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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, May 21. [Epub ahead of print] (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.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 Genetics)

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 (2009). Detection of non-neutral substitution rates on mammalian phylogenies, Genome Research, 20: 110-121. (Link to Genome Research)

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)

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 Genomics)

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)

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 Systems Biology)

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 Neuroscience)

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)

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)

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)

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)

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. Journal of Statistical Planning and Inference, 125: 85-100. (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)

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)