Jason Lieb, Ph.D. - Publications

Biology University of North Carolina, Chapel Hill, Chapel Hill, NC 
Specificity and Function in Protein-Genome Interactions

90 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
2016 Simon JM, Davis JP, Lee SE, Schaner MR, Gipson GR, Weiser M, Sartor RB, Herfarth HH, Rahbar R, Sadiq TS, Koruda MJ, McGovern DP, Lieb JD, Mohlke KL, Furey TS, et al. Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses. European Journal of Immunology. PMID 27159132 DOI: 10.1002/Eji.201546237  0.76
2015 Wiesenfahrt T, Berg JY, Nishimura EO, Robinson AG, Goszczynski B, Lieb JD, McGhee JD. The Function and Regulation of the GATA Factor ELT-2 in the C. elegans Endoderm. Development (Cambridge, England). PMID 26700680 DOI: 10.1242/dev.130914  0.76
2015 Schulz KN, Bondra ER, Moshe A, Villalta JE, Lieb JD, Kaplan T, McKay DJ, Harrison MM. Zelda is differentially required for chromatin accessibility, transcription-factor binding and gene expression in the early Drosophila embryo. Genome Research. PMID 26335634 DOI: 10.1101/Gr.192682.115  0.76
2015 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 11: e1005177. PMID 25919664 DOI: 10.1371/Journal.Pgen.1005177  0.76
2015 Osborne Nishimura E, Zhang JC, Werts AD, Goldstein B, Lieb JD. Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis. Plos Genetics. 11: e1005117. PMID 25875092 DOI: 10.1371/Journal.Pgen.1005117  0.76
2015 Fleming JD, Giresi PG, Lindahl-Allen M, Krall EB, Lieb JD, Struhl K. STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer. Epigenetics & Chromatin. 8: 7. PMID 25784959 DOI: 10.1186/1756-8935-8-7  0.76
2015 Lynch VJ, Nnamani MC, Kapusta A, Brayer K, Plaza SL, Mazur EC, Emera D, Sheikh SZ, Grützner F, Bauersachs S, Graf A, Young SL, Lieb JD, DeMayo FJ, Feschotte C, et al. Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Reports. 10: 551-61. PMID 25640180 DOI: 10.1016/J.Celrep.2014.12.052  0.76
2014 McKay DJ, Lieb JD. A split personality for nucleosomes. Cell. 159: 1249-51. PMID 25480289 DOI: 10.1016/J.Cell.2014.11.030  0.76
2014 Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR, Birney E. Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. Plos Genetics. 10: e1004798. PMID 25411781 DOI: 10.1371/Journal.Pgen.1004798  0.76
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, ... ... Lieb JD, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111  0.76
2014 Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... Lieb JD, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415  0.56
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, ... ... Lieb JD, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111  0.76
2014 Strome S, Kelly WG, Ercan S, Lieb JD. Regulation of the X chromosomes in Caenorhabditis elegans. Cold Spring Harbor Perspectives in Biology. 6. PMID 24591522 DOI: 10.1101/Cshperspect.A018366  0.76
2014 Annayev Y, Adar S, Chiou YY, Lieb JD, Sancar A, Ye R. Gene model 129 (Gm129) encodes a novel transcriptional repressor that modulates circadian gene expression. The Journal of Biological Chemistry. 289: 5013-24. PMID 24385426 DOI: 10.1074/Jbc.M113.534651  0.76
2014 Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, Ho TH, Kuan PF, Jonasch E, Furey TS, Prins JF, Lieb JD, Rathmell WK, Davis IJ. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Research. 24: 241-50. PMID 24158655 DOI: 10.1101/Gr.158253.113  0.76
2013 McKay DJ, Lieb JD. A common set of DNA regulatory elements shapes Drosophila appendages. Developmental Cell. 27: 306-18. PMID 24229644 DOI: 10.1016/J.Devcel.2013.10.009  0.76
2013 Berkseth M, Ikegami K, Arur S, Lieb JD, Zarkower D. TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination. Proceedings of the National Academy of Sciences of the United States of America. 110: 16033-8. PMID 24046365 DOI: 10.1073/Pnas.1312087110  0.76
2013 Lickwar CR, Mueller F, Lieb JD. Genome-wide measurement of protein-DNA binding dynamics using competition ChIP. Nature Protocols. 8: 1337-53. PMID 23764940 DOI: 10.1038/Nprot.2013.077  0.76
2013 Simon JM, Giresi PG, Davis IJ, Lieb JD. A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE). Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit21.26. PMID 23547014 DOI: 10.1002/0471142727.Mb2126S102  0.76
2013 Grohman JK, Gorelick RJ, Lickwar CR, Lieb JD, Bower BD, Znosko BM, Weeks KM. A guanosine-centric mechanism for RNA chaperone function. Science (New York, N.Y.). 340: 190-5. PMID 23470731 DOI: 10.1126/Science.1230715  0.76
2012 Vielle A, Lang J, Dong Y, Ercan S, Kotwaliwale C, Rechtsteiner A, Appert A, Chen QB, Dose A, Egelhofer T, Kimura H, Stempor P, Dernburg A, Lieb JD, Strome S, et al. H4K20me1 contributes to downregulation of X-linked genes for C. elegans dosage compensation. Plos Genetics. 8: e1002933. PMID 23028348 DOI: 10.1371/Journal.Pgen.1002933  0.76
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, ... ... Lieb JD, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  0.76
2012 Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, ... ... Lieb JD, et al. The accessible chromatin landscape of the human genome. Nature. 489: 75-82. PMID 22955617 DOI: 10.1038/Nature11232  0.76
2012 Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. Plos Genetics. 8: e1002771. PMID 22737086 DOI: 10.1371/Journal.Pgen.1002771  0.76
2012 Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, ... Lieb JD, et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods. 9: 609-14. PMID 22522655 DOI: 10.1038/Nmeth.1985  0.76
2012 Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature. 484: 251-5. PMID 22498630 DOI: 10.1038/Nature10985  0.76
2012 Gassmann R, Rechtsteiner A, Yuen KW, Muroyama A, Egelhofer T, Gaydos L, Barron F, Maddox P, Essex A, Monen J, Ercan S, Lieb JD, Oegema K, Strome S, Desai A. An inverse relationship to germline transcription defines centromeric chromatin in C. elegans. Nature. 484: 534-7. PMID 22495302 DOI: 10.1038/Nature10973  0.76
2012 Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature Protocols. 7: 256-67. PMID 22262007 DOI: 10.1038/Nprot.2011.444  0.76
2012 Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research. 22: 9-24. PMID 22090374 DOI: 10.1101/Gr.127597.111  0.76
2011 Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nature Genetics. 43: 1179-85. PMID 22019781 DOI: 10.1038/Ng.948  0.76
2011 Mansisidor AR, Cecere G, Hoersch S, Jensen MB, Kawli T, Kennedy LM, Chavez V, Tan MW, Lieb JD, Grishok A. A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in Caenorhabditis elegans. Plos Genetics. 7: e1002299. PMID 21980302 DOI: 10.1371/Journal.Pgen.1002299  0.76
2011 Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biology. 12: R67. PMID 21787385 DOI: 10.1186/Gb-2011-12-7-R67  0.76
2011 Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, ... ... Lieb JD, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research. 21: 1757-67. PMID 21750106 DOI: 10.1101/Gr.121541.111  0.76
2011 Hanlon SE, Rizzo JM, Tatomer DC, Lieb JD, Buck MJ. The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae. Plos One. 6: e19060. PMID 21552514 DOI: 10.1371/Journal.Pone.0019060  0.76
2011 Ercan S, Lubling Y, Segal E, Lieb JD. High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans. Genome Research. 21: 237-44. PMID 21177966 DOI: 10.1101/Gr.115931.110  0.76
2011 Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung MS, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P, Rosenbaum H, Shin H, Taing S, Takasaki T, Iniguez AL, ... ... Lieb JD, et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Research. 21: 227-36. PMID 21177964 DOI: 10.1101/Gr.115519.110  0.76
2011 Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, ... ... Lieb JD, et al. An assessment of histone-modification antibody quality. Nature Structural & Molecular Biology. 18: 91-3. PMID 21131980 DOI: 10.1038/Nsmb.1972  0.76
2010 Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, ... ... Lieb JD, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914  0.56
2010 Ikegami K, Egelhofer TA, Strome S, Lieb JD. Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biology. 11: R120. PMID 21176223 DOI: 10.1186/Gb-2010-11-12-R120  0.76
2010 Kaplan N, Hughes TR, Lieb JD, Widom J, Segal E. Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biology. 11: 140. PMID 21118582 DOI: 10.1186/Gb-2010-11-11-140  0.76
2010 Burns C, Stajich JE, Rechtsteiner A, Casselton L, Hanlon SE, Wilke SK, Savytskyy OP, Gathman AC, Lilly WW, Lieb JD, Zolan ME, Pukkila PJ. Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution. Plos Genetics. 6: e1001135. PMID 20885784 DOI: 10.1371/Journal.Pgen.1001135  0.76
2010 Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Human Molecular Genetics. 19: R204-9. PMID 20846943 DOI: 10.1093/Hmg/Ddq404  0.76
2010 Rechtsteiner A, Ercan S, Takasaki T, Phippen TM, Egelhofer TA, Wang W, Kimura H, Lieb JD, Strome S. The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. Plos Genetics. 6: e1001091. PMID 20824077 DOI: 10.1371/Journal.Pgen.1001091  0.76
2010 Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal E. Nucleosome sequence preferences influence in vivo nucleosome organization. Nature Structural & Molecular Biology. 17: 918-20; author reply. PMID 20683473 DOI: 10.1038/Nsmb0810-918  0.76
2010 McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science (New York, N.Y.). 328: 235-9. PMID 20299549 DOI: 10.1126/Science.1184655  0.76
2010 Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Field Y, Lieb JD, Widom J, Segal E, Hughes TR. High nucleosome occupancy is encoded at human regulatory sequences. Plos One. 5: e9129. PMID 20161746 DOI: 10.1371/Journal.Pone.0009129  0.76
2010 Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, Berney T, Montanya E, Mohlke KL, Lieb JD, Ferrer J. A map of open chromatin in human pancreatic islets. Nature Genetics. 42: 255-9. PMID 20118932 DOI: 10.1038/Ng.530  0.76
2009 Ercan S, Dick LL, Lieb JD. The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence. Current Biology : Cb. 19: 1777-87. PMID 19853451 DOI: 10.1016/J.Cub.2009.09.047  0.64
2009 Berchowitz LE, Hanlon SE, Lieb JD, Copenhaver GP. A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae. Genome Research. 19: 2245-57. PMID 19801530 DOI: 10.1101/Gr.096297.109  0.76
2009 Whittle CM, Lazakovitch E, Gronostajski RM, Lieb JD. DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I. Proceedings of the National Academy of Sciences of the United States of America. 106: 12049-54. PMID 19584245 DOI: 10.1073/Pnas.0812894106  0.76
2009 Azvolinsky A, Giresi PG, Lieb JD, Zakian VA. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Molecular Cell. 34: 722-34. PMID 19560424 DOI: 10.1016/J.Molcel.2009.05.022  0.76
2009 Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, et al. Unlocking the secrets of the genome. Nature. 459: 927-30. PMID 19536255 DOI: 10.1038/459927A  0.76
2009 Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ. Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. Plos Genetics. 5: e1000502. PMID 19503594 DOI: 10.1371/Journal.Pgen.1000502  0.76
2009 Ercan S, Lieb JD. C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 17: 215-27. PMID 19308702 DOI: 10.1007/S10577-008-9011-0  0.64
2009 Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods (San Diego, Calif.). 48: 233-9. PMID 19303047 DOI: 10.1016/J.Ymeth.2009.03.003  0.76
2009 Lickwar CR, Rao B, Shabalin AA, Nobel AB, Strahl BD, Lieb JD. The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency. Plos One. 4: e4886. PMID 19295910 DOI: 10.1371/Journal.Pone.0004886  0.76
2009 Field Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, Lubling Y, Lieb JD, Widom J, Segal E. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nature Genetics. 41: 438-45. PMID 19252487 DOI: 10.1038/Ng.324  0.76
2009 Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature. 458: 362-6. PMID 19092803 DOI: 10.1038/Nature07667  0.76
2008 Gossett AJ, Lieb JD. DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity. Csh Protocols. 2008: pdb.prot4972. PMID 21356788 DOI: 10.1101/Pdb.Prot4972  0.76
2008 Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, ... ... Lieb JD, et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Molecular Cell. 32: 878-87. PMID 19111667 DOI: 10.1016/J.Molcel.2008.11.020  0.76
2008 Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD. The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. Plos Genetics. 4: e1000187. PMID 18787694 DOI: 10.1371/Journal.Pgen.1000187  0.76
2008 Ercan S, Lieb JD. Chromatin proteins do double duty. Cell. 133: 763-5. PMID 18510918 DOI: 10.1016/J.Cell.2008.05.011  0.64
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, ... ... Lieb JD, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508  0.76
2007 Voth WP, Yu Y, Takahata S, Kretschmann KL, Lieb JD, Parker RL, Milash B, Stillman DJ. Forkhead proteins control the outcome of transcription factor binding by antiactivation. The Embo Journal. 26: 4324-34. PMID 17898805 DOI: 10.1038/sj.emboj.7601859  0.76
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Lieb JD, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.76
2007 Mieczkowski PA, Dominska M, Buck MJ, Lieb JD, Petes TD. Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 104: 3955-60. PMID 17360459 DOI: 10.1073/Pnas.0700412104  0.76
2007 Ercan S, Giresi PG, Whittle CM, Zhang X, Green RD, Lieb JD. X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nature Genetics. 39: 403-8. PMID 17293863 DOI: 10.1038/Ng1983  0.76
2007 Morris SA, Rao B, Garcia BA, Hake SB, Diaz RL, Shabanowitz J, Hunt DF, Allis CD, Lieb JD, Strahl BD. Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification. The Journal of Biological Chemistry. 282: 7632-40. PMID 17189264 DOI: 10.1074/Jbc.M607909200  0.76
2007 Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research. 17: 877-85. PMID 17179217 DOI: 10.1101/Gr.5533506  0.76
2007 Xiao T, Shibata Y, Rao B, Laribee RN, O'Rourke R, Buck MJ, Greenblatt JF, Krogan NJ, Lieb JD, Strahl BD. The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Molecular and Cellular Biology. 27: 721-31. PMID 17088384 DOI: 10.1128/Mcb.01628-06  0.76
2006 Buck MJ, Lieb JD. A chromatin-mediated mechanism for specification of conditional transcription factor targets. Nature Genetics. 38: 1446-51. PMID 17099712 DOI: 10.1038/Ng1917  0.76
2006 Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Research. 16: 1517-28. PMID 17053089 DOI: 10.1101/Gr.5655606  0.76
2006 Ercan S, Lieb JD. New evidence that DNA encodes its packaging. Nature Genetics. 38: 1104-5. PMID 17006463 DOI: 10.1038/Ng1006-1104  0.64
2006 Giresi PG, Lieb JD. How to find an opening (or lots of them). Nature Methods. 3: 501-2. PMID 16791206 DOI: 10.1038/Nmeth0706-501  0.76
2006 Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenetic and Genome Research. 114: 1-15. PMID 16717444 DOI: 10.1159/000091922  0.76
2006 Giresi PG, Gupta M, Lieb JD. Regulation of nucleosome stability as a mediator of chromatin function. Current Opinion in Genetics & Development. 16: 171-6. PMID 16503136 DOI: 10.1016/J.Gde.2006.02.003  0.76
2006 Mieczkowski PA, Dominska M, Buck MJ, Gerton JL, Lieb JD, Petes TD. Global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae. Molecular and Cellular Biology. 26: 1014-27. PMID 16428454 DOI: 10.1128/Mcb.26.3.1014-1027.2006  0.76
2005 Lieb JD, Clarke ND. Control of transcription through intragenic patterns of nucleosome composition. Cell. 123: 1187-90. PMID 16377560 DOI: 10.1016/J.Cell.2005.12.010  0.76
2005 Buck MJ, Nobel AB, Lieb JD. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biology. 6: R97. PMID 16277752 DOI: 10.1186/Gb-2005-6-11-R97  0.76
2005 Liu X, Noll DM, Lieb JD, Clarke ND. DIP-chip: rapid and accurate determination of DNA-binding specificity. Genome Research. 15: 421-7. PMID 15710749 DOI: 10.1101/Gr.3256505  0.76
2004 Hanlon SE, Lieb JD. Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Current Opinion in Genetics & Development. 14: 697-705. PMID 15531167 DOI: 10.1016/J.Gde.2004.09.008  0.76
2004 Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics. 83: 349-60. PMID 14986705 DOI: 10.1016/J.Ygeno.2003.11.004  0.76
2003 Nagy PL, Cleary ML, Brown PO, Lieb JD. Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. Proceedings of the National Academy of Sciences of the United States of America. 100: 6364-9. PMID 12750471 DOI: 10.1073/Pnas.1131966100  0.76
2003 Conlon EM, Liu XS, Lieb JD, Liu JS. Integrating regulatory motif discovery and genome-wide expression analysis. Proceedings of the National Academy of Sciences of the United States of America. 100: 3339-44. PMID 12626739 DOI: 10.1073/pnas.0630591100  0.76
2002 Chu DS, Dawes HE, Lieb JD, Chan RC, Kuo AF, Meyer BJ. A molecular link between gene-specific and chromosome-wide transcriptional repression. Genes & Development. 16: 796-805. PMID 11937488 DOI: 10.1101/Gad.972702  0.76
2001 Lieb JD, Liu X, Botstein D, Brown PO. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nature Genetics. 28: 327-34. PMID 11455386 DOI: 10.1038/Ng569  0.76
2000 Lieb JD, de Solorzano CO, Rodriguez EG, Jones A, Angelo M, Lockett S, Meyer BJ. The Caenorhabditis elegans dosage compensation machinery is recruited to X chromosome DNA attached to an autosome. Genetics. 156: 1603-21. PMID 11102361  0.76
1998 Lieb JD, Albrecht MR, Chuang PT, Meyer BJ. MIX-1: an essential component of the C. elegans mitotic machinery executes X chromosome dosage compensation. Cell. 92: 265-77. PMID 9458050 DOI: 10.1016/S0092-8674(00)80920-4  0.76
1996 Chuang PT, Lieb JD, Meyer BJ. Sex-specific assembly of a dosage compensation complex on the nematode X chromosome. Science (New York, N.Y.). 274: 1736-9. PMID 8939870 DOI: 10.1126/Science.274.5293.1736  0.76
1996 Lieb JD, Capowski EE, Meneely P, Meyer BJ. DPY-26, a link between dosage compensation and meiotic chromosome segregation in the nematode. Science (New York, N.Y.). 274: 1732-6. PMID 8939869 DOI: 10.1126/science.274.5293.1732  0.76
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