| Year |
Citation |
Score |
| 2018 |
Israel JW, Chappell GA, Simon JM, Pott S, Safi A, Lewis L, Cotney P, Boulos HS, Bodnar W, Lieb JD, Crawford GE, Furey TS, Rusyn I. Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription. Mammalian Genome : Official Journal of the International Mammalian Genome Society. PMID 29429127 DOI: 10.1007/S00335-018-9739-6 |
0.34 |
|
| 2016 |
Jeffers TE, Lieb JD. Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans. Genome Research. PMID 27979995 DOI: 10.1101/gr.208173.116 |
0.483 |
|
| 2016 |
Pearson JC, McKay DJ, Lieb JD, Crews ST. Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers. Development (Cambridge, England). 143: 3723-3732. PMID 27802137 DOI: 10.1242/Dev.136895 |
0.69 |
|
| 2016 |
Adar S, Hu J, Lieb JD, Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis. Proceedings of the National Academy of Sciences of the United States of America. PMID 27036006 DOI: 10.1073/Pnas.1603388113 |
0.337 |
|
| 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 |
0.371 |
|
| 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 |
0.729 |
|
| 2015 |
Burman B, Zhang ZZ, Pegoraro G, Lieb JD, Misteli T. Histone modifications predispose genome regions to breakage and translocation. Genes & Development. PMID 26104467 DOI: 10.1101/gad.262170.115 |
0.393 |
|
| 2015 |
Hu J, Adar S, Selby CP, Lieb JD, Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution. Genes & Development. 29: 948-60. PMID 25934506 DOI: 10.1101/Gad.261271.115 |
0.366 |
|
| 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 |
0.326 |
|
| 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 |
0.747 |
|
| 2015 |
McKay DJ, Klusza S, Penke TJ, Meers MP, Curry KP, McDaniel SL, Malek PY, Cooper SW, Tatomer DC, Lieb JD, Strahl BD, Duronio RJ, Matera AG. Interrogating the function of metazoan histones using engineered gene clusters. Developmental Cell. 32: 373-86. PMID 25669886 DOI: 10.1016/J.Devcel.2014.12.025 |
0.653 |
|
| 2014 |
McKay DJ, Lieb JD. A split personality for nucleosomes. Cell. 159: 1249-51. PMID 25480289 DOI: 10.1016/J.Cell.2014.11.030 |
0.634 |
|
| 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 |
0.339 |
|
| 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 |
0.814 |
|
| 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 |
0.455 |
|
| 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 |
0.316 |
|
| 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 |
0.326 |
|
| 2014 |
Burman B, Zhang Z, Burgess R, Roukos V, Lieb J, Misteli T. Abstract 2406: Epigenetics of chromosomal breakage sites and translocations Cancer Research. 74: 2406-2406. DOI: 10.1158/1538-7445.Am2014-2406 |
0.542 |
|
| 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 |
0.694 |
|
| 2013 |
Ikegami K, Lieb JD. Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans. Molecular Cell. 51: 840-9. PMID 24011592 DOI: 10.1016/j.molcel.2013.08.001 |
0.332 |
|
| 2013 |
Hilton IB, Simon JM, Lieb JD, Davis IJ, Damania B, Dittmer DP. The open chromatin landscape of Kaposi's sarcoma-associated herpesvirus. Journal of Virology. 87: 11831-42. PMID 23986576 DOI: 10.1128/Jvi.01685-13 |
0.511 |
|
| 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 |
0.802 |
|
| 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 |
0.75 |
|
| 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 |
0.721 |
|
| 2013 |
Rohner S, Kalck V, Wang X, Ikegami K, Lieb JD, Gasser SM, Meister P. Promoter- and RNA polymerase II-dependent hsp-16 gene association with nuclear pores in Caenorhabditis elegans. The Journal of Cell Biology. 200: 589-604. PMID 23460676 DOI: 10.1083/jcb.201207024 |
0.383 |
|
| 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 |
0.302 |
|
| 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 |
0.324 |
|
| 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 |
0.459 |
|
| 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 |
0.839 |
|
| 2012 |
Palpant T, Lieb J. Tuning gene expression with nucleosome-disfavoring sequences. Nature Genetics. 44: 735-6. PMID 22735583 DOI: 10.1038/Ng.2328 |
0.491 |
|
| 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 |
0.37 |
|
| 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 |
0.813 |
|
| 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 |
0.465 |
|
| 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 |
0.79 |
|
| 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 |
0.376 |
|
| 2012 |
Patel M, Simon JM, Iglesia MD, Wu SB, McFadden AW, Lieb JD, Davis IJ. Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription. Genome Research. 22: 259-70. PMID 22086061 DOI: 10.1101/gr.125666.111 |
0.332 |
|
| 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 |
0.762 |
|
| 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 |
0.791 |
|
| 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 |
0.429 |
|
| 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 |
0.413 |
|
| 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 |
0.395 |
|
| 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 |
0.824 |
|
| 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 |
0.346 |
|
| 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 |
0.309 |
|
| 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 |
0.344 |
|
| 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 |
0.343 |
|
| 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 |
0.358 |
|
| 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 |
0.788 |
|
| 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 |
0.367 |
|
| 2010 |
He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XS. Nucleosome dynamics define transcriptional enhancers. Nature Genetics. 42: 343-7. PMID 20208536 DOI: 10.1038/Ng.545 |
0.402 |
|
| 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 |
0.835 |
|
| 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 |
0.769 |
|
| 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 |
0.769 |
|
| 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 |
0.436 |
|
| 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 |
0.821 |
|
| 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 |
0.767 |
|
| 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 |
0.808 |
|
| 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 |
0.817 |
|
| 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 |
0.433 |
|
| 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 |
0.843 |
|
| 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 |
0.826 |
|
| 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 |
0.831 |
|
| 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 |
0.805 |
|
| 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 |
0.393 |
|
| 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 |
0.787 |
|
| 2007 |
Fang J, Hogan GJ, Liang G, Lieb JD, Zhang Y. The Saccharomyces cerevisiae histone demethylase Jhd1 fine-tunes the distribution of H3K36me2. Molecular and Cellular Biology. 27: 5055-65. PMID 17470555 DOI: 10.1128/Mcb.00127-07 |
0.341 |
|
| 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 |
0.406 |
|
| 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 |
0.808 |
|
| 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 |
0.652 |
|
| 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 |
0.79 |
|
| 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 |
0.624 |
|
| 2007 |
Ercan S, Whittle C, Lieb J. Chromatin immunoprecipitation from C. elegans embryos Nature Protocols. DOI: 10.1038/Nprot.2007.123 |
0.754 |
|
| 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 |
0.445 |
|
| 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 |
0.489 |
|
| 2006 |
Ercan S, Lieb JD. New evidence that DNA encodes its packaging. Nature Genetics. 38: 1104-5. PMID 17006463 DOI: 10.1038/Ng1006-1104 |
0.399 |
|
| 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 |
0.74 |
|
| 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 |
0.378 |
|
| 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 |
0.786 |
|
| 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 |
0.442 |
|
| 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 |
0.462 |
|
| 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 |
0.345 |
|
| 2005 |
Rao B, Shibata Y, Strahl BD, Lieb JD. Dimethylation of histone H3 at lysine 36 demarcates regulatory and nonregulatory chromatin genome-wide. Molecular and Cellular Biology. 25: 9447-59. PMID 16227595 DOI: 10.1128/Mcb.25.21.9447-9459.2005 |
0.684 |
|
| 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 |
0.37 |
|
| 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 |
0.487 |
|
| 2004 |
Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature Genetics. 36: 900-5. PMID 15247917 DOI: 10.1038/Ng1400 |
0.68 |
|
| 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 |
0.361 |
|
| 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 |
0.436 |
|
| 2003 |
Lieb JD. Genome-wide mapping of protein-DNA interactions by chromatin immunoprecipitation and DNA microarray hybridization. Methods in Molecular Biology (Clifton, N.J.). 224: 99-109. PMID 12710669 DOI: 10.1385/1-59259-364-X:99 |
0.367 |
|
| 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 |
0.32 |
|
| 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 |
0.807 |
|
| 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 |
0.483 |
|
| 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 |
0.502 |
|
| 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 |
0.481 |
|
| 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 |
0.506 |
|
| 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 |
0.462 |
|
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