.P. Sharp, T. Zhu, D.L. Swaney, J.R. Johnson, J. Von Dollen, H.R. Ramage, L. Satkamp, B. Newton, R. Hüttenhain, M.J. Petit, T. Baum, A. Everitt, O. Laufman, M. Tassetto, M. Shales, E. Stevenson, G.N. Iglesias, L. Shokat, S. Tripathi, V. Balasubramaniam, L.G. Webb, S. Aguirre, A.J. Willsey, A. Garcia-Sastre, K.S. Pollard, S. Cherry, A.V. Gamarnik, I. Marazzi, J. Taunton, A. Fernandez-Sesma, H.J. Bellen, R. Andino, N.J. Krogan (2018). Comparative flavivirus-host protein interaction mapping reveals mechanisms of dengue and zika virus pathogenesis, Cell, 175(7): 1931-1945.e18. (Link to Cell)
J. Ladau, Y. Shi, X. Jing, J.-S. He, L. Chen, X. Lin, N. Fierer, J.A. Gilbert, K.S. Pollard, H. Chu (2018). Climate change will lead to pronounced shifts in the diversity of soil microbial communities, mSystems, 3(5): e00167-18. (Link to mSystems) (Link to BioRxiv)
S.K. Wyman, A. Avila-Herrera, S. Nayfach, K.S. Pollard (2018). A most wanted list of conserved protein families with no known domains, PLoS ONE, 13(10): e0205749. (Link to PLoS) (Link to BioRxiv) (featured on PLoS Microbiome Channel)
P.H. Bradley, S. Nayfach, K.S. Pollard (2018). Phylogeny-corrected identification of microbial gene families relevant to human gut colonization, PLoS Computational Biology, 14(8): e1006242. (Link to PLoS) (Link to BioRxiv) (Press release)
D. Kostka, A.K. Holloway, K.S. Pollard (2018). Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages, Molecular Biology and Evolution, 35(8): 2034–2045. (Link to MBE) (Link to BioRxiv) (Highlighted by CARTA)
D. McDonald et al. (2018). American Gut: an open platform for citizen-science microbiome research, mSystems 3:
e00031-18. (Link to mSystems) (Link to BioRxiv)
S.A. Moquin, S. Thomas, S. Whalen, A. Warburton, S.G. Fernanadez, A.A. McBride, K.S. Pollard, J.L. Miranda (2018). The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation, J Virology, 92(3): e01413-17. (Link to JVI) (Editor’s Spotlight) (Link to BioRxiv)
P. Milgrom, J.A. Horst, S. Ludwig, M. Rothen, B.W. Chaffee, S. Lyalina, K.S. Pollard, J.L. DeRisi, L. Mancl (2018). 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, J Dentistry, 68: 72-78. (Link to J Dentistry)
2017
The Earth Microbiome Project Consortium (2017). A communal catalogue reveals Earth’s multiscale microbial diversity, Nature, 551(7681): 457-463. (Link to Nature)
L.F. Franchini, K.S. Pollard (2017). Human evolution: the non-coding revolution, BMC Biology, 15: 89. (Link to BMC Bio)
T.J. Sharpton, S. Lyalina, J. Loung, J. Pham, E.M. Deal, C. Armour, C. Gaulke, S. Sanjabi, K.S. Pollard (2017). Development of inflammatory bowel disease is linked to a longitudinal restructuring of the gut metagenome in mice, mSystems, 2(5): e00036-17. (Link to mSystems) (Link to BioRxiv)
F.R. Day, D.J. Thompson, H. Helgason, D.I. Chasman, H. Finucane, P. Sulem, K.S. Ruth, S. Whalen, …(114 others), K.S. Pollard, D.F. Easton, J.Y. Tung, J. Chang-Claude, D. Hinds, A. Murray, J.M. Murabito, K. Stefansson, K.K. Ong, J.R.B. Perry (2017). Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk, Nature Genetics, 49: 834–841. (Link to Nature)
C.M. Anderson, J. Hu, R. Thomas, T.B. Gainous, B. Celona, T. Sinha, D.E. Dickel, A.B. Heidt, S.M. Xu, B.G. Bruneau, K.S. Pollard, L.A. Pennacchio, B.L. Black (2017 Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites, Development, 144(7): 1235-1241. (Link to Development)
P.H. Bradley, K.S. Pollard (2017). Proteobacteria drive significant functional variability in the human gut microbiome, Microbiome, 5: 36. (Link to Microbiome) (Link to BioRxiv)
S. Engle, S. Whalen, A. Joshi, K.S. Pollard (2017). Unboxing cluster heatmaps, Proceedings of the 6th Symposium on Biological Data Visualization (BioVis), BMC Bioinformatics, 18: 63. (Link to BMC)
C.J. Guo, F.Y. Chang, T.P. Wyche, K.M. Backus, T.M. Acker, M. Funabashi, M. Taketani, M.S. Donia, S. Nayfach, K.S. Pollard, C.S. Craik, B.F. Cravatt, J. Clardy, C.A. Voigt, M.A. Fischbach (2017). Discovery of reactive microbiota-derived metabolites that inhibit host proteases, Cell, 168(3): 517-526. (Link to Cell)
R. Thomas, S. Thomas, A.K. Holloway, K.S. Pollard (2017). Features that define the best ChIP-seq peak calling algorithms, Briefings in Bioinformatics, 18(3): 441–450. (Link to Briefings)
2016
A.S. Devlin, A. Marcobal, D. Dodd, S. Nayfach, N. Plummer, T. Meyer, K.S. Pollard, J.L. Sonnenburg, M.A. Fischbach (2016). Modulation of a circulating uremic solute via rational genetic manipulation of the gut microbiota, Cell Host Microbe, 20(6): 709-715. (Link to Cell HM)
S. Nayfach, B. Rodriguez-Mueller, N. Garud, K.S. Pollard (2016). An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria, Genome Research, 26: 1612-1625. (Link to Genome Research)(Link to BioRxiv) (Also: Earlier BioRxiv version)
G. Mhuireach, B.R. Johnson, A.E. Altrichter, J. Ladau, J.F. Meadow, K.S. Pollard, J.L. Green (2016). Urban greenness influences airborne bacterial community composition, Science of the Total Environment, 571: 680-687. (Link to Sci Total Env)
K.S. Pollard (2016). Decoding Human Accelerated Regions, The Scientist. (Link to The Scientist)(Summary)
S. Nayfach, K.S. Pollard (2016). Towards accurate and quantitative comparative metagenomics, Cell, 166(5): 1103-1116. (Link to Cell)
M.J. Blaser, Z.G. Cardon, M.K. Cho, J.L. Dangl, T.J. Donohue, J.L. Green, R. Knight, M.E. Maxon, T.R. Northen, K.S. Pollard, E.L. Brodie (2016). Toward a predictive understanding of Earth’s microbiomes to address 21st century challenges, mBio 7(3): e00714-16. (Link to mBio)
S. Whalen, R.M. Truty, K.S. Pollard (2016). Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin, Nature Genetics, 48: 488-496. (Link to Nature)(GitHub Repo)(Link to bioRxiv)(News and Views) 
B. Booker, T. Friedrich, M.K. Mason, J.E. VanderMeer, J. Zhao, W.L. Eckalbar, M. Logan, N. Illing, K.S. Pollard, N. Ahituv (2016).Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD locus, PLoS Genetics, 12(1): e1005738. (Link to PLoS)
W.L. Eckalbar, S.A. Schlebusch, M.K. Mason, Z. Gill, A.V. Parker, B.M. Booker, S. Nishizaki, C. Muswamba-Nday, E. Terhune, K.A. Nevonen, N. Makki, T. Friedrich, J.E. VanderMeer, K.S. Pollard, L. Carbone, J.D. Wall, N. Illing, N. Ahituv (2016). Transcriptomic and epigenomic characterization of the developing bat wing, Nature Genetics, 48: 528-536. (Link to Nature)(Cover Image)
S.A. Myers, S. Peddada, N. Chatterjee, T. Freidrich, K. Tomodo, G. Krings, S. Thomas, M. Broeker, J. Maynard, M. Thomson, K.S. Pollard, S. Yamanaka, A.L. Burlingame, B. Panning (2016). SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells, eLife: 10647. (Link to eLife)
L. Luna-Zurita, C.U. Stirnimann, S. Glatt, B.L. Kaynak, S. Thomas, F. Baudin, M.A.H. Samee, D. He, E.M. Small, M. Mileikovsky, A. Nagy, A.K. Holloway, K.S. Pollard, C.W. Muller, B.G. Bruneau (2016). Complex interdependence regulates heterotypic transcription factor distribution and coordinates cardiogenesis, Cell, 164(5): 999-1014. (Link to Cell)
X. Wang, A.K. Pandey, M.K. Mulligan, E.G. Williams, K. Mozhui, Z. Li, V. Jovaisaite, L.D. Quarles, Z. Xiao, J. Huang, J.A. Capra, Z. Chen, W.L. Taylor, L. Bastarache, X. Niu, K.S. Pollard, D.C. Ciobanu, A.O. Reznik, A.V. Tishkov, I.B. Zhulin, J. Peng, S.F. Nelson, J.C. Denny, J. Auwerx, L. Lu, R.W. Williams (2016). Joint mouse-human phenome-wide association to test gene function and disease risk, Nature Communications, 7: 10464. (Link to Nature)
2015
A.K. Holloway, B.G. Bruneau, T. Sukonnik, J.L. Rubenstein, K.S. Pollard (2015). Accelerated evolution of enhancer hotspots in the mammalian ancestor, Molecular Biology and Evolution, 33(4): 1008-1018. (Link to MBE)(Blog Post)
S. Nayfach, P.H. Bradley, S.K. Wyman, T.J. Laurent, A. Williams, J.A. Eisen, K.S. Pollard, T.J. Sharpton (2015). Automated and accurate estimation of gene family abundance from shotgun metagenomes, PLoS Computational Biology, 11(11): e1004573. (Link to PLoS)(bioRxiv pre-print)
D. Kostka, T. Friedrich, A.K. Holloway, K.S. Pollard (2015). motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences, Statistics and Its Interface, 8(4): 463-476. (Link to SII) (ArXiv pre-print)
A.P. Alivisatos, M.J. Blaser, E.L. Brodie, M. Chun, J.L. Dangl, T.J. Donohue, P.C. Dorrestein, J.A. Gilbert, J.L. Green, J.K. Jansson, R. Knight, M.E. Maxon, M.J. McFall-Ngai, J.F. Miller, K.S. Pollard, E.G. Ruby, S.A. Taha, Unified Microbiome Initiative Consortium (2015). MICROBIOME. A unified initiative to harness Earth’s microbiomes, Science, 350(6260): 507-508. (Link to Science)
S. Nayfach, M.A. Fischbach, K.S. Pollard (2015). MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome, Bioinformatics, 31(20): 3368-3370. (Link to Bioinformatics)
C.F. Maurice, S.C.L. Knowles, J. Ladau, K.S. Pollard, A. Fenton, A.B. Pedersen, P.J. Turnbaugh (2015). Marked seasonal variation in the wild mouse gut microbiota, ISME Journal, 9: 2423-2434. (Link to ISME)
L.F. Franchini, K.S. Pollard (2015). Genomic approaches to studying human-specific developmental traits, Development, 142: 3100-3112. (Link to Development)
G.D.E. Haliburton, G.L. McKinsey, K.S. Pollard (2015). Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development, Neurogenetics, 17(1), 1-9. (Link to Neurogenetics)
L.F. Franchini, K.S. Pollard (2015). Can a few non-coding mutations make a human brain?, BioEssays, 37: 1054-1061. (Link to BioEssays)(Link to video abstract)
A. Avila-Herrera, K.S. Pollard (2015). Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species, BMC Bioinformatics, 16: 268. (Link to BMC)(BioRxiv pre-print)
K.S. Ramirez, M. Doring, N. Eisenhauer, C. Gardi, J. Ladau, J.W. Leff, G. Lentendu, Z. Lindo, M.C. Rillig, D. Russell, S. Scheu, M.G. St. John, F.T. de Vries, T. Wubet, W.H. van der Putten, D.H. Wall (2015). Toward a global platform for linking soil biodiversity data, Frontiers in Ecology and Evolution, 3: 91. (Link to FEE)
K.S. Smith, V.K. Yadav, B.S. Pedersen, R. Shaknovich, M.W. Geraci, K.S. Pollard, S. De (2015). Signatures of accelerated somatic evolution in gene promoters in multiple cancer types, Nucleic Acids Research, 43(11): 5307-5317. (Link to NAR)
A. Barberan, J. Ladau, J.W. Leff, K.S. Pollard, H.L. Menninger, R.R. Dunn, N. Fierer (2015). Continential-scale distributions of dust-associated bacteria and fungi, Proceedings of the National Academy of Sciences, 112(18): 5756-5761. (Link to PNAS)
S. Nayfach, K.S. Pollard (2015). Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome, Genome Biology, 16: 51. (Link to Genome Biology)(BioRxiv pre-print)(Blog post)
C.V. Theodoris, M. Li, M.P. White, L. Liu, D. He, K.S. Pollard, B.G. Bruneau, D. Srivastava (2015). Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency, Cell, 160(6): 1072-1086. (Link to Cell)(Press release)
C.N. Simonti, K.S. Pollard, S. Schroder, D. He, B.G. Bruneau, M. Ott, J.A. Capra (2015). Evolution of lysine acetylation in the RNA polymerase II C-terminal domain, BMC Evolutionary Biology, 15: 35. (Link to BMC)
K. Xu, E.E. Schadt, K.S. Pollard, P. Roussos, J.T. Dudley (2015). Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions, Molecular Biology and Evolution, 32(5): 1148-1160. (Link to MBE)
2014
C. Huttenhower, R. Knight, C.T. Brown, J.G. Caporaso, J.C. Clemente, D. Gevers, E.A. Franzosa, S.T. Kelley, D. Knights, R.E. Ley, A. Mahurkar, J. Ravel, The Scientists for Advancement of Microbiome Research, O. White (2014). Advancing the microbiome research community, Cell, 159(2): 227-230. (Link to Cell)
L. Carbone, R.A. Harris, S. Gnerre, K.R. Veeramah, B. Lorente-Galdos, J. Huddleston, et al. (2014). Gibbon genomes and the fast karyotype evolution of small apes, Nature, 513: 195-201. (Link to Nature)
M.J. Hubisz, K.S. Pollard (2014). Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution, Current Opinion in Genetics and Development, 29: 15-21. (Link to Curr Op)
N. Oksenberg, G.D.E. Haliburton, W.L. Eckalbar, I. Oren, S. Nishizaki, K. Murphy, K.S. Pollard, R.Y. Birnbaum, N. Ahituv (2014).Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes, Translational Psychiatry, 4: e431. (Link to Trans Psych)
P. Skewes-Cox, T.J. Sharpton, K.S. Pollard, J.L. DeRisi (2014). Profile hidden Markov models for the detection of viruses within metagenomic sequence data, PLoS ONE, 9(8): e105067. (Link to PLoS)
G.D. Erwin, R.M. Truty, D. Kostka, K.S. Pollard, J.A. Capra (2014). Integrating diverse datasets improves developmental enhancer prediction, PLoS Computational Biology, 10(6): e1003677. Top 10% most cited PLoS CB articles. (Link to PLoS) (ArXiv pre-print) (Link to Haldane’s Sieve)
J. Kidd, T.J. Sharpton, D. Bobo, P. Norman, A. Martin, M. Carpenter, M. Sikora, C. Gignoux, N. Nemat-Gorgani, A. Adams, M. Guadalupe, X. Guo, Q. Feng, Y. Li, X. Liu, P. Parham, E. Hoal, M. Feldman, K.S. Pollard, J. Wall, C. Bustamente, B. Henn (2014).Exome capture from saliva produces high quality genomic and metagenomic data, BMC Genomics, 15: 262. (Link to BMC)
N. Roan, H. Liu, S. Usmani, J. Neidleman, J. Muller, A. Avila-Herrera, A. Gawanbacht, O. Zirafi, S. Chu, M. Dong, S. Kumar, J. Smith, K.S. Pollard, M. Fandrich, F. Kirchhoff, J. Munch, E. Witkowska, W. Greene (2014). Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection, Journal of Virology, 88(13): 7221-7234. (Link to JVI)
>M.M. Finucane, T.J. Sharpton, T.J. Laurent, K.S. Pollard (2014). A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter, PLoS ONE 9(1): e84689. (Link to PLoS)
2013
S. Schroder, E. Herker, F. Itzen, D. He, S. Thomas, D. Gilchrist, K. Kaehlcke, S. Cho, K.S. Pollard, J.A. Capra, M. Schnolzer, P.A. Cole, M. Geyer, B.G. Bruneau, K. Adelman, M. Ott (2013). Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells, Molecular Cell, 52(3): 314-324. (Link to Mol Cell)
N. Fierer, J. Ladau, J.C. Clemente, J.W. Leff, S.M. Owens, K.S. Pollard, R. Knight, J.A. Gilbert, R.L. McCulley (2013). Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States, Science, 342(6158): 621-624. (Link to Science)(Nature News)(Press Release)
J.A. Capra, G.D. Erwin, G. McKinsey, J.L.R. Rubenstein, K.S. Pollard (2013). Many human accelerated regions are developmental enhancers, Philosophical Transactions of the Royal Society B, 368: 20130025. (Link to PTRSB) (Highlighted in CARTA Newsletter)(Press release)
J.A. Capra, M. Stolzer, D. Durrand, K.S. Pollard (2013). How old is my gene? Trends in Genetics, 29(11): 659-668. (Link to TIGs)
D.G. Lemay, K.S. Pollard, W.F. Martin, C.F. Zadrowksi, J. Hernandez, I. Korf, M. Rijnkels (2013). From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome, PLoS ONE, 8(9): e75030. (Link to PLoS)(Highlighted in Genomeweb Daily Scan)
R.P. Smith, S.J. Riesenfeld, A.K. Holloway, Q. Li, K.K. Murphy, N.M. Feliciano, L. Orecchia, N. Oksenber, K.S. Pollard, N. Ahituv (2013). A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design, Genome Biology, 14: R72. (Link to Genome Biology)(Editor’s Pick)
S.J. Riesenfeld, K.S. Pollard (2013). Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis, BMC Genomics, 14: 419. (Link to BMC)
J.A. Capra, M.J. Hubisz, D. Kostka, K.S. Pollard, A. Siepel (2013). A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes, PLoS Genetics, 9(8): e1003684. (Link to PLoS)
J. Ladau, T.J. Sharpton, M.M. Finucane, G. Jospin, S.W. Kembel, J. O’Dwyer, A.F. Koeppel, J.L. Green, K.S. Pollard (2013). Global marine bacterial diversity peaks at high latitudes in winter, ISME Journal, 7: 1669-1677. (Link to ISME)
2012
K.S. Pollard (2012). The genetics of humanness, in What makes us human? Answers from evolutionary anthropology, J.M. Calcagno, A. Fuentes (Editors), Evolutionary Anthropology, 21: 182-194. (Link to Evolutionary Anthropology)
T.J. Sharpton, G. Jospin, D. Wu, M.G. Langille, K.S. Pollard, J.A. Eisen (2012). Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource, BMC Bioinformatics, 13(1): 264. (Link to BMC)
J.A. Wamstad, J.M. Alexander, R.M. Truty, A. Shrikumar, F. Li, K.E. Eilertson, H. Ding, J.N. Wylie, A.R. Pico, J.A. Capra, G. Erwin, S.J. Kattman, G.M. Keller, D. Srivastava, S.S. Levine, K.S. Pollard, A.K. Holloway, L.A. Boyer, B.G. Bruneau (2012). Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage, Cell, 151(1): 206-220. (Link to Cell)
D.G. Lemay, W.F. Martin, A.S. Hinrichs, M. Rijnkels, J.B. German, I. Korf, K.S. Pollard (2012). G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes, BMC Bioinformatics, 13: 253. (Link to BMC)
J.A. Capra, A.G. Williams, K.S. Pollard (2012). ProteinHistorian: Tools for the comparative analysis of eukaryote protein origin, PLoS Computational Biology, 8(6): e1002567. (Link to PLoS)(Selected for PLoS Software Collection)
K.M. Wylie, R.M. Truty, T.J. Sharpton, K.A. Mihindukulasuriya, Y. Zhou, H. Gao, E. Sodergren, G.M. Weinstock, K.S. Pollard (2012).Novel bacterial taxa in the human microbiome, PLoS ONE, 7(6): e3529 (HMP Companion Paper Collection). (Link to PLoS)
The Human Microbiome Project Consortium (2012). Structure, function and diversity of the human microbiome in an adult reference population, Nature, 486: 207-214. (Link to Nature)(Press Release)
The Human Microbiome Project Consortium (2012). A framework for human microbiome research, Nature, 486: 215-221. (Link to Nature)
H.A. Burbano, R.E. Green, T. Maricic, C. Lalueza-Fox-C, M. de la Rasilla, A. Rosas, J. Kelso, K.S. Pollard, M. Lachmann, S. Paabo (2012). Analysis of human accelerated DNA regions using archaic hominin genomes, PLoS ONE, 7(3):e32877. (Link to PLoS)
2011
K. Lindblad-Toh, M. Garber, O. Zuk, B.J. Parker, S. Washieti, P. Kheradpour, J. Ernst, G. Jordan, E. Maucell, L.D. Ward, C.B. Lowe, A.K. Holloway, …(46 others), K.S. Pollard, J.S. Pedersen, E.S. Lander, M. Kellis (2011). A high-resolution map of human evolutionary constraint using 29 mammals, Nature, 478: 476-482. (Link to Nature) (Press Release)
D. Kostka, M.J. Hubisz, A. Siepel, K.S. Pollard (2011). The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome, Molecular Biology and Evolution, 29(3): 1047-1057. (Link to MBE)
S.W. Kembel, J.A. Eisen, K.S. Pollard, J.L. Green (2011). The phylogenetic diversity of metagenomes, PLoS ONE, 6(8): e23214. (Link to PLoS)
J.C. Roach, G. Glusman, R. Hubley, S.Z. Montsaroff, A.K. Holloway, D.E. Mauldin, D. Srivastava, W. Garg, K.S. Pollard, D.J. Galas, L. Hood, A.F.A. Smit (2011). Chromosomal haplotypes by genetic phasing of human families, The American Journal of Human Genetics, 89: 1-16. (Link to AJHG)
S. Katzman, J.A. Capra, D. Haussler, K.S. Pollard (2011). Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hotspots, Genome Biology and Evolution, 3: 614-626. (Link to GBE)
M.D. Hirschey, T. Shimazu, J.A. Capra, K.S. Pollard, E. Verdin (2011). SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2, Aging, 3(6), 635—642. . (Link to Aging)
J.A. Capra, K.S. Pollard (2011). Substitution patterns are GC-biased in divergent sequences across the metazoans, Genome Biology and Evolution, 3: 516-527. (Link to GBE)
K. Paeschke, J.A. Capra, V. A. Zaklan (2011). DNA replication through G-quadruplex motifs is promoted by the saccharomyces cerevisiae Pif1 DNA helices, Cell, 145(5): 678-691. (Link to Cell) (Highlighted on Nature Reviews Molecular Cellular Biology)
N. Lambert, M. Lambot , A. Bilheu, V. Albert, Y. Englert, F. Libert, J. Noel, C. Sotiriou, A.K. Holloway, K.S. Pollard, V. Detours, P. Vanderhaeghen (2011). Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution, PLoS ONE, March, 6(3): e17753. (Link to PLoS)
M.J. Hubisz, K.S. Pollard, A. Siepel (2011). PHAST and RPHAST: phylogenetic analysis with space/time models, Briefings in Bioinformatics, (12)1: 41-51. (Link to Briefings)
J.K. Takeuchi, X. Lou, J.M. Alexander, H. Sugizaki, P. Delgado-OlguÃn, A.K. Holloway, A.D. Mori, J.N. Wylie, C. Munson, Y. Zhu, Y.Q. Zhou, R.F. Yeh, R.M. Henkelman, R.P. Harvey, D. Metzger, P. Chambon, D.Y.R. Stainier, K.S. Pollard, I.C. Scott, B.G. Bruneau (2011). Chromatin remodelling complex dosage modulates transcription factor function in heart development, Nature Communications, 2: article 187. (Link to Nature)
T.J. Sharpton, S.J. Riesenfeld, S.W. Kembel, J. Ladau, J.P. O’Dwyer, J.L. Green, J.A. Eisen, K.S. Pollard (2011). PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data, PLoS Computational Biology, 7(1): e1001061. (Link to PLoS) (Highlighted on Genome Web)
2010
J.A. Capra, K.S. Pollard, M. Singh (2010). Novel genes exhibit distinct patterns of function acquisition and network integration,Genome Biology, 11: R127. (Link to Genome Biology)(Highlighted on Genome Web)
X. Wang, R. Agarwala, J.A. Capra, Z. Chen, D.M. Church, D.C. Ciobanu, Z. Li, L. Lu, K. Mozhui, M.K. Mulligan, S.F. Nelson, K.S. Pollard, W.L. Taylor, D.B. Thomason, R.W. Williams (2010). High-throughput sequencing of the DBA/2J mouse genome, BMC Bioinformatics, 11 (Suppl 4): O7. (Link To BMC)
D.I. Ritter, Q. Li, D. Kostka, K.S. Pollard, S. Guo, J.H. Chuang (2010). The importance of being cis: Evolution of orthologous fish and mammalian enhancer activity, Molecluar Biology and Evolution, 27(10): 2322-2332. (Link to MBE) (EMBO blog about the article)
D. Kostka, M.W. Hahn, K.S. Pollard (2010). Non-coding sequences near duplicated genes evolve rapidly, Genome Biology and Evolution, 2: 518-533. (Link to GBE)
J. Ladau, S.J. Ryan (2010). MPowering ecologists: community assembly tools for community assembly rules, Oikos, July, 119(7): 1064-1069. (Link to JSTOR)
J.A. Capra, L. Carbone, S.J. Riesenfeld, J.D. Wall (2010). Genomics through the lens of next-generation sequencing, Genome Biology, 11:306. (Link to Genome Biology)
S. Katzman, A.D. Kern, K.S. Pollard, S.R. Salama, D. Haussler (2010). GC-biased evolution near human accelerated regions, PLoS Genetics, 6(5): e1000960. (Link to PLoS)
S.L. Taylor, K.S. Pollard (2010). Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes, Genetics Research, 92: 39-53. (Link to Genetics Research)
K.S. Pollard, M.J. Hubisz, K.R. Rosenbloom, A. Siepel (2010). Detection of non-neutral substitution rates on mammalian phylogenies, Genome Research, 20: 110-121. (Link to Genome Research)
2009
F. Hsieh, S.-C. Chen, K.S. Pollard (2009). A nearly exhaustive search for CpG islands on whole chromosomes, The International Journal of Biostatistics, 5(1): article 14. (Link to IJB)
D.G. Lemay, D.J. Lynn, W.F. Martin, M.C. Neville, T.M. Casey, G. Rincon, E.V. Kriventseva, W.C. Barris, A.S. Hinrichs, A.J. Molenaar, K.S. Pollard, N.J. Maqbool, K. Singh, R. Murney, E.M. Zdobnov, R.L. Tellam, J.F. Medrano, J.B. German, M. Rijnkels (2009). The bovine lactation genome: insights into the evolution of mammalian milk, Genome Biology, 10:R43. (Link to Genome Biology) (Reviewed in Nature Reviews Genetics) (Reviewed in Journal of Biology)
K.S. Pollard (2009). What makes us human? Scientific American, May: 44-49 (cover story). (Link to SciAm) (Coverage on ABC News)
J. Berglund, K.S. Pollard, M.T. Webster (2009). Hotspots of biased nucleotide substitutions in human genes, PLoS Biology, 7(1): e1000026. (Link to PLoS)(Selected for Faculty of 1000)
S.L. Taylor, K.S. Pollard (2009). Hypothesis tests for point-mass mixture data with application to `omics data with many zero values, Statistical Applications in Genetics and Molecular Biology, 8(1): article 8. (Link to SAGMB)
A.E. Cozen, M.T. Weirauch, K.S. Pollard, D.L. Bernick, J.M. Stuart, T.M. Lowe (2009). Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum, Journal of Bacteriology, 191(3): 782-794. (Link to J Bact)
2008
K.S. Pollard, M.J. van der Laan (2008). Supervised distance matrices, Statistical Applications in Genetics and Molecular Biology, 7(1): article 33. (Link to SAGMB)
W.L. Walker, I.H. Liao, D.L. Gilbert, B. Wong, K.S. Pollard, C.E. McCulloch, L. Lit, F.R. Sharp (2008). Empirical Bayes accommodation of batch-effects in microarray data using identical replicate reference samples: Application to RNA expression profiling of blood from Duchenne muscular dystrophy patients, BMC Genomics, 9: 494. (Link to BMC)
A.K. Holloway, D.J. Begun, A. Siepel, K.S. Pollard (2008). Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster, Genome Research, 18: 1592-1601. (Link to Genome Research)
S.L. Taylor, K.S. Pollard (2008). Evaluation of two methods to estimate and monitor bird populations, PLoS ONE, 3(8): e3047. (Link to PLoS)
K.S. Pollard, D. Serre, X. Wang, H. Tao, E. Grundberg, T.J. Hudson, A.G. Clark, K. Frazer (2008). A genome-wide approach to identifying novel-imprinted genes, Human Genetics, 122(6): 625-634. (Link to Human Genetics)
2007
S.L. Taylor, D. Temple Lang, K.S. Pollard (2007). Improvements to the multiple testing package multtest, R News 7(3): 52-55. (Link to R News)
D.G. Lemay, M.C. Neville, M.C. Rudolph, K.S. Pollard, J.B. German (2007). Gene regulatory networks in lactation: identification of global principles using bioinformatics, BMC Systems Biology, 1: 56. (Link to BMC)
T.R. Dreszer, G.D. Wall, D. Haussler, K.S. Pollard (2007). Biased clustered substitutions in the human genome: the footprints of male driven biased gene conversion, Genome Research, 17: 1420-1430. (Link to Genome Research)
T.R. Magalhaes, J. Palmer, P. Tomancak, K.S. Pollard (2007). Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach, BMC Neuroscience, 8: 59. (Link to BMC)
2006
K.S. Pollard, S.R. Salama, B. King, A.D. Kern, T. Dreszer, S. Katzman, A. Siepel, J.S. Pedersen, G. Bejerano, R. Baertsch, K.R. Rosenbloom, J. Kent, D. Haussler (2006). Forces shaping the fastest evolving regions in the human genome, PLoS Genetics, 2(10): e168. (Details of accelerated regions) (Link to PLoS)
K.S. Pollard, S.R. Salama, N. Lambert, M.A. Lambot, S. Coppens, J.S. Pedersen, S. Katzman, B. King, C. Onodera, A. Siepel, A.D. Kern, C. Dehay, H. Igel, M. Ares, Jr., P. Vanderhaeghen, D. Haussler (2006). An RNA gene expressed during cortical development evolved rapidly in humans, Nature, 443: 167-172. (Link to Nature) (Press Release) (Faculty of 1000)
A. Siepel, K.S. Pollard, D. Haussler (2006). New methods for detecting lineage-specific selection, Proceedings of the 10th International Conference on Research in Computational Molecular Biology: 190-205. (PDF)
K.L. Schneider, K.S. Pollard, R. Baertsch, A. Pohl, T.M. Lowe (2006). The UCSC Archaeal Genome Browser, Nucleic Acids Research; 34, Database issue: D407-D410. (Link to NAR)
2005
The Chimpanzee Sequencing and Analysis Consortium (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437: 69-87. (Link to Nature) (Press Release)
N.G. Salomonis, N. Cotte, A.C. Zambon, K.S. Pollard, K. Vranizan, S.W. Doniger, G. Dolganov, B.R. Conklin (2005). Identifying genetic networks underlying myometrial transition to labor. Genome Biology, 6: R12. (Link to Genome Biology)
K.S. Pollard, S. Dudoit, M.J. van der Laan (2005). Multiple Testing Procedures: R multtest Package and Applications to Genomics, inBioinformatics and Computational Biology Solutions Using R and Bioconductor, R. Gentleman, V. Carey, W. Huber, R. Irizarry, S. Dudoit (Editors). Springer (Statistics for Biology and Health Series), pp. 251-272. (Buy at Amazon.com) (PDF)
K.S. Pollard, M.J. van der Laan (2005). Cluster Analysis of Genomic Data, in Bioinformatics and Computational Biology Solutions Using R and Bioconductor, R. Gentleman, V. Carey, W. Huber, R. Irizarry, S. Dudoit (Editors). Springer (Statistics for Biology and Health Series), pp. 209-228. (Buy at Amazon.com) (PDF)
K.S. Pollard, M.D. Birkner, S. Dudoit, M.J. van der Laan (2005). Test statistics null distributions in multiple testing: simulation studies and applications to genomics. Numero double special Statistique et Biopuces, Journal de la Société Française de Statistique, Vol. 146(1-2): 77-115. (Tech Report)
M.D. Birkner, K.S. Pollard, S. Dudoit, M.J. van der Laan (2005). Multiple testing procedures and applications to genomics. U.C. Berkeley Division of Biostatistics Working Paper Series. Working Paper 168. (PDF)
2004
M.J. van der Laan, S. Dudoit, K.S. Pollard (2004). 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, 3(1): article 15. (PDF)
M.J. van der Laan, S. Dudoit, K.S. Pollard (2004). Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Statistical Applications in Genetics and Molecular Biology, 3(1): article 14. (PDF)
S. Dudoit, M.J. van der Laan, K.S. Pollard (2004). Multiple testing. Part I. Single-step procedures for control of general type I error rates. Statistical Applications in Genetics and Molecular Biology, 3(1): article 13. (PDF)
K.S. Pollard, M.J. van der Laan (2004). Choice of null distribution in resampling-based multiple testing. Journal of Statistical Planning and Inference, 125: 85-100. (Link to JSPI).
2003
M.J. van der Laan, K.S. Pollard, J. Bryan (2003). A new partitioning around medoids algorithm. Journal of Statistical Computation and Simulation, 73(8): 575-584. (PDF)
K.S. Pollard, M.J. van der Laan (2003). Multiple testing for gene expression data: an investigation of null distributions with consequences for the permutation test. Proceedings of the 2003 International MultiConference in Computer Science and Engineering, METMBS’03 Conference: 3-9. (PDF)
2002
K.S. Pollard, M.J. van der Laan (2002). Resampling-based multiple testing: Asymptotic control of type I error and applications to gene expression data. U.C. Berkeley Division of Biostatistics Working Paper Series. Working Paper 121. (PDF)
K.S. Pollard, M.J. van der Laan (2002). New methods for identifying significant clusters in gene expression data. 2002 Proceedings of the American Statistical Association, Biometrics Section [CD-ROM]. (PDF)
K.S. Pollard, M.J. van der Laan (2002). A method to identify significant clusters in gene expression data. Proceedings of SCI 2002, Vol. II: 318-325. (Link to COBRA)
K.S. Pollard,M.J. van der Laan (2002). Statistical inference for simultaneous clustering of gene expression data, in Nonlinear Estimation and Classification, D.D. Denison, M.H. Hansen, C. Holmes, B. Mallick, B. Yu (Editors). Springer-Verlag, pp. 305-320. (Buy at Amazon.com) (PDF)
J. Bryan, K.S. Pollard, M.J. van der Laan (2002). Paired and unpaired comparison and clustering with gene expression data. Statistica Sinica, 12(1): 87-110. (PDF)
K.S. Pollard, M.J. van der Laan (2002). Statistical inference for simultaneous clustering of gene expression data. Mathematical Biosciences, 176(1): 99-121. (Link to Math Biosciences) (PDF)
2001
M.J. van der Laan, K.S. Pollard (2001). Hybrid clustering of gene expression data with visualization and the bootstrap. Journal of Statistical Planning and Inference, 2003, 117: 275-303. (PDF) (Link to JSPI)