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Publications

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)

S. Nayfach, K.S. Pollard (2014). Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome, bioRxiv. (Link to bioRxiv)(Blog post)

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. (Link to PLoS) (Link to arXiv) (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)

D. Kostka, T. Friedrich, A.K. Holloway, K.S. Pollard (2014). motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences, ArXiv: 1402.0042. (Link to arXiv)(Accepted at Statistics and Its Interface)

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: 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 Evoltionary 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. Linblad-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). (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-Olguín, 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)

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.

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 indentifying 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)(Selected for 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, 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. 251-272. (Buy at Amazon.com)(Tech Report)

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. 209-229. (Buy at Amazon.com) (Tech Report)

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. Numéro double spécial 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. (PDF)

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)(PS)

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. (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)