Sunduz Keles, Ph.D. - Publications

Affiliations: 
University of Wisconsin, Madison, Madison, WI 
 2003 University of California, Berkeley, Berkeley, CA 

111 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Xu X, Qiao D, Dong C, Mann M, Garofalo RP, Keles S, Brasier AR. The SWI/SNF-Related, Matrix Associated, Actin-Dependent Regulator of Chromatin A4 Core Complex Represses Respiratory Syncytial Virus-Induced Syncytia Formation and Subepithelial Myofibroblast Transition. Frontiers in Immunology. 12: 633654. PMID 33732255 DOI: 10.3389/fimmu.2021.633654  0.01
2021 Huang K, Wu Y, Shin J, Zheng Y, Siahpirani AF, Lin Y, Ni Z, Chen J, You J, Keles S, Wang D, Roy S, Lu Q. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. Plos Genetics. 17: e1009309. PMID 33539344 DOI: 10.1371/journal.pgen.1009309  0.01
2020 Zwifelhofer NM, Cai X, Liao R, Mao B, Conn DJ, Mehta C, Keles S, Xia Y, Bresnick EH. GATA factor-regulated solute carrier ensemble reveals a nucleoside transporter-dependent differentiation mechanism. Plos Genetics. 16: e1009286. PMID 33370779 DOI: 10.1371/journal.pgen.1009286  0.01
2020 Liu P, Soukup AA, Bresnick EH, Dewey CN, Keles S. PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Genome Research. PMID 32958497 DOI: 10.1101/Gr.252445.119  0.01
2020 Johnson KD, Conn DJ, Shishkova E, Katsumura KR, Liu P, Shen S, Ranheim EA, Kraus SG, Wang W, Calvo KR, Hsu AP, Holland SM, Coon JJ, Keles S, Bresnick EH. Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories. The Journal of Experimental Medicine. 217. PMID 32736380 DOI: 10.1084/Jem.20191526  0.01
2020 Zheng Y, Zhou P, Keleş S. FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection. Methods (San Diego, Calif.). PMID 32663510 DOI: 10.1016/J.Ymeth.2020.07.001  0.01
2020 Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH. Discovering How Heme Controls Genome Function Through Heme-omics. Cell Reports. 31: 107832. PMID 32610133 DOI: 10.1016/J.Celrep.2020.107832  0.01
2020 Chen F, Keleş S. SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins. Genome Biology. 21: 139. PMID 32532357 DOI: 10.1186/S13059-020-02039-7  0.01
2020 Damaschke NA, Gawdzik J, Avilla M, Yang B, Svaren J, Roopra A, Luo JH, Yu YP, Keles S, Jarrard DF. CTCF loss mediates unique DNA hypermethylation landscapes in human cancers. Clinical Epigenetics. 12: 80. PMID 32503656 DOI: 10.1186/S13148-020-00869-7  0.01
2020 Lee H, Lee YS, Harenda Q, Pietrzak S, Oktay HZ, Schreiber S, Liao Y, Sonthalia S, Ciecko AE, Chen YG, Keles S, Sridharan R, Engin F. Beta Cell Dedifferentiation Induced by IRE1α Deletion Prevents Type 1 Diabetes. Cell Metabolism. PMID 32220307 DOI: 10.1016/J.Cmet.2020.03.002  0.01
2020 Patel NJ, Hogan KJ, Rizk E, Stewart K, Madrid A, Meethal SV, Alisch R, Borth L, Papale LA, Ondoma S, Gorges LR, Weber K, Lake W, Bauer A, Hariharan N, ... ... Keles S, et al. Correction to: Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny. Molecular Neurobiology. PMID 32002788 DOI: 10.1007/S12035-020-01886-6  0.01
2020 Patel NJ, Hogan KJ, Rizk E, Stewart K, Madrid A, Vadakkadath Meethal S, Alisch R, Borth L, Papale LA, Ondoma S, Gorges LR, Weber K, Lake W, Bauer A, Hariharan N, ... ... Keles S, et al. Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny. Molecular Neurobiology. PMID 31919777 DOI: 10.1007/S12035-019-01812-5  0.01
2019 Zheng Y, Keleş S. FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. Nature Methods. PMID 31712779 DOI: 10.1038/S41592-019-0624-3  0.01
2019 Rojo C, Zhang Q, Keleş S. iFunMed: Integrative functional mediation analysis of GWAS and eQTL studies. Genetic Epidemiology. PMID 31328826 DOI: 10.1002/Gepi.22217  0.01
2019 Preston MA, Porter DF, Chen F, Buter N, Lapointe CP, Keles S, Kimble J, Wickens M. Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase. Nature Methods. PMID 30988468 DOI: 10.1038/S41592-019-0370-6  0.01
2019 Zheng Y, Ay F, Keles S. Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. Elife. 8. PMID 30702424 DOI: 10.7554/Elife.38070  0.01
2019 Soukup AA, Zheng Y, Mehta C, Wu J, Liu P, Cao M, Hofmann I, Zhou Y, Zhang J, Johnson KD, Choi K, Keles S, Bresnick EH. Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer. The Journal of Clinical Investigation. PMID 30620726 DOI: 10.1172/Jci122694  0.01
2019 Wickens M, Preston MA, Porter D, Chen F, Buter N, Lapointe CP, Keles S, Kimble J. TRAID-seq: Unbiased analysis of RNA tailing enzyme activity at single-nucleotide resolution Protocol Exchange. DOI: 10.1038/Protex.2019.016  0.01
2018 Shin S, Hudson R, Harrison C, Craven M, Keles S. atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding. Bioinformatics (Oxford, England). PMID 30534948 DOI: 10.1093/Bioinformatics/Bty1010  0.01
2018 Tanimura N, Liao R, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang Y, Zheng Y, Keles S, Xu J, Coon JJ, Bresnick EH. GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism. Developmental Cell. PMID 30122630 DOI: 10.1016/J.Devcel.2018.07.022  0.01
2018 Bresnick EH, Hewitt KJ, Mehta C, Keles S, Paulson RF, Johnson KD. Mechanisms of erythrocyte development and regeneration: implications for regenerative medicine and beyond. Development (Cambridge, England). 145. PMID 29321181 DOI: 10.1242/Dev.151423  0.01
2018 Zheng Y, Ay F, Keles S. Author response: Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies Elife. DOI: 10.7554/Elife.38070.103  0.01
2017 Zhang Q, Keles S. An empirical Bayes test for allelic-imbalance detection in ChIP-seq. Biostatistics (Oxford, England). PMID 29126153 DOI: 10.1093/Biostatistics/Kxx060  0.01
2017 Beauchene NA, Mettert EL, Moore LJ, Keleş S, Willey ER, Kiley PJ. O2 availability impacts iron homeostasis in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087312 DOI: 10.1073/Pnas.1707189114  0.01
2017 Welch R, Chung D, Grass J, Landick R, Keles S. Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments. Nucleic Acids Research. 45: e145. PMID 28911122 DOI: 10.1093/Nar/Gkx594  0.01
2017 Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, Coon JJ, Kim JS, Dewey CN, Keles S, Hao S, Paulson RF, Bresnick EH. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Developmental Cell. 42: 213-225.e4. PMID 28787589 DOI: 10.1016/J.Devcel.2017.07.009  0.01
2017 Shin S, Keleş S. Annotation Regression for Genome-Wide Association Studies with an Application to Psychiatric Genomic Consortium Data. Statistics in Biosciences. 9: 50-72. PMID 28781711 DOI: 10.1007/S12561-016-9154-Z  0.01
2017 Otlu B, Firtina C, Keles S, Tastan O. GLANET: Genomic Loci ANnotation and Enrichment Tool. Bioinformatics (Oxford, England). PMID 28541490 DOI: 10.1093/Bioinformatics/Btx326  0.01
2017 Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Goke J, Mueller NS, ... ... Keles S, et al. Predicting gene expression in massively parallel reporter assays: a comparative study. Human Mutation. PMID 28220625 DOI: 10.1002/Humu.23197  0.01
2016 Zuo C, Chen K, Hewitt KJ, Bresnick EH, Keleş S. A Hierarchical Framework for State-Space Matrix Inference and Clustering. The Annals of Applied Statistics. 10: 1348-1372. PMID 29910842 DOI: 10.1214/16-Aoas938  0.01
2016 Kim T, Havighurst T, Kim K, Hebbring SJ, Ye Z, Aylward J, Keles S, Xu YG, Spiegelman VS. RNA-Binding Protein IGF2BP1 in Cutaneous Squamous Cell Carcinoma. The Journal of Investigative Dermatology. PMID 27856289 DOI: 10.1016/J.Jid.2016.10.042  0.01
2016 Zuo C, Chen K, Keleş S. A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27835030 DOI: 10.1089/Cmb.2016.0138  0.01
2016 Papale LA, Li S, Madrid A, Zhang Q, Chen L, Chopra P, Jin P, Keleş S, Alisch RS. Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress. Neurobiology of Disease. PMID 27576189 DOI: 10.1016/J.Nbd.2016.08.014  1
2016 Liu P, Sanalkumar R, Bresnick EH, Keleş S, Dewey CN. Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Genome Research. PMID 27405803 DOI: 10.1101/Gr.199174.115  0.01
2016 Li R, Dong Q, Yuan X, Zeng X, Gao Y, Chiao C, Li H, Zhao X, Keles S, Wang Z, Chang Q. Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome. Plos Genetics. 12: e1006129. PMID 27352031 DOI: 10.1371/Journal.Pgen.1006129  1
2016 Capowski EE, Wright LS, Liang K, Phillips MJ, Wallace K, Petelinsek A, Hagstrom A, Pinilla I, Borys K, Lien J, Min JH, Keles S, Thomson JA, Gamm DM. Regulation of WNT Signaling by VSX2 during Optic Vesicle Patterning in Human Induced Pluripotent Stem Cells. Stem Cells (Dayton, Ohio). PMID 27301076 DOI: 10.1002/Stem.2414  1
2016 Hewitt KJ, Johnson KD, Gao X, Keles S, Bresnick EH. The Hematopoietic Stem and Progenitor Cell Cistrome: GATA Factor-Dependent cis-Regulatory Mechanisms. Current Topics in Developmental Biology. 118: 45-76. PMID 27137654 DOI: 10.1016/Bs.Ctdb.2016.01.002  1
2016 Zhang Q, Zeng X, Younkin S, Kawli T, Snyder MP, Keleş S. Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection. Bmc Bioinformatics. 17: 96. PMID 26908256 DOI: 10.1186/S12859-016-0957-1  1
2016 Damaschke NA, Yang B, Montgomery A, Svaren J, Roopra A, Luo J, Keles S, Jarrard D. Abstract 4434: CTCF acts as a master regulator to direct epigenetic events important for tumor development and progression Cancer Research. 76: 4434-4434. DOI: 10.1158/1538-7445.Am2016-4434  0.01
2015 Wang A, Welch R, Zhao B, Ta T, Keleş S, Johannsen E. EBNA3 proteins regulate EBNA2 binding to distinct RBPJ genomic sites. Journal of Virology. PMID 26719268 DOI: 10.1128/Jvi.02737-15  0.01
2015 Beauchene NA, Myers KS, Chung D, Park DM, Weisnicht AM, Keleş S, Kiley PJ. Impact of Anaerobiosis on Expression of the Iron-Responsive Fur and RyhB Regulons. Mbio. 6. PMID 26670385 DOI: 10.1128/Mbio.01947-15  1
2015 Xiong L, Kuan PF, Tian J, Keles S, Wang S. Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data. Cancer Informatics. 13: 123-131. PMID 26609213 DOI: 10.4137/Cin.S16353  0.01
2015 Li S, Papale LA, Zhang Q, Madrid A, Chen L, Chopra P, Keleş S, Jin P, Alisch RS. Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress. Neurobiology of Disease. PMID 26598390 DOI: 10.1016/J.Nbd.2015.11.010  1
2015 Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keleş S. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. Plos Computational Biology. 11: e1004491. PMID 26484757 DOI: 10.1371/Journal.Pcbi.1004491  1
2015 Papale LA, Zhang Q, Li S, Chen K, Keleş S, Alisch RS. Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism. Human Molecular Genetics. 24: 7121-31. PMID 26423458 DOI: 10.1093/Hmg/Ddv411  0.01
2015 Marty AJ, Broman AT, Zarnowski R, Dwyer TG, Bond LM, Lounes-Hadj Sahraoui A, Fontaine J, Ntambi JM, Keleş S, Kendziorski C, Gauthier GM. Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis. Plos Pathogens. 11: e1004959. PMID 26114571 DOI: 10.1371/Journal.Ppat.1004959  1
2015 Hewitt KJ, Kim DH, Devadas P, Prathibha R, Zuo C, Sanalkumar R, Johnson KD, Kang YA, Kim JS, Dewey CN, Keles S, Bresnick EH. Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome. Molecular Cell. 59: 62-74. PMID 26073540 DOI: 10.1016/J.Molcel.2015.05.020  1
2015 Lopez-Anido C, Sun G, Koenning M, Srinivasan R, Hung HA, Emery B, Keles S, Svaren J. Differential Sox10 genomic occupancy in myelinating glia. Glia. PMID 25974668 DOI: 10.1002/Glia.22855  0.01
2015 Hung HA, Sun G, Keles S, Svaren J. Dynamic regulation of Schwann cell enhancers after peripheral nerve injury. The Journal of Biological Chemistry. 290: 6937-50. PMID 25614629 DOI: 10.1074/Jbc.M114.622878  1
2015 Yao C, Chen BH, Joehanes R, Otlu B, Zhang X, Liu C, Huan T, Tastan O, Cupples LA, Meigs JB, Fox CS, Freedman JE, Courchesne P, O'Donnell CJ, Munson PJ, ... Keles S, et al. Integromic analysis of genetic variation and gene expression identifies networks for cardiovascular disease phenotypes. Circulation. 131: 536-49. PMID 25533967 DOI: 10.1161/Circulationaha.114.010696  1
2015 Lopez-Anido C, Sun G, Koenning M, Srinivasan R, Hung HA, Emery B, Keles S, Svaren J. Differential Sox10 genomic occupancy in myelinating glia Glia. DOI: 10.1002/glia.22855  1
2014 Alisch RS, Chopra P, Fox AS, Chen K, White AT, Roseboom PH, Keles S, Kalin NH. Differentially methylated plasticity genes in the amygdala of young primates are linked to anxious temperament, an at risk phenotype for anxiety and depressive disorders. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 34: 15548-56. PMID 25411484 DOI: 10.1523/Jneurosci.3338-14.2014  1
2014 Zhang Q, Keleş S. CNV-guided multi-read allocation for ChIP-seq. Bioinformatics (Oxford, England). 30: 2860-7. PMID 24966364 DOI: 10.1093/Bioinformatics/Btu402  0.01
2014 Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, et al. A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology. 32: 1202-12. PMID 24880487 DOI: 10.1038/nbt.2877  1
2014 DeVilbiss AW, Sanalkumar R, Johnson KD, Keles S, Bresnick EH. Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points. Experimental Hematology. 42: 618-29. PMID 24816274 DOI: 10.1016/J.Exphem.2014.05.004  1
2014 Hewitt KJ, Sanalkumar R, Johnson KD, Keles S, Bresnick EH. Epigenetic and genetic mechanisms in red cell biology. Current Opinion in Hematology. 21: 155-64. PMID 24722192 DOI: 10.1097/Moh.0000000000000034  1
2014 Zuo C, Keleş S. A statistical framework for power calculations in ChIP-seq experiments. Bioinformatics (Oxford, England). 30: 753-60. PMID 23665773 DOI: 10.1093/Bioinformatics/Btt200  0.04
2013 Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keleş S. dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data. Plos Computational Biology. 9: e1003246. PMID 24146601 DOI: 10.1371/Journal.Pcbi.1003246  1
2013 Bellesi M, Pfister-Genskow M, Maret S, Keles S, Tononi G, Cirelli C. Effects of sleep and wake on oligodendrocytes and their precursors. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 33: 14288-300. PMID 24005282 DOI: 10.1523/Jneurosci.5102-12.2013  1
2013 Shanle EK, Zhao Z, Hawse J, Wisinski K, Keles S, Yuan M, Xu W. Research resource: global identification of estrogen receptor β target genes in triple negative breast cancer cells. Molecular Endocrinology (Baltimore, Md.). 27: 1762-75. PMID 23979844 DOI: 10.1210/Me.2013-1164  1
2013 Zeng X, Sanalkumar R, Bresnick EH, Li H, Chang Q, KeleÅŸ S. jMOSAiCS: joint analysis of multiple ChIP-seq datasets. Genome Biology. 14: R38. PMID 23844871 DOI: 10.1186/Gb-2013-14-4-R38  1
2013 Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, KeleÅŸ S, Landick R, Kiley PJ. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. Plos Genetics. 9: e1003565. PMID 23818864 DOI: 10.1371/Journal.Pgen.1003565  1
2012 Johnson KD, Hsu AP, Ryu MJ, Wang J, Gao X, Boyer ME, Liu Y, Lee Y, Calvo KR, Keles S, Zhang J, Holland SM, Bresnick EH. Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity. The Journal of Clinical Investigation. 122: 3692-704. PMID 22996659 DOI: 10.1172/Jci61623  1
2012 Liang K, KeleÅŸ S. Normalization of ChIP-seq data with control. Bmc Bioinformatics. 13: 199. PMID 22883957 DOI: 10.1186/1471-2105-13-199  1
2012 Srinivasan R, Sun G, Keles S, Jones EA, Jang SW, Krueger C, Moran JJ, Svaren J. Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve. Nucleic Acids Research. 40: 6449-60. PMID 22492709 DOI: 10.1093/Nar/Gks313  1
2012 Huebert DJ, Kuan PF, Keleş S, Gasch AP. Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Molecular and Cellular Biology. 32: 1645-53. PMID 22354995 DOI: 10.1128/Mcb.06170-11  1
2012 Powell E, Shanle E, Brinkman A, Li J, Keles S, Wisinski KB, Huang W, Xu W. Identification of estrogen receptor dimer selective ligands reveals growth-inhibitory effects on cells that co-express ERα and ERβ. Plos One. 7: e30993. PMID 22347418 DOI: 10.1371/Journal.Pone.0030993  1
2012 Qiu C, Kershner A, Wang Y, Holley CP, Wilinski D, Keles S, Kimble J, Wickens M, Hall TM. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket. The Journal of Biological Chemistry. 287: 6949-57. PMID 22205700 DOI: 10.1074/Jbc.M111.326264  1
2012 Yang X, Qiao D, Meyer K, Pier T, Keles S, Friedl A. Angiogenesis induced by signal transducer and activator of transcription 5A (STAT5A) is dependent on autocrine activity of proliferin. The Journal of Biological Chemistry. 287: 6490-502. PMID 22199350 DOI: 10.1074/Jbc.M111.254631  1
2012 Jones EA, Brewer MH, Srinivasan R, Krueger C, Sun G, Charney KN, Keles S, Antonellis A, Svaren J. Distal enhancers upstream of the Charcot-Marie-Tooth type 1A disease gene PMP22. Human Molecular Genetics. 21: 1581-91. PMID 22180461 DOI: 10.1093/Hmg/Ddr595  1
2012 Liang K, Keles S. Detecting differential binding of transcription factors with ChIP-seq. Bioinformatics (Oxford, England). 28: 121-2. PMID 22057161 DOI: 10.1093/Bioinformatics/Btr605  1
2012 Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Molecular and Cellular Biology. 32: 226-39. PMID 22025678 DOI: 10.1128/Mcb.06166-11  1
2012 Qiu C, Kershner A, Wang Y, Holley CH, Wilinski D, Keles S, Kimble J, Wickens M, Hall TMT. Divergence of PUF protein specificity through variations in an RNA-binding pocket Journal of Biological Chemistry. DOI: 10.2210/Pdb3V71/Pdb  0.01
2011 Kuan PF, Chung D, Pan G, Thomson JA, Stewart R, Keleş S. A Statistical Framework for the Analysis of ChIP-Seq Data. Journal of the American Statistical Association. 106: 891-903. PMID 26478641 DOI: 10.1198/Jasa.2011.Ap09706  1
2011 Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proceedings of the National Academy of Sciences of the United States of America. 108: 13641-6. PMID 21808000 DOI: 10.1073/Pnas.1108440108  1
2011 Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, KeleÅŸ S. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. Plos Computational Biology. 7: e1002111. PMID 21779159 DOI: 10.1371/Journal.Pcbi.1002111  1
2010 Jang SW, Srinivasan R, Jones EA, Sun G, Keles S, Krueger C, Chang LW, Nagarajan R, Svaren J. Locus-wide identification of Egr2/Krox20 regulatory targets in myelin genes. Journal of Neurochemistry. 115: 1409-20. PMID 21044070 DOI: 10.1111/J.1471-4159.2010.07045.X  1
2010 Tietjen JR, Zhang DW, Rodríguez-Molina JB, White BE, Akhtar MS, Heidemann M, Li X, Chapman RD, Shokat K, Keles S, Eick D, Ansari AZ. Chemical-genomic dissection of the CTD code Nature Structural and Molecular Biology. 17: 1154-1161. PMID 20802488 DOI: 10.1038/Nsmb.1900  1
2010 Bresnick EH, Lee HY, Fujiwara T, Johnson KD, Keles S. GATA switches as developmental drivers. The Journal of Biological Chemistry. 285: 31087-93. PMID 20670937 DOI: 10.1074/Jbc.R110.159079  1
2010 Chung D, Keles S. Sparse partial least squares classification for high dimensional data. Statistical Applications in Genetics and Molecular Biology. 9: Article17. PMID 20361856 DOI: 10.2202/1544-6115.1492  1
2010 Eng KH, Kvitek DJ, Keles S, Gasch AP. Transient genotype-by-environment interactions following environmental shock provide a source of expression variation for essential genes. Genetics. 184: 587-93. PMID 19966067 DOI: 10.1534/Genetics.109.107268  1
2010 Bochkov YA, Hanson KM, Keles S, Brockman-Schneider RA, Jarjour NN, Gern JE. Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma Mucosal Immunology. 3: 69-80. PMID 19710636 DOI: 10.1038/Mi.2009.109  1
2009 Bravo HC, Wright S, Eng KH, Keles S, Wahba G. Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming. Journal of Machine Learning Research : Jmlr. 5: 41-48. PMID 22081761  1
2009 Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Molecular Cell. 36: 667-81. PMID 19941826 DOI: 10.1016/J.Molcel.2009.11.001  1
2009 Peters JM, Mooney RA, Kuan PF, Rowland JL, Keles S, Landick R. Rho directs widespread termination of intragenic and stable RNA transcription. Proceedings of the National Academy of Sciences of the United States of America. 106: 15406-11. PMID 19706412 DOI: 10.1073/Pnas.0903846106  1
2009 Kuan PF, Huebert D, Gasch A, Keles S. A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions. Statistical Applications in Genetics and Molecular Biology. 8: Article29. PMID 19572828 DOI: 10.2202/1544-6115.1454  1
2009 Koh YY, Opperman L, Stumpf C, Mandan A, Keles S, Wickens M. A single C. elegans PUF protein binds RNA in multiple modes. Rna (New York, N.Y.). 15: 1090-9. PMID 19369425 DOI: 10.1261/Rna.1545309  1
2009 Chun H, Keles S. Expression quantitative trait loci mapping with multivariate sparse partial least squares regression. Genetics. 182: 79-90. PMID 19270271 DOI: 10.1534/Genetics.109.100362  0.01
2008 Wozniak RJ, Keles S, Lugus JJ, Young KH, Boyer ME, Tran TM, Choi K, Bresnick EH. Molecular hallmarks of endogenous chromatin complexes containing master regulators of hematopoiesis. Molecular and Cellular Biology. 28: 6681-94. PMID 18779319 DOI: 10.1128/Mcb.01061-08  1
2008 Keleş S, Warren CL, Carlson CD, Ansari AZ. CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data. Nucleic Acids Research. 36: 3171-84. PMID 18411210 DOI: 10.1093/Nar/Gkn057  1
2008 Wei H, Kuan PF, Tian S, Yang C, Nie J, Sengupta S, Ruotti V, Jonsdottir GA, Keles S, Thomson JA, Stewart R. A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Research. 36: 2926-38. PMID 18385155 DOI: 10.1093/Nar/Gkn133  1
2008 Jörnsten R, Keleş S. Mixture models with multiple levels, with application to the analysis of multifactor gene expression data. Biostatistics (Oxford, England). 9: 540-54. PMID 18256042 DOI: 10.1093/Biostatistics/Kxm051  0.01
2008 Shim H, Keles S. Integrating quantitative information from ChIP-chip experiments into motif finding. Biostatistics (Oxford, England). 9: 51-65. PMID 17533175 DOI: 10.1093/Biostatistics/Kxm014  1
2008 Keleş S, Chun H. Comments on: Augmenting the bootstrap to analyze high dimensional genomic data : C to the ridge regularized covariance estimator with bagging Test. 17: 36-39. DOI: 10.1007/S11749-008-0104-Z  1
2007 Isogai Y, Keles S, Prestel M, Hochheimer A, Tjian R. Transcription of histone gene cluster by differential core-promoter factors. Genes & Development. 21: 2936-49. PMID 17978101 DOI: 10.1101/Gad.1608807  1
2007 Goff LA, Davila J, Jörnsten R, Keles S, Hart RP. Bioinformatic analysis of neural stem cell differentiation. Journal of Biomolecular Techniques : Jbt. 18: 205-12. PMID 17916793  1
2007 Sweitzer NK, Shenoy M, Stein JH, Keles S, Palta M, LeCaire T, Mitchell GF. Increases in central aortic impedance precede alterations in arterial stiffness measures in type 1 diabetes. Diabetes Care. 30: 2886-91. PMID 17686834 DOI: 10.2337/Dc07-0191  1
2007 Hopkins DR, Keles S, Greenspan DS. The bone morphogenetic protein 1/Tolloid-like metalloproteinases. Matrix Biology : Journal of the International Society For Matrix Biology. 26: 508-23. PMID 17560775 DOI: 10.1016/J.Matbio.2007.05.004  1
2007 Keleş S. Mixture modeling for genome-wide localization of transcription factors. Biometrics. 63: 10-21. PMID 17447925 DOI: 10.1111/J.1541-0420.2005.00659.X  0.01
2007 Bembom O, Keles S, van der Laan MJ. Supervised detection of conserved motifs in DNA sequences with cosmo. Statistical Applications in Genetics and Molecular Biology. 6: Article8. PMID 17402923 DOI: 10.2202/1544-6115.1260  1
2007 Isogai Y, Takada S, Tjian R, Kele? S. Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription. The Embo Journal. 26: 79-89. PMID 17170711 DOI: 10.1038/Sj.Emboj.7601448  1
2006 Keleş S, van der Laan MJ, Dudoit S, Cawley SE. Multiple testing methods for ChIP-Chip high density oligonucleotide array data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 579-613. PMID 16706714 DOI: 10.1089/Cmb.2006.13.579  1
2005 Lu F, Keles S, Wright SJ, Wahba G. Framework for kernel regularization with application to protein clustering. Proceedings of the National Academy of Sciences of the United States of America. 102: 12332-7. PMID 16109767 DOI: 10.1073/Pnas.0505411102  1
2005 Cinar H, Keles S, Jin Y. Expression profiling of GABAergic motor neurons in Caenorhabditis elegans. Current Biology : Cb. 15: 340-6. PMID 15723795 DOI: 10.1016/J.Cub.2005.02.025  1
2004 van der Laan MJ, Dudoit S, Keles S. Asymptotic optimality of likelihood-based cross-validation. Statistical Applications in Genetics and Molecular Biology. 3: Article4. PMID 16646820 DOI: 10.2202/1544-6115.1036  1
2004 Keles S, van der Laan MJ, Vulpe C. Regulatory motif finding by logic regression. Bioinformatics (Oxford, England). 20: 2799-811. PMID 15166027 DOI: 10.1093/Bioinformatics/Bth333  1
2004 De Freitas JM, Kim JH, Poynton H, Su T, Wintz H, Fox T, Holman P, Loguinov A, Keles S, van der Laan M, Vulpe C. Exploratory and confirmatory gene expression profiling of mac1Delta. The Journal of Biological Chemistry. 279: 4450-8. PMID 14534306 DOI: 10.1074/Jbc.M212308200  1
2004 Kele? S, Van Der Laan M, Dudoit S. Asymptotically optimal model selection method with right censored outcomes Bernoulli. 10: 1011-1037. DOI: 10.3150/Bj/1106314848  1
2003 Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB. Supervised detection of regulatory motifs in DNA sequences. Statistical Applications in Genetics and Molecular Biology. 2: Article5. PMID 16646783 DOI: 10.2202/1544-6115.1015  1
2002 Kele? S, van der Laan M, Eisen MB. Identification of regulatory elements using a feature selection method. Bioinformatics (Oxford, England). 18: 1167-75. PMID 12217908 DOI: 10.1093/Bioinformatics/18.9.1167  1
2002 Keles S, Laan MJvd, Robins JM. Estimation of the Bivariate Survival Function with Generalized Bivariate Right Censored Data Structures Handbook of Statistics. 23: 143-173. DOI: 10.1016/S0169-7161(03)23008-X  0.2
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