Using ReMap ? Please cite the corresponding paper !

ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
Fayrouz Hammal, Pierre De Langen, Aurélie Bergon, Fabrice Lopez, Benoit Ballester. Under review

PDF ACCESS ReMap 2022 Under review

Papers citing ReMap

Year DOI Pubmed ID Citation
2021
10.1186/s13073-021-00880-4
33926515
Crosstalk between microRNA expression and DNA methylation drives the hormone-dependent phenotype of breast cancer. Aure MR, Fleischer T, Bjørklund S, Ankill J, Castro-Mondragon JA, Børresen-Dale AL, Tost J, Sahlberg KK, Mathelier A, Tekpli X, Kristensen VN Genome medicine 2021 Apr 29;13(1):72 10.1186/s13073-021-00880-4

2021
10.1186/s13072-021-00390-y
33741028
Molecular and computational approaches to map regulatory elements in 3D chromatin structure. Lee BH, Rhie SK Epigenetics & chromatin 2021 Mar 19;14(1):14 10.1186/s13072-021-00390-y

2021
10.1093/nargab/lqaa054
33575605
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data. Luu PL, Ong PT, Dinh TP, Clark SJ NAR genomics and bioinformatics 2020 Sep;2(3):lqaa054 10.1093/nargab/lqaa054

2021
10.3389/fimmu.2020.596173
33643286
The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment. Odia T, Malherbe ST, Meier S, Maasdorp E, Kleynhans L, du Plessis N, Loxton AG, Zak DE, Thompson E, Duffy FJ, Kuivaniemi H, Ronacher K, Winter J, Walzl G, Tromp G Frontiers in immunology 2020;11:596173 10.3389/fimmu.2020.596173

2021
10.18632/aging.202353
33493135
Cell lineage-specific methylome and genome alterations in gout. Tseng CC, Liao WT, Wong MC, Chen CJ, Lee SC, Yen JH, Chang SJ Aging 2021 Jan 20;13(3):3843-3865 10.18632/aging.202353

2021
10.1186/s13059-021-02261-x
33482911
Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer. Huang KK, Huang J, Wu JKL, Lee M, Tay ST, Kumar V, Ramnarayanan K, Padmanabhan N, Xu C, Tan ALK, Chan C, Kappei D, Göke J, Tan P Genome biology 2021 Jan 22;22(1):44 10.1186/s13059-021-02261-x

2021
10.1016/j.jbc.2021.100291
33453283
Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis. Koay TW, Osterhof C, Orlando IMC, Keppner A, Andre D, Yousefian S, Alonso MS, Correia M, Markworth R, Schödel J, Hankeln T, Hoogewijs D The Journal of biological chemistry 2021 Jan 13;:100291 10.1016/j.jbc.2021.100291

2021
10.1161/ATVBAHA.120.314978
33406884
MEF2 (Myocyte Enhancer Factor 2) Is Essential for Endothelial Homeostasis and the Atheroprotective Gene Expression Program. Lu YW, Martino N, Gerlach BD, Lamar JM, Vincent PA, Adam AP, Schwarz JJ Arteriosclerosis, thrombosis, and vascular biology 2021 Mar;41(3):1105-1123 10.1161/ATVBAHA.120.314978

2021
10.1093/nargab/lqab022
33860225
BARTweb: a web server for transcriptional regulator association analysis. Ma W, Wang Z, Zhang Y, Magee NE, Feng Y, Shi R, Chen Y, Zang C NAR genomics and bioinformatics 2021 Jun;3(2):lqab022 10.1093/nargab/lqab022

2020
10.1186/s12864-019-5535-2
32039697
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. Wang R, Wang Y, Zhang X, Zhang Y, Du X, Fang Y, Li G BMC genomics 2019 May 8;20(Suppl 3):296 10.1186/s12864-019-5535-2

2020
10.1016/j.cels.2020.04.004
32550271
MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. Zhang R, Ma J Cell systems 2020 May 20;10(5):397-407.e5 10.1016/j.cels.2020.04.004

2020
10.3390/cancers12051140
32370157
SNAI1-Driven Sequential EMT Changes Attributed by Selective Chromatin Enrichment of RAD21 and GRHL2. Sundararajan V, Tan M, Zea Tan T, Pang QY, Ye J, Chung VY, Huang RY Cancers 2020 May 2;12(5) 10.3390/cancers12051140

2020
10.1186/s13059-020-01996-3
32393327
Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. Ambrosini G, Vorontsov I, Penzar D, Groux R, Fornes O, Nikolaeva DD, Ballester B, Grau J, Grosse I, Makeev V, Kulakovskiy I, Bucher P Genome biology 2020 May 11;21(1):114 10.1186/s13059-020-01996-3

2020
10.1038/s42003-020-0937-x
32358504
Single-cell expression and Mendelian randomization analyses identify blood genes associated with lifespan and chronic diseases. Chignon A, Bon-Baret V, Boulanger MC, Li Z, Argaud D, Bossé Y, Thériault S, Arsenault BJ, Mathieu P Communications biology 2020 May 1;3(1):206 10.1038/s42003-020-0937-x

2020
10.3389/fgene.2020.00072
32153638
Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules. Ronzio M, Zambelli F, Dolfini D, Mantovani R, Pavesi G Frontiers in genetics 2020;11:72 10.3389/fgene.2020.00072

2020
10.3389/fgene.2020.00053
32117461
epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis. Zhou Y, Sun Y, Huang D, Li MJ Frontiers in genetics 2020;11:53 10.3389/fgene.2020.00053

2020
10.1038/s41467-019-13888-7
31913281
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J, Zaugg JB Nature communications 2020 Jan 8;11(1):124 10.1038/s41467-019-13888-7

2020
10.1038/s41467-019-13983-9
32024846
Integrative pathway enrichment analysis of multivariate omics data. Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, Reimand J Nature communications 2020 Feb 5;11(1):735 10.1038/s41467-019-13983-9

2020
10.1038/s41467-019-14098-x
31949157
Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer. Achinger-Kawecka J, Valdes-Mora F, Luu PL, Giles KA, Caldon CE, Qu W, Nair S, Soto S, Locke WJ, Yeo-Teh NS, Gould CM, Du Q, Smith GC, Ramos IR, Fernandez KF, Hoon DS, Gee JMW, Stirzaker C, Clark SJ Nature communications 2020 Jan 16;11(1):320 10.1038/s41467-019-14098-x

2020
10.1681/ASN.2019030289
31919106
Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy. Guo J, Rackham OJL, Sandholm N, He B, Österholm AM, Valo E, Harjutsalo V, Forsblom C, Toppila I, Parkkonen M, Li Q, Zhu W, Harmston N, Chothani S, Öhman MK, Eng E, Sun Y, Petretto E, Groop PH, Tryggvason K Journal of the American Society of Nephrology : JASN 2020 Feb;31(2):309-323 10.1681/ASN.2019030289

2020
10.1186/s12864-019-6436-0
31914926
CNCC: an analysis tool to determine genome-wide DNA break end structure at single-nucleotide resolution. Szlachta K, Raimer HM, Comeau LD, Wang YH BMC genomics 2020 Jan 8;21(1):25 10.1186/s12864-019-6436-0

2020
10.1186/s13059-020-02087-z
32718321
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance. D'Anna F, Van Dyck L, Xiong J, Zhao H, Berrens RV, Qian J, Bieniasz-Krzywiec P, Chandra V, Schoonjans L, Matthews J, De Smedt J, Minnoye L, Amorim R, Khorasanizadeh S, Yu Q, Zhao L, De Borre M, Savvides SN, Simon MC, Carmeliet P, Reik W, Rastinejad F, Mazzone M, Thienpont B, Lambrechts D Genome biology 2020 Jul 27;21(1):182 10.1186/s13059-020-02087-z

2020
10.1038/s41588-019-0537-1
31911677
Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. Fachal L, Aschard H, Beesley J, Barnes DR, Allen J, Kar S, Pooley KA, Dennis J, Michailidou K, Turman C, Soucy P, Lemaçon A, Lush M, Tyrer JP, Ghoussaini M, Moradi Marjaneh M, Jiang X, Agata S, Aittomäki K, Alonso MR, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Aronson KJ, Arun BK, Auber B, Auer PL, Azzollini J, Balmaña J, Barkardottir RB, Barrowdale D, Beeghly-Fadiel A, Benitez J, Bermisheva M, Białkowska K, Blanco AM, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borg A, Bosse K, Brauch H, Brenner H, Briceno I, Brock IW, Brooks-Wilson A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldés T, Caligo MA, Camp NJ, Campbell I, Canzian F, Carroll JS, Carter BD, Castelao JE, Chiquette J, Christiansen H, Chung WK, Claes KBM, Clarke CL, Collée JM, Cornelissen S, Couch FJ, Cox A, Cross SS, Cybulski C, Czene K, Daly MB, de la Hoya M, Devilee P, Diez O, Ding YC, Dite GS, Domchek SM, Dörk T, Dos-Santos-Silva I, Droit A, Dubois S, Dumont M, Duran M, Durcan L, Dwek M, Eccles DM, Engel C, Eriksson M, Evans DG, Fasching PA, Fletcher O, Floris G, Flyger H, Foretova L, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gago-Dominguez M, Gambino G, Ganz PA, Gapstur SM, Garber J, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Tibiletti MG, Greene MH, Grip M, Gronwald J, Grundy A, Guénel P, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Harrington PA, Hartikainen JM, Hartman M, He W, Healey CS, Heemskerk-Gerritsen BAM, Heyworth J, Hillemanns P, Hogervorst FBL, Hollestelle A, Hooning MJ, Hopper JL, Howell A, Huang G, Hulick PJ, Imyanitov EN, Isaacs C, Iwasaki M, Jager A, Jakimovska M, Jakubowska A, James PA, Janavicius R, Jankowitz RC, John EM, Johnson N, Jones ME, Jukkola-Vuorinen A, Jung A, Kaaks R, Kang D, Kapoor PM, Karlan BY, Keeman R, Kerin MJ, Khusnutdinova E, Kiiski JI, Kirk J, Kitahara CM, Ko YD, Konstantopoulou I, Kosma VM, Koutros S, Kubelka-Sabit K, Kwong A, Kyriacou K, Laitman Y, Lambrechts D, Lee E, Leslie G, Lester J, Lesueur F, Lindblom A, Lo WY, Long J, Lophatananon A, Loud JT, Lubiński J, MacInnis RJ, Maishman T, Makalic E, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Matsuo K, Maurer T, Mavroudis D, Mayes R, McGuffog L, McLean C, Mebirouk N, Meindl A, Miller A, Miller N, Montagna M, Moreno F, Muir K, Mulligan AM, Muñoz-Garzon VM, Muranen TA, Narod SA, Nassir R, Nathanson KL, Neuhausen SL, Nevanlinna H, Neven P, Nielsen FC, Nikitina-Zake L, Norman A, Offit K, Olah E, Olopade OI, Olsson H, Orr N, Osorio A, Pankratz VS, Papp J, Park SK, Park-Simon TW, Parsons MT, Paul J, Pedersen IS, Peissel B, Peshkin B, Peterlongo P, Peto J, Plaseska-Karanfilska D, Prajzendanc K, Prentice R, Presneau N, Prokofyeva D, Pujana MA, Pylkäs K, Radice P, Ramus SJ, Rantala J, Rau-Murthy R, Rennert G, Risch HA, Robson M, Romero A, Rossing M, Saloustros E, Sánchez-Herrero E, Sandler DP, Santamariña M, Saunders C, Sawyer EJ, Scheuner MT, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schöttker B, Schürmann P, Scott C, Scott RJ, Senter L, Seynaeve CM, Shah M, Sharma P, Shen CY, Shu XO, Singer CF, Slavin TP, Smichkoska S, Southey MC, Spinelli JJ, Spurdle AB, Stone J, Stoppa-Lyonnet D, Sutter C, Swerdlow AJ, Tamimi RM, Tan YY, Tapper WJ, Taylor JA, Teixeira MR, Tengström M, Teo SH, Terry MB, Teulé A, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Torres D, Torres-Mejía G, Troester MA, Truong T, Tung N, Tzardi M, Ulmer HU, Vachon CM, van Asperen CJ, van der Kolk LE, van Rensburg EJ, Vega A, Viel A, Vijai J, Vogel MJ, Wang Q, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wildiers H, Winqvist R, Wolk A, Wu AH, Yannoukakos D, Zhang Y, Zheng W, Hunter D, Pharoah PDP, Chang-Claude J, García-Closas M, Schmidt MK, Milne RL, Kristensen VN, French JD, Edwards SL, Antoniou AC, Chenevix-Trench G, Simard J, Easton DF, Kraft P, Dunning AM Nature genetics 2020 Jan;52(1):56-73 10.1038/s41588-019-0537-1

2020
10.1186/s13059-019-1877-y
31910858
Chromatin interactome mapping at 139 independent breast cancer risk signals. Beesley J, Sivakumaran H, Moradi Marjaneh M, Lima LG, Hillman KM, Kaufmann S, Tuano N, Hussein N, Ham S, Mukhopadhyay P, Kazakoff S, Lee JS, Michailidou K, Barnes DR, Antoniou AC, Fachal L, Dunning AM, Easton DF, Waddell N, Rosenbluh J, Möller A, Chenevix-Trench G, French JD, Edwards SL Genome biology 2020 Jan 7;21(1):8 10.1186/s13059-019-1877-y

2020
10.3390/ijms21134702
32630231
Systemic Investigation of Promoter-wide Methylome and Genome Variations in Gout. Tseng CC, Wong MC, Liao WT, Chen CJ, Lee SC, Yen JH, Chang SJ International journal of molecular sciences 2020 Jul 1;21(13) 10.3390/ijms21134702

2020
10.1186/s13072-020-00345-9
32505195
Linker histone epitopes are hidden by in situ higher-order chromatin structure. Teif VB, Gould TJ, Clarkson CT, Boyd L, Antwi EB, Ishaque N, Olins AL, Olins DE Epigenetics & chromatin 2020 Jun 6;13(1):26 10.1186/s13072-020-00345-9

2020
10.1038/s41598-020-69791-5
32737375
Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. Minchington TG, Griffiths-Jones S, Papalopulu N Scientific reports 2020 Jul 31;10(1):12960 10.1038/s41598-020-69791-5

2020
10.1093/nar/gkaa806
33045741
LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. Chen J, Zhang J, Gao Y, Li Y, Feng C, Song C, Ning Z, Zhou X, Zhao J, Feng M, Zhang Y, Wei L, Pan Q, Jiang Y, Qian F, Han J, Yang Y, Wang Q, Li C Nucleic acids research 2021 Jan 8;49(D1):D969-D980 10.1093/nar/gkaa806

2020
10.1371/journal.pone.0243332
33347457
Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. Sharipov RN, Kondrakhin YV, Ryabova AS, Yevshin IS, Kolpakov FA PloS one 2020;15(12):e0243332 10.1371/journal.pone.0243332

2020
10.3389/fgene.2020.00730
32765587
ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. Manjunath M, Zhang Y, Zhang S, Roy S, Perez-Pinera P, Song JS Frontiers in genetics 2020;11:730 10.3389/fgene.2020.00730

2020
10.1016/j.celrep.2020.108426
33238122
Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression. Lin L, Holmes B, Shen MW, Kammeron D, Geijsen N, Gifford DK, Sherwood RI Cell reports 2020 Nov 24;33(8):108426 10.1016/j.celrep.2020.108426

2020
10.1126/sciadv.aba5933
33188013
Dedifferentiation and neuronal repression define familial Alzheimer's disease. Caldwell AB, Liu Q, Schroth GP, Galasko DR, Yuan SH, Wagner SL, Subramaniam S Science advances 2020 Nov;6(46) 10.1126/sciadv.aba5933

2020
10.1093/database/baaa071
33186463
Exploring functionally annotated transcriptional consensus regulatory elements with CONREL. Dalfovo D, Valentini S, Romanel A Database : the journal of biological databases and curation 2020 Jan 1;2020 10.1093/database/baaa071

2020
10.1093/nar/gkaa922
33095866
VARAdb: a comprehensive variation annotation database for human. Pan Q, Liu YJ, Bai XF, Han XL, Jiang Y, Ai B, Shi SS, Wang F, Xu MC, Wang YZ, Zhao J, Chen JX, Zhang J, Li XC, Zhu J, Zhang GR, Wang QY, Li CQ Nucleic acids research 2021 Jan 8;49(D1):D1431-D1444 10.1093/nar/gkaa922

2020
10.1038/s41467-020-18839-1
33060578
Aberrant methylation underlies insulin gene expression in human insulinoma. Karakose E, Wang H, Inabnet W, Thakker RV, Libutti S, Fernandez-Ranvier G, Suh H, Stevenson M, Kinoshita Y, Donovan M, Antipin Y, Li Y, Liu X, Jin F, Wang P, Uzilov A, Argmann C, Schadt EE, Stewart AF, Scott DK, Lambertini L Nature communications 2020 Oct 15;11(1):5210 10.1038/s41467-020-18839-1

2020
10.1038/s41467-020-19962-9
33268804
Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations. Grujic O, Phung TN, Kwon SB, Arneson A, Lee Y, Lohmueller KE, Ernst J Nature communications 2020 Dec 2;11(1):6168 10.1038/s41467-020-19962-9

2020
10.1186/s13073-020-00779-6
32977850
Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci. Li T, Ortiz-Fernández L, Andrés-León E, Ciudad L, Javierre BM, López-Isac E, Guillén-Del-Castillo A, Simeón-Aznar CP, Ballestar E, Martin J Genome medicine 2020 Sep 25;12(1):81 10.1186/s13073-020-00779-6

2020
10.2217/epi-2020-0048
32914644
Genome-wide resolution peripheral blood methylome profiling reveals signatures for cholestatic liver disease. Moore RM, Sun Z, Juran BD, Lazaridis KN Epigenomics 2020 Aug;12(16):1363-1375 10.2217/epi-2020-0048

2020
10.1093/nar/gkaa729
32890394
Genome-wide binding of SEPALLATA3 and AGAMOUS complexes determined by sequential DNA-affinity purification sequencing. Lai X, Stigliani A, Lucas J, Hugouvieux V, Parcy F, Zubieta C Nucleic acids research 2020 Sep 25;48(17):9637-9648 10.1093/nar/gkaa729

2020
10.1186/s12885-020-07318-x
32859160
A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer. Cario CL, Chen E, Leong L, Emami NC, Lopez K, Tenggara I, Simko JP, Friedlander TW, Li PS, Paris PL, Carroll PR, Witte JS BMC cancer 2020 Aug 28;20(1):820 10.1186/s12885-020-07318-x

2020
10.1038/s41419-020-02800-7
32826850
Combined treatment with CBP and BET inhibitors reverses inadvertent activation of detrimental super enhancer programs in DIPG cells. Wiese M, Hamdan FH, Kubiak K, Diederichs C, Gielen GH, Nussbaumer G, Carcaboso AM, Hulleman E, Johnsen SA, Kramm CM Cell death & disease 2020 Aug 21;11(8):673 10.1038/s41419-020-02800-7

2020
10.1016/j.gpb.2019.09.006
32858223
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets. Zhang Q, Liu W, Zhang HM, Xie GY, Miao YR, Xia M, Guo AY Genomics, proteomics & bioinformatics 2020 Apr;18(2):120-128 10.1016/j.gpb.2019.09.006

2020
10.1038/s41467-020-18527-0
32958757
A predictable conserved DNA base composition signature defines human core DNA replication origins. Akerman I, Kasaai B, Bazarova A, Sang PB, Peiffer I, Artufel M, Derelle R, Smith G, Rodriguez-Martinez M, Romano M, Kinet S, Tino P, Theillet C, Taylor N, Ballester B, Méchali M Nature communications 2020 Sep 21;11(1):4826 10.1038/s41467-020-18527-0

2019
10.1093/nar/gkz302
31028388
SEanalysis: a web tool for super-enhancer associated regulatory analysis. Qian FC, Li XC, Guo JC, Zhao JM, Li YY, Tang ZD, Zhou LW, Zhang J, Bai XF, Jiang Y, Pan Q, Wang QY, Li EM, Li CQ, Xu LY, Lin DC Nucleic acids research 2019 Jul 2;47(W1):W248-W255 10.1093/nar/gkz302

2019
10.1080/15592294.2019.1621140
31177910
Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure. Hou Y, Li F, Zhang R, Li S, Liu H, Qin ZS, Sun X Epigenetics 2019 Sep;14(9):894-911 10.1080/15592294.2019.1621140

2019
10.1093/nar/gkz446
31114921
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Keenan AB, Torre D, Lachmann A, Leong AK, Wojciechowicz ML, Utti V, Jagodnik KM, Kropiwnicki E, Wang Z, Ma'ayan A Nucleic acids research 2019 Jul 2;47(W1):W212-W224 10.1093/nar/gkz446

2019
10.3892/ijo.2019.4786
31081062
INKA2, a novel p53 target that interacts with the serine/threonine kinase PAK4. Liu YY, Tanikawa C, Ueda K, Matsuda K International journal of oncology 2019 Jun;54(6):1907-1920 10.3892/ijo.2019.4786

2019
10.1289/EHP3398
31039056
Associations between Maternal Tobacco Smoke Exposure and the Cord Blood [Formula: see text] DNA Methylome. Howe CG, Zhou M, Wang X, Pittman GS, Thompson IJ, Campbell MR, Bastain TM, Grubbs BH, Salam MT, Hoyo C, Bell DA, Smith AD, Breton CV Environmental health perspectives 2019 Apr;127(4):47009 10.1289/EHP3398

2019
10.1093/nar/gkz320
31045203
TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes. González A, Artufel M, Rihet P Nucleic acids research 2019 Aug 22;47(14):e79 10.1093/nar/gkz320

2019
10.3390/cancers11040507
30974831
Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer. Huang S, Xu W, Hu P, Lakowski TM Cancers 2019 Apr 10;11(4) 10.3390/cancers11040507

2019
10.1371/journal.pgen.1008007
30807572
Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci. Gong J, Wang F, Xiao B, Panjwani N, Lin F, Keenan K, Avolio J, Esmaeili M, Zhang L, He G, Soave D, Mastromatteo S, Baskurt Z, Kim S, O'Neal WK, Polineni D, Blackman SM, Corvol H, Cutting GR, Drumm M, Knowles MR, Rommens JM, Sun L, Strug LJ PLoS genetics 2019 Feb;15(2):e1008007 10.1371/journal.pgen.1008007

2019
10.3390/ijms20071616
30939743
Mechanism of Action for HDAC Inhibitors-Insights from Omics Approaches. Li W, Sun Z International journal of molecular sciences 2019 Apr 1;20(7) 10.3390/ijms20071616

2019
30864321
SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs. Anand S, Kalesinskas L, Smail C, Tanigawa Y Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2019;24:184-195

2019
10.1093/bioinformatics/btz150
30824903
RECAP reveals the true statistical significance of ChIP-seq peak calls. Chitpin JG, Awdeh A, Perkins TJ Bioinformatics (Oxford, England) 2019 Oct 1;35(19):3592-3598 10.1093/bioinformatics/btz150

2019
10.1038/s41467-018-08126-5
30664627
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin JW Nature communications 2019 Jan 21;10(1):360 10.1038/s41467-018-08126-5

2019
10.1016/j.jpain.2018.12.008
30639570
Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsurgical Pain and Anxiety in Children: A Prospective, Pilot Study. Chidambaran V, Zhang X, Geisler K, Stubbeman BL, Chen X, Weirauch MT, Meller J, Ji H The journal of pain 2019 Jul;20(7):771-785 10.1016/j.jpain.2018.12.008

2019
10.1016/j.ccell.2019.01.004
30753827
DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns. Skvortsova K., Masle-Farquhar E., Luu P. L., Song J. Z., Qu W., Zotenko E., Gould C. M., Du Q., Peters T. J., Colino-Sanguino Y., Pidsley R., Nair S. S., Khoury A., Smith G. C., Miosge L. A., Reed J. H., Kench J. G., Rubin M. A., Horvath L., Bogdanovic O., Lim S. M., Polo J. M., Goodnow C. C., Stirzaker C. and Clark S. J. Cancer Cell. 2019;35(2):297-314 e8. Epub 2019/02/13.

2019
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2019
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2019
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2019
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2019
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2019
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2019
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2019
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2019
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2019
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2019
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A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. Levitsky V, Zemlyanskaya E, Oshchepkov D, Podkolodnaya O, Ignatieva E, Grosse I, Mironova V, Merkulova T Nucleic acids research 2019 Dec 2;47(21):e139 10.1093/nar/gkz800

2019
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2019
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2019
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2019
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2019
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2019
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2019
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Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. Liu X, Helenius D, Skotte L, Beaumont RN, Wielscher M, Geller F, Juodakis J, Mahajan A, Bradfield JP, Lin FTJ, Vogelezang S, Bustamante M, Ahluwalia TS, Pitkänen N, Wang CA, Bacelis J, Borges MC, Zhang G, Bedell BA, Rossi RM, Skogstrand K, Peng S, Thompson WK, Appadurai V, Lawlor DA, Kalliala I, Power C, McCarthy MI, Boyd HA, Marazita ML, Hakonarson H, Hayes MG, Scholtens DM, Rivadeneira F, Jaddoe VWV, Vinding RK, Bisgaard H, Knight BA, Pahkala K, Raitakari O, Helgeland Ø, Johansson S, Njølstad PR, Fadista J, Schork AJ, Nudel R, Miller DE, Chen X, Weirauch MT, Mortensen PB, Børglum AD, Nordentoft M, Mors O, Hao K, Ryckman KK, Hougaard DM, Kottyan LC, Pennell CE, Lyytikainen LP, Bønnelykke K, Vrijheid M, Felix JF, Lowe WL Jr, Grant SFA, Hyppönen E, Jacobsson B, Jarvelin MR, Muglia LJ, Murray JC, Freathy RM, Werge TM, Melbye M, Buil A, Feenstra B Nature communications 2019 Sep 2;10(1):3927 10.1038/s41467-019-11881-8

2019
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2019
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The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways. Ochsner SA, Abraham D, Martin K, Ding W, McOwiti A, Kankanamge W, Wang Z, Andreano K, Hamilton RA, Chen Y, Hamilton A, Gantner ML, Dehart M, Qu S, Hilsenbeck SG, Becnel LB, Bridges D, Ma'ayan A, Huss JM, Stossi F, Foulds CE, Kralli A, McDonnell DP, McKenna NJ Scientific data 2019 Oct 31;6(1):252 10.1038/s41597-019-0193-4

2019
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The role of GRHL2 and epigenetic remodeling in epithelial-mesenchymal plasticity in ovarian cancer cells. Chung VY, Tan TZ, Ye J, Huang RL, Lai HC, Kappei D, Wollmann H, Guccione E, Huang RY Communications biology 2019;2:272 10.1038/s42003-019-0506-3

2018
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The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. Rigden DJ, Fernández XM Nucleic acids research 2018 Jan 4;46(D1):D1-D7 10.1093/nar/gkx1235

2018
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Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. Dong X, Cuevas-Diaz Duran R, You Y, Wu JQ Journal of visualized experiments : JoVE 2018 Apr 16;(134) 10.3791/57547

2018
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Nasal DNA methylation is associated with childhood asthma. Zhang X, Biagini Myers JM, Burleson JD, Ulm A, Bryan KS, Chen X, Weirauch MT, Baker TA, Butsch Kovacic MS, Ji H Epigenomics 2018 May;10(5):629-641 10.2217/epi-2017-0127

2018
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Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Harley JB, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen AF, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman KM, Kottyan LC, Weirauch MT Nature genetics 2018 May;50(5):699-707 10.1038/s41588-018-0102-3

2018
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Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region. Khor SS, Morino R, Nakazono K, Kamitsuji S, Akita M, Kawajiri M, Yamasaki T, Kami A, Hoshi Y, Tada A, Ishikawa K, Hine M, Kobayashi M, Kurume N, Kamatani N, Tokunaga K, Johnson TA Scientific reports 2018 Jan 18;8(1):1069 10.1038/s41598-017-18241-w

2018
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The next generation of melanocyte data: Genetic, epigenetic, and transcriptional resource datasets and analysis tools. Loftus S. K. Pigment Cell Melanoma Res. 2018;31(3):442-447. Epub 2018/01/18.

2018
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Systematic target function annotation of human transcription factors. Li YF, Altman RB BMC biology 2018 Jan 10;16(1):4 10.1186/s12915-017-0469-0

2018
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Parkinson's disease genetic risk in a midbrain neuronal cell line. Pierce S. E., Tyson T., Booms A., Prahl J. and Coetzee G. A. Neurobiol Dis. 2018;114:53-64. Epub 2018/02/28.

2018
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Genetic variants with gene regulatory effects are associated with diisocyanate-induced asthma. Bernstein D. I., Lummus Z. L., Kesavalu B., Yao J., Kottyan L., Miller D., Cartier A., Cruz M. J., Lemiere C., Munoz X., Quirce S., Tarlo S., Sastre J., Boulet L. P., Weirauch M. T. and Kaufman K. J Allergy Clin Immunol. 2018;142(3):959-969. Epub 2018/07/04.

2018
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The quality agenda: governance and regulation of preschool teachers’ work. Grant S., Comber B., Danby S., Theobald M. and Thorpe K. Cambridge Journal of Education. 2018;48(4):515-532.

2018
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Japanese GWAS identifies variants for bust-size, dysmenorrhea, and menstrual fever that are eQTLs for relevant protein-coding or long non-coding RNAs. Hirata T, Koga K, Johnson TA, Morino R, Nakazono K, Kamitsuji S, Akita M, Kawajiri M, Kami A, Hoshi Y, Tada A, Ishikawa K, Hine M, Kobayashi M, Kurume N, Fujii T, Kamatani N, Osuga Y Scientific reports 2018 May 31;8(1):8502 10.1038/s41598-018-25065-9

2018
10.1002/1878-0261.12327
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Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration. Cioni B, Nevedomskaya E, Melis MHM, van Burgsteden J, Stelloo S, Hodel E, Spinozzi D, de Jong J, van der Poel H, de Boer JP, Wessels LFA, Zwart W, Bergman AM Molecular oncology 2018 Aug;12(8):1308-1323 10.1002/1878-0261.12327

2018
10.1093/eep/dvy020
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Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome. Zhang X, Chen X, Weirauch MT, Zhang X, Burleson JD, Brandt EB, Ji H Environmental epigenetics 2018 Jul;4(3):dvy020 10.1093/eep/dvy020

2018
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LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. Nagraj VP, Magee NE, Sheffield NC Nucleic acids research 2018 Jul 2;46(W1):W194-W199 10.1093/nar/gky464

2018
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<i>TFmapper</i>: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data. Zeng J, Li G International journal of biological sciences 2018;14(12):1724-1731 10.7150/ijbs.28850

2018
10.1371/journal.pone.0209096
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Genome-wide association study (GWAS) of ovarian cancer in Japanese predicted regulatory variants in 22q13.1. Yodsurang V, Tang Y, Takahashi Y, Tanikawa C, Kamatani Y, Takahashi A, Momozawa Y, Fuse N, Sugawara J, Shimizu A, Fukushima A, Hishida A, Furusyo N, Naito M, Wakai K, Yamaji T, Sawada N, Iwasaki M, Tsugane S, Hirata M, Murakami Y, Kubo M, Matsuda K PloS one 2018;13(12):e0209096 10.1371/journal.pone.0209096

2018
10.1093/nar/gky1210
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A map of direct TF-DNA interactions in the human genome. Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A Nucleic acids research 2019 Feb 28;47(4):e21 10.1093/nar/gky1210

2018
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ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis. Rotinen M, You S, Yang J, Coetzee SG, Reis-Sobreiro M, Huang WC, Huang F, Pan X, Yáñez A, Hazelett DJ, Chu CY, Steadman K, Morrissey CM, Nelson PS, Corey E, Chung LWK, Freedland SJ, Di Vizio D, Garraway IP, Murali R, Knudsen BS, Freeman MR Nature medicine 2018 Dec;24(12):1887-1898 10.1038/s41591-018-0241-1

2018
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Genome-wide association study in Japanese females identifies fifteen novel skin-related trait associations. Endo C, Johnson TA, Morino R, Nakazono K, Kamitsuji S, Akita M, Kawajiri M, Yamasaki T, Kami A, Hoshi Y, Tada A, Ishikawa K, Hine M, Kobayashi M, Kurume N, Tsunemi Y, Kamatani N, Kawashima M Scientific reports 2018 Jun 12;8(1):8974 10.1038/s41598-018-27145-2

2018
10.1093/nar/gky1094
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Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen CH, Brown M, Zhang X, Meyer CA, Liu XS Nucleic acids research 2019 Jan 8;47(D1):D729-D735 10.1093/nar/gky1094

2018
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Insights into mammalian transcription control by systematic analysis of ChIP sequencing data. Devailly G, Joshi A BMC bioinformatics 2018 Nov 20;19(Suppl 14):409 10.1186/s12859-018-2377-x

2018
10.1093/nar/gky1095
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The UCSC Genome Browser database: 2019 update. Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ Nucleic acids research 2019 Jan 8;47(D1):D853-D858 10.1093/nar/gky1095

2018
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ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. Oki S, Ohta T, Shioi G, Hatanaka H, Ogasawara O, Okuda Y, Kawaji H, Nakaki R, Sese J, Meno C EMBO reports 2018 Dec;19(12) 10.15252/embr.201846255

2018
10.1093/nar/gky1081
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PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, Kuo PL, Zheng HQ, Chang WC Nucleic acids research 2019 Jan 8;47(D1):D1155-D1163 10.1093/nar/gky1081

2018
10.1186/s13104-018-3856-x
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Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data. Vorontsov IE, Fedorova AD, Yevshin IS, Sharipov RN, Kolpakov FA, Makeev VJ, Kulakovskiy IV BMC research notes 2018 Oct 23;11(1):756 10.1186/s13104-018-3856-x

2018
10.1074/jbc.RA118.002462
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c-Myc is a novel <i>Leishmania</i> virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages. Colineau L, Lambertz U, Fornes O, Wasserman WW, Reiner NE The Journal of biological chemistry 2018 Aug 17;293(33):12805-12819 10.1074/jbc.RA118.002462

2018
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MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations. Fornes O, Gheorghe M, Richmond PA, Arenillas DJ, Wasserman WW, Mathelier A Scientific data 2018 Jul 24;5:180141 10.1038/sdata.2018.141

2017
10.1016/j.immuni.2017.11.021
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Transcription Factor IRF4 Promotes CD8(+) T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection. Man K., Gabriel S. S., Liao Y., Gloury R., Preston S., Henstridge D. C., Pellegrini M., Zehn D., Berberich-Siebelt F., Febbraio M. A., Shi W. and Kallies A. Immunity. 2017;47(6):1129-1141 e5. Epub 2017/12/17.

2017
10.1093/nar/gkx377
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CHD1 regulates cell fate determination by activation of differentiation-induced genes. Baumgart SJ, Najafova Z, Hossan T, Xie W, Nagarajan S, Kari V, Ditzel N, Kassem M, Johnsen SA Nucleic acids research 2017 Jul 27;45(13):7722-7735 10.1093/nar/gkx377

2017
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Tracing ‘the Social’ in Processes of Rural Development in Kyrgyzstan. Dergousoff D. Forum for Development Studies. 2017;44(3):473-492.

2017
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Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning. Dozmorov M. G. Bioinformatics. 2017;33(20):3323-3330. Epub 2017/10/14.

2017
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Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. Andrews E, Wang Y, Xia T, Cheng W, Cheng C PLoS computational biology 2017 Jan;13(1):e1005340 10.1371/journal.pcbi.1005340

2017
10.1186/s12864-016-3450-3
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Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. Yang CC, Chen MH, Lin SY, Andrews EH, Cheng C, Liu CC, Chen JJ BMC genomics 2017 Jan 10;18(1):61 10.1186/s12864-016-3450-3

2017
10.1093/hmg/ddw290
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Cystic fibrosis gene modifier SLC26A9 modulates airway response to CFTR-directed therapeutics. Strug LJ, Gonska T, He G, Keenan K, Ip W, Boëlle PY, Lin F, Panjwani N, Gong J, Li W, Soave D, Xiao B, Tullis E, Rabin H, Parkins MD, Price A, Zuberbuhler PC, Corvol H, Ratjen F, Sun L, Bear CE, Rommens JM Human molecular genetics 2016 Oct 15;25(20):4590-4600 10.1093/hmg/ddw290

2017
10.1093/nar/gkx212
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Histone deacetylase class-I inhibition promotes epithelial gene expression in pancreatic cancer cells in a BRD4- and MYC-dependent manner. Mishra VK, Wegwitz F, Kosinsky RL, Sen M, Baumgartner R, Wulff T, Siveke JT, Schildhaus HU, Najafova Z, Kari V, Kohlhof H, Hessmann E, Johnsen SA Nucleic acids research 2017 Jun 20;45(11):6334-6349 10.1093/nar/gkx212

2017
10.1158/2159-8290.CD-16-1032
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Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME Cancer discovery 2017 Aug;7(8):868-883 10.1158/2159-8290.CD-16-1032

2017
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ConTra v3: a tool to identify transcription factor binding sites across species, update 2017. Kreft L, Soete A, Hulpiau P, Botzki A, Saeys Y, De Bleser P Nucleic acids research 2017 Jul 3;45(W1):W490-W494 10.1093/nar/gkx376

2017
10.1371/journal.pone.0187818
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Beyond genome-wide scan: Association of a cis-regulatory NCR3 variant with mild malaria in a population living in the Republic of Congo. Baaklini S, Afridi S, Nguyen TN, Koukouikila-Koussounda F, Ndounga M, Imbert J, Torres M, Pradel L, Ntoumi F, Rihet P PloS one 2017;12(11):e0187818 10.1371/journal.pone.0187818

2017
10.1038/s41598-017-01765-6
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Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis. Gangwar I, Kumar Sharma N, Panzade G, Awasthi S, Agrawal A, Shankar R Scientific reports 2017 May 8;7(1):1554 10.1038/s41598-017-01765-6

2017
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DNA methylation at the mu-1 opioid receptor gene (<i>OPRM1</i>) promoter predicts preoperative, acute, and chronic postsurgical pain after spine fusion. Chidambaran V, Zhang X, Martin LJ, Ding L, Weirauch MT, Geisler K, Stubbeman BL, Sadhasivam S, Ji H Pharmacogenomics and personalized medicine 2017;10:157-168 10.2147/PGPM.S132691

2017
10.1056/NEJMoa1612665
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Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. Zhang G, Feenstra B, Bacelis J, Liu X, Muglia LM, Juodakis J, Miller DE, Litterman N, Jiang PP, Russell L, Hinds DA, Hu Y, Weirauch MT, Chen X, Chavan AR, Wagner GP, Pavličev M, Nnamani MC, Maziarz J, Karjalainen MK, Rämet M, Sengpiel V, Geller F, Boyd HA, Palotie A, Momany A, Bedell B, Ryckman KK, Huusko JM, Forney CR, Kottyan LC, Hallman M, Teramo K, Nohr EA, Davey Smith G, Melbye M, Jacobsson B, Muglia LJ The New England journal of medicine 2017 Sep 21;377(12):1156-1167 10.1056/NEJMoa1612665

2017
10.18632/oncotarget.19608
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Identification of a p53-repressed gene module in breast cancer cells. Miyamoto T, Tanikawa C, Yodsurang V, Zhang YZ, Imoto S, Yamaguchi R, Miyano S, Nakagawa H, Matsuda K Oncotarget 2017 Aug 22;8(34):55821-55836 10.18632/oncotarget.19608

2017
10.1186/s13072-017-0153-1
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Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state. Mauser R, Kungulovski G, Keup C, Reinhardt R, Jeltsch A Epigenetics & chromatin 2017 Sep 25;10(1):45 10.1186/s13072-017-0153-1

2017
10.3389/fgene.2017.00140
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Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach. Ye Y, Gao L, Zhang S Frontiers in genetics 2017;8:140 10.3389/fgene.2017.00140

2017
10.1093/bioinformatics/btx709
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Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. Cario CL, Witte JS Bioinformatics (Oxford, England) 2018 Mar 15;34(6):936-942 10.1093/bioinformatics/btx709

2017
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DNA methylation at enhancers identifies distinct breast cancer lineages. Fleischer T, Tekpli X, Mathelier A, Wang S, Nebdal D, Dhakal HP, Sahlberg KK, Schlichting E, Børresen-Dale AL, Borgen E, Naume B, Eskeland R, Frigessi A, Tost J, Hurtado A, Kristensen VN Nature communications 2017 Nov 9;8(1):1379 10.1038/s41467-017-00510-x

2017
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ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B Nucleic acids research 2018 Jan 4;46(D1):D267-D275 10.1093/nar/gkx1092

2017
10.1093/nar/gkx1126
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A Nucleic acids research 2018 Jan 4;46(D1):D260-D266 10.1093/nar/gkx1126

2017
10.1158/2159-8290.CD-16-1022
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Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma. Qamra A., Xing M., Padmanabhan N., Kwok J. J. T., Zhang S., Xu C., Leong Y. S., Lee Lim A. P., Tang Q., Ooi W. F., Suling Lin J., Nandi T., Yao X., Ong X., Lee M., Tay S. T., Keng A. T. L., Gondo Santoso E., Ng C. C. Y., Ng A., Jusakul A., Smoot D., Ashktorab H., Rha S. Y., Yeoh K. G., Peng Yong W., Chow P. K. H., Chan W. H., Ong H. S., Soo K. C., Kim K. M., Wong W. K., Rozen S. G., Teh B. T., Kappei D., Lee J., Connolly J. and Tan P. Cancer Discov. 2017;7(6):630-651. Epub 2017/03/23.

2017
10.1038/nn.4587
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A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease. Huang KL, Marcora E, Pimenova AA, Di Narzo AF, Kapoor M, Jin SC, Harari O, Bertelsen S, Fairfax BP, Czajkowski J, Chouraki V, Grenier-Boley B, Bellenguez C, Deming Y, McKenzie A, Raj T, Renton AE, Budde J, Smith A, Fitzpatrick A, Bis JC, DeStefano A, Adams HHH, Ikram MA, van der Lee S, Del-Aguila JL, Fernandez MV, Ibañez L, Sims R, Escott-Price V, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Lambert JC, van Duijn C, Launer L, Seshadri S, Williams J, Amouyel P, Schellenberg GD, Zhang B, Borecki I, Kauwe JSK, Cruchaga C, Hao K, Goate AM Nature neuroscience 2017 Aug;20(8):1052-1061 10.1038/nn.4587

2017
10.1038/s41598-017-07226-4
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Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma. Batmanov K, Wang W, Bjørås M, Delabie J, Wang J Scientific reports 2017 Aug 1;7(1):7040 10.1038/s41598-017-07226-4

2017
10.1186/s12859-017-1708-7
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Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. Khan A, Mathelier A BMC bioinformatics 2017 May 31;18(1):287 10.1186/s12859-017-1708-7

2017
10.1038/s41598-017-08754-9
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Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. Ferrero G, Miano V, Beccuti M, Balbo G, De Bortoli M, Cordero F Scientific reports 2017 Aug 17;7(1):8564 10.1038/s41598-017-08754-9

2017
10.1038/gene.2017.13
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Association of a functional TNF variant with Plasmodium falciparum parasitaemia in a congolese population. Nguyen TN, Baaklini S, Koukouikila-Koussounda F, Ndounga M, Torres M, Pradel L, Ntoumi F, Rihet P Genes and immunity 2017 Sep;18(3):152-157 10.1038/gene.2017.13

2016
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ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition. Zhu L., Guo W. L., Deng S. P. and Huang D. S. IEEE/ACM Trans Comput Biol Bioinform. 2016;13(1):55-63. Epub 2016/02/18.

2016
10.1186/s12859-016-1274-4
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ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XS BMC bioinformatics 2016 Oct 3;17(1):404 10.1186/s12859-016-1274-4

2016
10.1038/ncomms12983
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Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity. Ooi WF, Xing M, Xu C, Yao X, Ramlee MK, Lim MC, Cao F, Lim K, Babu D, Poon LF, Lin Suling J, Qamra A, Irwanto A, Qu Zhengzhong J, Nandi T, Lee-Lim AP, Chan YS, Tay ST, Lee MH, Davies JO, Wong WK, Soo KC, Chan WH, Ong HS, Chow P, Wong CY, Rha SY, Liu J, Hillmer AM, Hughes JR, Rozen S, Teh BT, Fullwood MJ, Li S, Tan P Nature communications 2016 Sep 28;7:12983 10.1038/ncomms12983

2016
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Collaborative Completion of Transcription Factor Binding Profiles via Local Sensitive Unified Embedding. Zhu L., Guo W. L., Lu C. and Huang D. S. IEEE Trans Nanobioscience. 2016;15(8):946-958. Epub 2016/11/16.

2016
10.1002/acn3.320
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A microRNA-328 binding site in PAX6 is associated with centrotemporal spikes of rolandic epilepsy. Panjwani N, Wilson MD, Addis L, Crosbie J, Wirrell E, Auvin S, Caraballo RH, Kinali M, McCormick D, Oren C, Taylor J, Trounce J, Clarke T, Akman CI, Kugler SL, Mandelbaum DE, McGoldrick P, Wolf SM, Arnold P, Schachar R, Pal DK, Strug LJ Annals of clinical and translational neurology 2016 Jul;3(7):512-22 10.1002/acn3.320

2016
10.3791/54093
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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA). Miller DE, Patel ZH, Lu X, Lynch AT, Weirauch MT, Kottyan LC Journal of visualized experiments : JoVE 2016 Aug 21;(114) 10.3791/54093

2016
10.1093/nar/gkw826
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BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire. Najafova Z, Tirado-Magallanes R, Subramaniam M, Hossan T, Schmidt G, Nagarajan S, Baumgart SJ, Mishra VK, Bedi U, Hesse E, Knapp S, Hawse JR, Johnsen SA Nucleic acids research 2017 Jan 9;45(1):127-141 10.1093/nar/gkw826

2016
10.1093/bib/bbw023
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Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. Nakato R, Shirahige K Briefings in bioinformatics 2017 Mar 1;18(2):279-290 10.1093/bib/bbw023

2016
10.1016/j.joca.2016.03.007
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Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses. Dunn SL, Soul J, Anand S, Schwartz JM, Boot-Handford RP, Hardingham TE Osteoarthritis and cartilage 2016 Aug;24(8):1431-40 10.1016/j.joca.2016.03.007

2016
10.1126/science.aad7993
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Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JSY, Martinez-Gil L, Fenouil R, Chen X, Edwards M, Metreveli G, Jordan S, Peralta Z, Munoz-Fontela C, Bouvier N, Merad M, Jin J, Weirauch M, Heinz S, Benner C, van Bakel H, Basler C, García-Sastre A, Bukreyev A, Marazzi I Science (New York, N.Y.) 2016 May 27;352(6289):aad7993 10.1126/science.aad7993

2016
10.1093/nar/gkw477
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Goldmine integrates information placing genomic ranges into meaningful biological contexts. Bhasin JM, Ting AH Nucleic acids research 2016 Jul 8;44(12):5550-6 10.1093/nar/gkw477

2016
10.1038/srep36111
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Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay. Trypsteen W, Mohammadi P, Van Hecke C, Mestdagh P, Lefever S, Saeys Y, De Bleser P, Vandesompele J, Ciuffi A, Vandekerckhove L, De Spiegelaere W Scientific reports 2016 Oct 26;6:36111 10.1038/srep36111

2015
10.1371/journal.pgen.1005734
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The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney. O'Brown ZK, Van Nostrand EL, Higgins JP, Kim SK PLoS genetics 2015 Dec;11(12):e1005734 10.1371/journal.pgen.1005734

2015
10.1093/nar/gkv607
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By the company they keep: interaction networks define the binding ability of transcription factors. Cirillo D, Botta-Orfila T, Tartaglia GG Nucleic acids research 2015 Oct 30;43(19):e125 10.1093/nar/gkv607

2015
10.15252/emmm.201505424
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Androgen receptor profiling predicts prostate cancer outcome. Stelloo S, Nevedomskaya E, van der Poel HG, de Jong J, van Leenders GJ, Jenster G, Wessels LF, Bergman AM, Zwart W EMBO molecular medicine 2015 Nov;7(11):1450-64 10.15252/emmm.201505424

2015
10.1093/bioinformatics/btv612
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LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Sheffield NC, Bock C Bioinformatics (Oxford, England) 2016 Feb 15;32(4):587-9 10.1093/bioinformatics/btv612

2015
10.1093/nar/gkv1281
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Modeling co-occupancy of transcription factors using chromatin features. Liu L, Zhao W, Zhou X Nucleic acids research 2016 Mar 18;44(5):e49 10.1093/nar/gkv1281

2014
10.1093/nar/gku1280
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Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B Nucleic acids research 2015 Feb 27;43(4):e27 10.1093/nar/gku1280

Year DOI Pubmed ID Citation