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Lijia Ma - Publications

Affiliations: 
University of Chicago, Chicago, IL 
Area:
TF regulation
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36 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 Sheng T, Ho SWT, Ooi WF, Xu C, Xing M, Padmanabhan N, Huang KK, Ma L, Ray M, Guo YA, Sim NL, Anene-Nzelu CG, Chang MM, Razavi-Mohseni M, Beer MA, et al. Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer. Genome Medicine. 13: 158. PMID 34635154 DOI: 10.1186/s13073-021-00970-3  0.485
2020 Lee D, Shi M, Moran J, Wall M, Zhang J, Liu J, Fitzgerald D, Kyono Y, Ma L, White KP, Gerstein M. STARRPeaker: uniform processing and accurate identification of STARR-seq active regions. Genome Biology. 21: 298. PMID 33292397 DOI: 10.1186/s13059-020-02194-x  0.674
2020 Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, ... ... Ma L, et al. An integrative ENCODE resource for cancer genomics. Nature Communications. 11: 3696. PMID 32728046 DOI: 10.1038/S41467-020-14743-W  0.743
2020 Song Q, Ni K, Liu M, Li Y, Wang L, Wang Y, Liu Y, Yu Z, Qi Y, Lu Z, Ma L. Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screen. Genome Biology. 21: 136. PMID 32513233 DOI: 10.1186/s13059-020-02044-w  0.316
2020 Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, ... ... Ma L, et al. Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer. The Journal of Clinical Investigation. PMID 32364535 DOI: 10.1172/Jci126726  0.633
2020 Shu X, Cao J, Cheng M, Xiang S, Gao M, Li T, Ying X, Wang F, Yue Y, Lu Z, Dai Q, Cui X, Ma L, Wang Y, He C, et al. A metabolic labeling method detects mA transcriptome-wide at single base resolution. Nature Chemical Biology. PMID 32341503 DOI: 10.1038/S41589-020-0526-9  0.322
2017 Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, ... ... Ma L, et al. The modERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics. PMID 29284660 DOI: 10.1534/Genetics.117.300657  0.718
2017 Ma L, Zhao B, Chen K, Thomas A, Tuteja JH, He X, He C, White K. Evolution of transcript modification by N6-methyladenosine in primates. Genome Research. PMID 28052920 DOI: 10.1101/Gr.212563.116  0.5
2015 Chen F, Ma H, Ma C, Ni Y, Zhang X, Wei H, Meng Y, Zhao M, Ma L. The complete mitochondrial genome sequence and gene organization of Amblychaeturichthys hexanema (Gobiidae: Amblychaeturichthys) with phylogenetic consideration. Mitochondrial Dna. 1-2. PMID 26642097 DOI: 10.3109/19401736.2015.1106503  0.322
2015 Li X, Gao S, Tang Y, Li L, Zhang F, Feng B, Fang Z, Ma L, Zhao C. Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes. Bmc Genomics. 16: 976. PMID 26581444 DOI: 10.1186/s12864-015-2196-7  0.349
2015 Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, et al. Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. PMID 26560031 DOI: 10.1038/Nature16075  0.351
2015 Chen C, Wu ZT, Ma LL, Ni X, Lin YF, Wang L, Chen KP, Huang CG, Pan G. Organic anion-transporting polypeptides contribute to the hepatic uptake of berberine. Xenobiotica; the Fate of Foreign Compounds in Biological Systems. 1-9. PMID 26068524 DOI: 10.3109/00498254.2015.1042537  0.458
2015 Ma L, Zhao W, Zhu F, Yuan F, Xie N, Li T, Wang P, Tong T. Global Characteristics of CSIG-Associated Gene Expression Changes in Human HEK293 Cells and the Implications for CSIG Regulating Cell Proliferation and Senescence. Frontiers in Endocrinology. 6: 69. PMID 26029164 DOI: 10.3389/fendo.2015.00069  0.324
2015 Shen W, Wang D, Ye B, Shi M, Ma L, Zhang Y, Zhao Z. GC3-biased gene domains in mammalian genomes. Bioinformatics (Oxford, England). PMID 26019240 DOI: 10.1093/bioinformatics/btv329  0.328
2014 Ozdemir A, Ma L, White KP, Stathopoulos A. Su(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos. Developmental Cell. 31: 100-13. PMID 25313963 DOI: 10.1016/J.Devcel.2014.08.005  0.597
2014 Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S. Transcription factor networks in Drosophila melanogaster. Cell Reports. 8: 2031-43. PMID 25242320 DOI: 10.1016/J.Celrep.2014.08.038  0.574
2014 Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, ... Ma L, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/Nature13668  0.79
2014 Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, et al. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 512: 400-5. PMID 25164749 DOI: 10.1038/Nature13497  0.562
2014 Oh H, Slattery M, Ma L, White KP, Mann RS, Irvine KD. Yorkie promotes transcription by recruiting a histone methyltransferase complex. Cell Reports. 8: 449-59. PMID 25017066 DOI: 10.1016/J.Celrep.2014.06.017  0.571
2014 Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, et al. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Research. 24: 1224-35. PMID 24985916 DOI: 10.1101/Gr.168807.113  0.776
2014 Arthur RK, Ma L, Slattery M, Spokony RF, Ostapenko A, Nègre N, White KP. Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification. Genome Research. 24: 1115-24. PMID 24985914 DOI: 10.1101/Gr.162008.113  0.77
2013 Slattery M, Voutev R, Ma L, Nègre N, White KP, Mann RS. Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. Plos Genetics. 9: e1003753. PMID 24039600 DOI: 10.1371/Journal.Pgen.1003753  0.746
2013 Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD. Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes. Cell Reports. 3: 309-18. PMID 23395637 DOI: 10.1016/J.Celrep.2013.01.008  0.639
2013 Kittler R, Zhou J, Hua S, Ma L, Liu Y, Pendleton E, Cheng C, Gerstein M, White KP. A comprehensive nuclear receptor network for breast cancer cells. Cell Reports. 3: 538-51. PMID 23375374 DOI: 10.1016/J.Celrep.2013.01.004  0.747
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, ... ... Ma L, 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  0.555
2012 Song X, Wang D, Ma L, Chen Z, Li P, Cui X, Liu C, Cao S, Chu C, Tao Y, Cao X. Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development. The Plant Journal : For Cell and Molecular Biology. 71: 378-89. PMID 22443269 DOI: 10.1111/J.1365-313X.2012.05001.X  0.304
2011 Slattery M, Ma L, Négre N, White KP, Mann RS. Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. Plos One. 6: e14686. PMID 21483663 DOI: 10.1371/Journal.Pone.0014686  0.759
2011 Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, et al. A cis-regulatory map of the Drosophila genome. Nature. 471: 527-31. PMID 21430782 DOI: 10.1038/Nature09990  0.804
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  0.771
2010 Xiang H, Zhu J, Chen Q, Dai F, Li X, Li M, Zhang H, Zhang G, Li D, Dong Y, Zhao L, Lin Y, Cheng D, Yu J, Sun J, ... ... Ma L, et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nature Biotechnology. 28: 516-20. PMID 20436463 DOI: 10.1038/Nbt.1626  0.489
2010 Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, ... ... Ma L, et al. The sequence and de novo assembly of the giant panda genome. Nature. 463: 311-7. PMID 20010809 DOI: 10.1038/Nature08696  0.398
2010 Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, ... ... Ma L, et al. Erratum: The sequence and de novo assembly of the giant panda genome Nature. 463: 1106-1106. DOI: 10.1038/Nature08846  0.331
2009 Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, ... ... Ma L, et al. The genome of the cucumber, Cucumis sativus L. Nature Genetics. 41: 1275-81. PMID 19881527 DOI: 10.1038/Ng.475  0.406
2009 Li G, Ma L, Song C, Yang Z, Wang X, Huang H, Li Y, Li R, Zhang X, Yang H, Wang J, Wang J. The YH database: the first Asian diploid genome database. Nucleic Acids Research. 37: D1025-8. PMID 19073702 DOI: 10.1093/Nar/Gkn966  0.392
2008 Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, ... ... Ma L, et al. The diploid genome sequence of an Asian individual. Nature. 456: 60-5. PMID 18987735 DOI: 10.1038/Nature07484  0.367
2007 Li S, Ma L, Li H, Vang S, Hu Y, Bolund L, Wang J. Snap: an integrated SNP annotation platform. Nucleic Acids Research. 35: D707-10. PMID 17135198 DOI: 10.1093/Nar/Gkl969  0.393
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