Ecosyste.ms: Papers

10.7554/eLife.00808

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation
Cited by: 159
Author(s): William S. Kruesi, Leighton J. Core, Colin T. Waters, John T. Lis, Barbara J Meyer
Software Mentions: 3
Published: over 11 years ago

10.1016/j.xcrm.2020.100146

Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
Cited by: 22
Author(s): Nils Rother, Cansu Yanginlar, R.G.H. Lindeboom, Siroon Bekkering, Mandy M. T. van Leent, Baranca Buijsers, Inge Jonkman, Mark de Graaf, Marijke P Baltissen, Lieke A. Lamers, Niels P. Riksen, Zahi A. Fayad, Willem J. M. Mulder, Luuk B. Hilbrands, Leo A. B. Joosten, Mihai G. Netea, Michiel Vermeulen, Johan van der Vlag, Raphaël Duivenvoorden
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1002728

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
Cited by: 66
Author(s): Julia Heisig, D. F. Weber, Eva Englberger, Anja Winkler, Susanne Kneitz, Wing-Kin Sung, Elmar Wolf, Martin Eilers, Wei Chia-Lin, Manfred Gessler
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.1007999

Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes
Cited by: 7
Author(s): Aria Ronsmans, Maxime Wéry, Ugo Szachnowski, Camille Gautier, Marc Descrimes, Evelyne Dubois, Antonin Morillon, Isabelle Georis
Software Mentions: 3
Published: over 5 years ago

10.1038/s41420-020-0264-5

Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells
Cited by: 6
Author(s): Fei He, Hao Wu, Libing Zhou, Qing Lin, Yin Chen, Yi Sun
Software Mentions: 3
Published: over 4 years ago

10.1186/s12920-014-0071-z

PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders
Cited by: 10
Author(s): Zheng Zhao, Yongsheng Li, Hong Chen, Jianping Lu, Peter M. Thompson, Juan Chen, Zishan Wang, Juan Xu, Xu Chun, Xia Li
Software Mentions: 3
Published: almost 10 years ago

10.1038/celldisc.2015.8

The PRC2-associated factor C17orf96 is a novel CpG island regulator in mouse ES cells
Cited by: 26
Author(s): Robert Liefke, Yang Shi
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1004183

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis
Cited by: 116
Author(s): Luis Solans, Jesús Gonzalo-Asensio, Claudia Sala, Andrej Benjak, Swapna Uplekar, Jacques Rougemont, Christophe Guilhot, Wladimir Malaga, Carlos Martı́n, Stewart T. Cole
Software Mentions: 3
Published: over 10 years ago

10.1111/jcmm.15323

The proteasome activator PA200 regulates expression of genes involved in cell survival upon selective mitochondrial inhibition in neuroblastoma cells
Cited by: 5
Author(s): Abdennour Douida, Frank Batista, Agnieszka Robaszkiewicz, Pál Botó, Azzam Aladdin, Mónika Szenykiv, Rita Czinege, László Virág, Krisztina Tar
Software Mentions: 3
Published: over 4 years ago

10.1111/jcmm.16750

Identification and characterization of N6‐methyladenosine modification of circRNAs in glioblastoma
Cited by: 8
Author(s): Yuhao Zhang, Xiuchao Geng, Jintao Xu, Qiang Li, Liangchao Hao, Zhaomu Zeng, Menglin Xiao, Jia Song, Fulin Liu, Chuan Fang, Hong Wang
Software Mentions: 3
Published: over 3 years ago

10.1038/cddis.2017.468

The histone code reader Spin1 controls skeletal muscle development
Cited by: 12
Author(s): Holger Greschik, Delphine Duteil, Nadia Messaddeq, Dominica Willmann, Laura Arrigoni, Manuela Sum, Manfred Jung, Daniel Metzger, Thomas Manke, Thomas Günther, Roland Schüle
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12284-021-00515-7

A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling
Cited by: 5
Author(s): Chao Zhou, Xiaoyun Liu, Xinglei Li, Hanlin Zhou, Sijia Wang, Yanfei Zhu, Yonghong Zhang, Sanhe Li, Aiqing You, Lei Zhou, Zhengquan He
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1004851

A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation
Cited by: 62
Author(s): Catherine Creppe, Anna M. Palau, Roberto Malinverni, Vanesa Valero, Marcus Buschbeck
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pgen.1006793

MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain
Cited by: 110
Author(s): Sabine Lagger, John C. Connelly, Gabriele Schweikert, Shaun Webb, Jim Selfridge, Bernard Ramsahoye, Miao Yu, Chuan He, Guido Sanguinetti, Lawrence C. Sowers, Malcolm D. Walkinshaw, Adrian Bird
Software Mentions: 3
Published: over 7 years ago

10.1186/s13073-017-0481-6

Nuclear Wiskott–Aldrich syndrome protein co-regulates T cell factor 1-mediated transcription in T cells
Cited by: 16
Author(s): Nikolai V. Kuznetsov, Bader Almuzzaini, Joanna S. Kritikou, Marisa A. P. Baptista, Mariana M.S. Oliveira, Márton Keszei, Scott B. Snapper, Piergiorgio Percipalle, Lisa S. Westerberg
Software Mentions: 3
Published: about 7 years ago

10.1038/cddis.2017.48

Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4
Cited by: 30
Author(s): Josefina Castex, Dominica Willmann, Toufike Kanouni, Laura Arrigoni, Yan Li, Marcel Friedrich, Michael Schleicher, Simon Wöhrle, Mark Pearson, Norbert Kraut, Michaël Méret, Thomas Manke, Eric Metzger, Roland Schüle, Thomas Günther
Software Mentions: 3
Published: over 7 years ago

10.1038/s41419-020-2333-3

UHRF1-repressed 5’-hydroxymethylcytosine is essential for the male meiotic prophase I
Cited by: 9
Author(s): Hongjie Pan, Ning Jiang, Shenfei Sun, Hanwei Jiang, Jianze Xu, Xiaohua Jiang, Qian Gao, Liang Li, Haili Wu, Huajun Zheng, Qi Qi, Tianqi Li, Meixing Zhang, Lingling Zhang, Xiaofeng Wan, Xinhua Lin, Jiemin Wong, Qinghua Shi, Li R
Software Mentions: 3
Published: over 4 years ago

10.1186/s13073-015-0180-0

The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells
Cited by: 14
Author(s): Robert Liefke, Indra M. Windhof-Jaidhauser, Jochen Gaedcke, Gabriela Salinas-Riester, Feizhen Wu, Michael Ghadimi, Sebastian Dango
Software Mentions: 3
Published: over 9 years ago

10.1186/gm536

Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases
Cited by: 21
Author(s): Gareth A. Wilson, Lee M. Butcher, Holly R. Foster, Andrew Feber, Christian Roos, Lutz Walter, Grzegorz Woszczek, Stephan Beck, Christopher G. Bell
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13073-016-0310-3

Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis
Cited by: 18
Author(s): Valeriya Malysheva, Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem, Hinrich Gronemeyer
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-017-4169-5

CGDV: a webtool for circular visualization of genomics and transcriptomics data
Cited by: 3
Author(s): Vineet Jha, Gulzar Singh, Sanjiv Kumar, Amol D. Sonawane, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1005680

LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes
Cited by: 54
Author(s): Hanqian L. Carlson, Jeffrey J. Quinn, Yul W. Yang, Chelsea K. Thornburg, Howard Y. Chang, H. Scott Stadler
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1004714

The Master Activator of IncA/C Conjugative Plasmids Stimulates Genomic Islands and Multidrug Resistance Dissemination
Cited by: 97
Author(s): Nicolas Carraro, Dominick Matteau, Peng Luo, Sébastien Rodrigue, Vincent Burrus
Software Mentions: 3
Published: about 10 years ago

10.1038/s41418-019-0362-1

ALDH1A3-regulated long non-coding RNA NRAD1 is a potential novel target for triple-negative breast tumors and cancer stem cells
Cited by: 79
Author(s): Dejan Vidovic, Thomas T. Huynh, Prathyusha Konda, Cheryl A. Dean, Brianne M. Cruickshank, Mohammad Sultan, Krysta M. Coyle, Shashi Gujar, Paola Marcato
Software Mentions: 3
Published: over 5 years ago

10.1186/s13073-017-0452-y

Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability
Cited by: 28
Author(s): Claudio Reggiani, Sandra Coppens, Tayeb Sékhara, Ivan K. Dimov, Bruno Pichon, Nicolas Lufin, Marie Claude Addor, Elga Fabia Belligni, María Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gérard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
Software Mentions: 3
Published: over 7 years ago

10.1186/s40104-021-00577-z

The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs
Cited by: 15
Author(s): Jin Yue, Xinhua Hou, Xin Liu, Ligang Wang, Hongmei Gao, Fuping Zhao, Lisong Shi, Liangyu Shi, Yan Hua, Tianyu Deng, Jianfei Gong, Lixian Wang, Longchao Zhang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1005870

Systems Level Analyses Reveal Multiple Regulatory Activities of CodY Controlling Metabolism, Motility and Virulence in Listeria monocytogenes
Cited by: 55
Author(s): Lior Lobel, Anat A. Herskovits
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-015-1445-0

Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells
Cited by: 28
Author(s): Daniel J. Trombly, Troy W. Whitfield, Srivatsan Padmanabhan, Jonathan A. R. Gordon, Jane B. Lian, André J. van Wijnen, Sayyed K. Zaidi, Janet L. Stein
Software Mentions: 3
Published: over 9 years ago

10.1186/s13059-020-01984-7

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
Cited by: 45
Author(s): Zhilian Jia, Jingwei Li, Xijin Ge, Yonghu Wu, Ya Guo, Qiang Wu
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009542

Genome-wide proximity between RNA polymerase and DNA topoisomerase I supports transcription in Streptococcus pneumoniae
Cited by: 7
Author(s): Marı́a José Ferrándiz, Pablo Hernández, Adela G. de la Campa
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers11111685

Intra-Patient Heterogeneity of Circulating Tumor Cells and Circulating Tumor DNA in Blood of Melanoma Patients
Cited by: 21
Author(s): Katharina Gorges, Lisa Wiltfang, Tobias M. Gorges, Alexander Sartori, Lina Hildebrandt, Laura Keller, Beate Volkmer, Sven Peine, Anna Babayan, Ingrid Moll, Stefan W. Schneider, Sören Twarock, Peter Mohr, Jens W. Fischer, Klaus Pantel
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1003459

SNF5 Is an Essential Executor of Epigenetic Regulation during Differentiation
Cited by: 44
Author(s): Jueng Soo You, Daniel D. De Carvalho, Chao Dai, Minmin Liu, Kurinji Pandiyan, Xianghong Jasmine Zhou, Gangning Liang, Peter A. Jones
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pgen.1004916

PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination
Cited by: 125
Author(s): Christopher L. Baker, Shimpei Kajita, Michael Walker, Ruth L. Saxl, Narayanan Raghupathy, Kwangbom Choi, Petko M. Petkov, Kenneth Paigen
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2164-14-666

Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Cited by: 62
Author(s): Pablo Cingolani, Xiaoyi Cao, Radhika S. Khetani, Chieh Chun Chen, Melissa Coon, Alya’a Sammak, Aliccia Bollig‐Fischer, Susan Land, Yun Huang, Matthew E. Hudson, Mark D. Garfinkel, Sheng Zhong, Gene E. Robinson, Douglas M. Ruden
Software Mentions: 3
Published: about 11 years ago

10.1186/s12859-018-2577-4

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis
Cited by: 2
Author(s): Dejian Zhao, Deyou Zheng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-019-1691-6

Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification
Cited by: 28
Author(s): Daryl M. Gohl, Alessandro Magli, John Garbe, Aaron Becker, Darrell M. Johnson, Shea Anderson, Benjamin Auch, Bradley Billstein, Elyse Froehling, Shana L. McDevitt, Kenneth B. Beckman
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-020-01976-7

Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium
Cited by: 10
Author(s): Juri Kazakevych, Jérémy Denizot, Anke Liebert, Mariana Portovedo, Mia Mosavie, Payal Jain, Claudia Stellato, Claire M. Fraser, Renan Oliveira Corrêa, Marina Célestine, Raphaël Mattiuz, Hanneke Okkenhaug, Jim Miller, Marco Aurélio Ramirez Vinolo, Marc Veldhoen, Patrick Varga‐Weisz
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-020-02150-9

A novel antiviral lncRNA, EDAL, shields a T309 O-GlcNAcylation site to promote EZH2 lysosomal degradation
Cited by: 34
Author(s): Baokun Sui, Dong Chen, Wei Liu, Qiong Wu, Bin Tian, Yingying Li, Jing Hou, Shiyong Liu, Juan Xie, Hao Jiang, Zhidan Luo, Lei Lv, Fei Huang, Ruiming Li, Chengguang Zhang, Yuling Tian, Min Cui, Ming Zhou, Huanchun Chen, Zhen F. Fu, Yi Zhang, Ling Zhao
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-13-50

Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages
Cited by: 68
Author(s): Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R. Steffensen, Carsten Carlberg
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pcbi.1003711

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
Cited by: 421
Author(s): Mahmoud Ghandi, Dongwon Lee, M. Mohammad-Noori, M Beer
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pcbi.1005720

Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb
Cited by: 16
Author(s): Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler Garvin, Ingrid Plajzer-Frick, Catherine S. Pickle, Jennifer A. Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E. Dickel, Axel Visel, Len A. Pennacchio
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0214723

Identification of factors associated with duplicate rate in ChIP-seq data
Cited by: 6
Author(s): Shulan Tian, Shu‐Lin Peng, Michael Kalmbach, Krutika S. Gaonkar, Aditya Bhagwate, Wei Ding, Jeanette E. Eckel‐Passow, Huihuang Yan, Susan L. Slager
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-016-1023-z

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells
Cited by: 54
Author(s): Xiaoli Zhang, Jun Wu, Jian Wang, Tingting Shen, Hua Li, Jun Lü, Yunzhao Gu, Yani Kang, Chee-Hong Wong, Chew Yee Ngan, Zongshu Shao, Ji Wu, Xiaodong Zhao
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-015-2285-7

cChIP-seq: a robust small-scale method for investigation of histone modifications
Cited by: 13
Author(s): Cristina Valensisi, Jo Ling Liao, Colin Andrus, Stephanie L. Battle, R. David Hawkins
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.21666

A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress
Cited by: 86
Author(s): Alicia N. McMurchy, Przemyslaw Stempor, Tessa Gaarenstroom, Brian Wysolmerski, Dong Yan, Darya Aussianikava, Alex Appert, Ni Huang, Paulina Kolasinska-Zwierz, Alexandra Sapetschnig, Eric A. Miska, Julie Ahringer
Software Mentions: 3
Published: over 7 years ago

10.1016/j.cell.2011.12.029

RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3
Cited by: 504
Author(s): Lígia Tavares, Emilia Dimitrova, David Oxley, Judith Webster, Raymond A. Poot, Jeroen Demmers, Karel Bezstarosti, Stephen Taylor, Hiroki Ura, Hiroshi Koide, Anton Wutz, Miguel Vidal, Sarah Elderkin, Neil Brockdorff
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12859-020-3430-0

MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq
Cited by: 13
Author(s): Yiqian Zhang, Michiaki Hamada
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1002968

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
Cited by: 199
Author(s): Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, J Stamatoyannopoulos, Jason Ernst, M Kellis, Bing Ren
Software Mentions: 3
Published: over 11 years ago

10.1186/s13059-015-0696-z

FOXM1 binds directly to non-consensus sequences in the human genome
Cited by: 47
Author(s): Deborah A. Sanders, Michael V. Gormally, Giovanni Marsico, Dario Beraldi, David Tannahill, Shankar Balasubramanian
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0242211

Ikaros antagonizes DNA binding by STAT5 in pre-B cells
Cited by: 7
Author(s): Beate Heizmann, Stéphanie Le Gras, Célestine Simand, Patricia Marchal, Susan Chan, Philippe Kastner
Software Mentions: 3
Published: about 4 years ago

10.1186/s12915-015-0159-8

Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline
Cited by: 58
Author(s): Ho-Su Sin, Andrey V. Kartashov, Kazuteru Hasegawa, Artem Barski, Satoshi H. Namekawa
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pcbi.1003501

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
Cited by: 75
Author(s): Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-13-147

Genome-wide analysis of Pax8 binding provides new insights into thyroid functions
Cited by: 40
Author(s): Sergio Ruiz‐Llorente, Enrique Carrillo Santa de Pau, Ana Sastre-Perona, Cristina Montero‐Conde, Gonzalo Goméz-López, James A. Fagin, Alfonso Valencia, David G. Pisano, Pilar Santisteban
Software Mentions: 3
Published: over 12 years ago

10.1186/gb-2009-10-12-r142

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
Cited by: 63
Author(s): Desmond S. Lun, Ashley M. Sherrid, Brian Weiner, David R. Sherman, James E. Galagan
Software Mentions: 3
Published: almost 16 years ago

10.1534/genetics.118.301674

MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in <i>Caenorhabditis elegans</i>
Cited by: 30
Author(s): Martina Hajdůšková, Gülkız Baytek, Ena Kolundžić, Alexander Gosdschan, Marlon Kazmierczak, Andreas Ofenbauer, Maria Lena Beato del Rosal, Sergej Herzog, Nida Fatima, Philipp Mertins, Stefanie Müthel, Baris Tursun
Software Mentions: 3
Published: about 6 years ago

10.3390/genes10050348

Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver
Cited by: 6
Author(s): Yu Luan, Lu Zhang, Mingyang Hu, Yongming Xu, Ye Hou, Xinyun Li, Zhao Song, Yi‐Fang Zhao, Changchun Li
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0148321

ePIANNO: ePIgenomics ANNOtation tool
Cited by: 4
Author(s): Chia-Hsin Liu, Bing-Ching Ho, Chun Ling Chen, Yun‐chien Chang, Yi Chiung Hsu, Yu Cheng Li, Shin Sheng Yuan, Yi Huan Huang, Chi Chen Chang, Ker Chau Li, Hsuan Yu Chen
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0126143

The Intraperitoneal Transcriptome of the Opportunistic Pathogen Enterococcus faecalis in Mice
Cited by: 29
Author(s): Cécile Muller, Margherita Cacaci, Nicolas Sauvageot, Maurizio Sanguinetti, Thomas Rattei, Thomas Eder, Jean‐Christophe Giard, Jörn Kalinowski, Torsten Hain, Axel Hartke
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-019-5602-8

A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe
Cited by: 16
Author(s): Dane Vassiliadis, Koon Ho Wong, Alex Andrianopoulos, Brendon J. Monahan
Software Mentions: 3
Published: over 5 years ago

10.3389/fvets.2021.659840

Differential DNA Methylation and Gene Expression Between ALV-J-Positive and ALV-J-Negative Chickens
Cited by: 3
Author(s): Yongde Yan, Huihua Zhang, Shuang Gao, Huanmin Zhang, Xinheng Zhang, Weiguo Chen, Wencheng Lin, Qingmei Xie
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pbio.3000094

Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila
Cited by: 26
Author(s): Chris Ellison, Doris Bachtrog
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pbio.2003389

Aging alters the epigenetic asymmetry of HSC division
Cited by: 94
Author(s): Maria Carolina Florian, Markus Klose, Mehmet Saçma, Jelena Jablanovic, Luke Knudson, Kalpana Nattamai, Gina Marka, Angelika Vollmer, Karin Soller, Vadim Sakk, Nina Cabezas-Wallscheid, Yi Zheng, Medhanie Mulaw, Ingmar Glauche, Hartmut Geiger
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0016344

Genomewide Analyses Define Different Modes of Transcriptional Regulation by Peroxisome Proliferator-Activated Receptor-β/δ (PPARβ/δ)
Cited by: 76
Author(s): Till Adhikary, Kerstin Kaddatz, Florian Finkernagel, Anne Schönbauer, Wolfgang Meißner, Maren Scharfe, Michael Jarek, Helmut Blöcker, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 3
Published: almost 14 years ago

10.3389/fphys.2018.01755

The Use of Targeted Next Generation Sequencing to Explore Candidate Regulators of TGF-β1’s Impact on Kidney Cells
Cited by: 7
Author(s): Bo Wang, Guanyu Ji, Haroon Naeem, Junwen Wang, Phillip Kantharidis, David Powell, Sharon D. Ricardo
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pbio.1000550

Co-Evolution of Transcriptional Silencing Proteins and the DNA Elements Specifying Their Assembly
Cited by: 38
Author(s): Oliver A. Zill, Devin R. Scannell, Lenny Teytelman, Jasper Rine
Software Mentions: 3
Published: almost 14 years ago

10.1186/1471-2164-14-193

Dynamic regulation of epigenomic landscapes during hematopoiesis
Cited by: 45
Author(s): Brian J. Abraham, Kairong Cui, Qingsong Tang, Keji Zhao
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0089187

Miz1 Deficiency in the Mammary Gland Causes a Lactation Defect by Attenuated Stat5 Expression and Phosphorylation
Cited by: 7
Author(s): Adrián Sanz-Moreno, David Fuhrmann, Elmar Wolf, Björn von Eyß, Martin Eilers, Hans–Peter Elsässer
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-14-128

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Cited by: 4,562
Author(s): Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R. Clark, Avi Ma’ayan
Software Mentions: 3
Published: over 11 years ago

10.3389/fnins.2020.00472

Genes Bound by ΔFosB in Different Conditions With Recurrent Seizures Regulate Similar Neuronal Functions
Cited by: 3
Author(s): Gabriel S. Stephens, Chia-Hsuan Fu, Corey P St Romain, Yi Zheng, Justin J. Botterill, Helen E. Scharfman, Yin Liu, Jeannie Chin
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0155378

CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells
Cited by: 7
Author(s): Laurie A. Steiner, Vincent P. Schulz, Yelena Makismova, Kimberly Lezon-Geyda, Patrick G. Gallagher
Software Mentions: 3
Published: over 8 years ago

10.1186/1746-4811-7-11

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
Cited by: 60
Author(s): Jose M. Muiño, Kerstin Kaufmann, Roeland Chj van Ham, Gerco C. Angenent, Paweł Krajewski
Software Mentions: 3
Published: almost 14 years ago

10.3389/fimmu.2019.00667

NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation
Cited by: 11
Author(s): Satyajeet P. Khare, Ankitha Shetty, Rahul Biradar, Indumathi Patta, Zhi Chen, Ameya Sathe, Puli Chandramouli Reddy, Riitta Lahesmaa, Sanjeev Galande
Software Mentions: 3
Published: over 5 years ago

10.3389/fnins.2019.00460

Identification of Cholecystokinin by Genome-Wide Profiling as Potential Mediator of Serotonin-Dependent Behavioral Effects of Maternal Separation in the Amygdala
Cited by: 10
Author(s): Magdalena Weidner, Roy Lardenoije, Lars Eijssen, Floriana Mogavero, Lilian P. M. T. De Groodt, Sandy Popp, Rupert Palme, Konrad U. Förstner, Tatyana Strekalova, Harry W.M. Steinbusch, Angelika G. Schmitt-Böhrer, Jeffrey Glennon, Jonas Waider, Daniël L.A. van den Hove, Klaus–Peter Lesch
Software Mentions: 3
Published: over 5 years ago

10.1111/pbi.12988

Multi‐omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process
Cited by: 81
Author(s): Jianying Li, Maojun Wang, Yajun Li, Qinghua Zhang, Keith Lindsey, Henry Daniell, Shuangxia Jin, Xianlong Zhang
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0140077

GATA1 and PU.1 Bind to Ribosomal Protein Genes in Erythroid Cells: Implications for Ribosomopathies
Cited by: 14
Author(s): Elsa P. Amanatiadou, Giorgio L. Papadopoulos, John Strouboulis, Ioannis S. Vizirianakis
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0066807

The Rice NAD+-Dependent Histone Deacetylase OsSRT1 Targets Preferentially to Stress- and Metabolism-Related Genes and Transposable Elements
Cited by: 38
Author(s): Xiaochao Zhong, Hua Zhang, Yu Zhao, Qianwen Sun, Yongfeng Hu, Hai Peng, Dao‐Xiu Zhou
Software Mentions: 3
Published: over 11 years ago

10.3389/fvets.2015.00068

Cystoisospora suis – A Model of Mammalian Cystoisosporosis
Cited by: 22
Author(s): Aruna Shrestha, Ahmed Abdelfattah, Barbara Freudenschuss, Barbara Hinney, Nicola Palmieri, Bärbel Ruttkowski, Anja Joachim
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.9442

Genome-wide Cas9 binding specificity in Saccharomyces cerevisiae
Cited by: 3
Author(s): Zachary J Waldrip, Piroon Jenjaroenpun, Oktawia A DeYoung, Intawat Nookaew, Sean D. Taverna, Kevin D. Raney, Alan J. Tackett
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2015.00188

Emerging applications of read profiles towards the functional annotation of the genome
Cited by: 9
Author(s): Sachin Pundhir, Panayiota Poirazi, Jan Gorodkin
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0062547

p63 Attenuates Epithelial to Mesenchymal Potential in an Experimental Prostate Cell Model
Cited by: 29
Author(s): Jan Roger Olsen, Anne Margrete Øyan, Kari Rostad, Margrete R. Hellem, Jie Liu, Lisha Li, David Micklem, Hallvard Haugen, James B. Lorens, Varda Rotter, Xisong Ke, Biaoyang Lin, Karl‐Henning Kalland
Software Mentions: 3
Published: over 11 years ago

10.3389/fgene.2019.00936

Enhancer LncRNAs Influence Chromatin Interactions in Different Ways
Cited by: 32
Author(s): Yue Hou, Rong Xin Zhang, Xiao Sun
Software Mentions: 3
Published: about 5 years ago

10.1186/s13071-019-3615-4

DNA methylation and hydroxymethylation profiles reveal possible role of highly methylated TLR signaling on Fasciola gigantica excretory/secretory products (FgESPs) modulation of buffalo dendritic cells
Cited by: 8
Author(s): Xuefang Mei, Wei Shi, Yao‐Yao Zhang, Bin Zhu, Yu-Rui Wang, Lin-jing Hou, Wei Zhao, Jian Li, Dongying Wang, Honglin Luo, Weiyi Huang
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-12-593

A co-ordinated interaction between CTCF and ER in breast cancer cells
Cited by: 56
Author(s): Caryn S. Ross-Innes, Gordon D. Brown, Jason S. Carroll
Software Mentions: 3
Published: almost 13 years ago

10.3390/v13040544

Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis
Cited by: 4
Author(s): Liana V. Basova, Alexander Lindsey, Anne Marie McGovern, Ronald J. Ellis, Maria Cecília Garibaldi Marcondes
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-15-494

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
Cited by: 2
Author(s): Lucas D. Ward, Junbai Wang, Harmen J. Bussemaker
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-14-99

Nuclear Factor I genomic binding associates with chromatin boundaries
Cited by: 25
Author(s): Milos Pjanic, Christoph D. Schmid, Armelle Gaussin, Giovanna Ambrosini, Jozef Adamčík, Petar Pjanić, Genta Plasari, Jan Kerschgens, Giovani Dietler, Philipp Bücher, Nicolas Mermod
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2014.00277

Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae
Cited by: 14
Author(s): Elena Gómez-Díaz, Ana Rivero, Fabrice Chandre, Victor G. Corcés
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-15-331

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells
Cited by: 40
Author(s): Suhn Kyong Rhie, Dennis J. Hazelett, Simon Coetzee, Chunli Yan, Houtan Noushmehr
Software Mentions: 3
Published: over 10 years ago

10.3389/fcell.2021.682561

Genome-Wide Histone H3K27 Acetylation Profiling Identified Genes Correlated With Prognosis in Papillary Thyroid Carcinoma
Cited by: 7
Author(s): Luyao Zhang, Dan Xiong, Qian Liu, Yiling Luo, Yuhan Tian, Xi Xiao, Ye Sang, Yihao Liu, Shubin Hong, Shuang Yu, Jie Li, Weiming Lv, Yanbing Li, Zhonghui Tang, Rengyun Liu, Qian Zhong, Hang Xiao
Software Mentions: 3
Published: over 3 years ago

10.1186/s13072-019-0276-7

Ovarian dysfunction following prenatal exposure to an insecticide, chlordecone, associates with altered epigenetic features
Cited by: 16
Author(s): Louis Legoff, Ouzna Dali, Shereen Cynthia D’Cruz, Antonio Suglia, Aurore Gély-Pernot, Chloé Hémery, Pierre-Yves Kernanec, Abbassia Demmouche, Christine Kervarrec, Sergei G. Tevosian, Luc Multigner, Fátima Smagulova
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.00842

Epitranscriptomic N4-Acetylcytidine Profiling in CD4+ T Cells of Systemic Lupus Erythematosus
Cited by: 18
Author(s): Gangqiang Guo, Xinyu Shi, Huijing Wang, Lele Ye, Xinya Tong, Kejing Yan, Ning Ding, Chaosheng Chen, Huidi Zhang, Xiangyang Xue
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-017-3719-1

Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern
Cited by: 42
Author(s): Xiaochun Tao, Jianning Chen, Yanzhi Jiang, Yingying Wei, Chen Yan, Huaming Xu, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Surong Shuai, Lin Bai, Haifeng Liu, Jideng Ma, Long Jin, Anxiang Wen, Qin Wang, Guangxiang Zhu, Meng Xie, Jiayun Wu, Tao He, Chunyu Huang, Xiang Gao, Xuewei Li
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2021.740866

Interplay Between BALL and CREB Binding Protein Maintains H3K27 Acetylation on Active Genes in Drosophila
Cited by: 2
Author(s): Ammad Shaukat, Muhammad Haider Farooq Khan, Hina Ahmad, Zain Umer, Muhammad Tariq
Software Mentions: 3
Published: about 3 years ago

10.3389/fcell.2021.655201

Polycomb Factor PHF19 Controls Cell Growth and Differentiation Toward Erythroid Pathway in Chronic Myeloid Leukemia Cells
Cited by: 6
Author(s): Marc García-Montolio, Cecilia Ballaré, Enrique Blanco, Arantxa Gutiérrez, Sergi Aranda, Antonio Gómez, Chung Hoow Kok, David T. Yeung, Timothy P. Hughes, Pedro Vizán, Luciano Di Croce
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.590672

Integrative Epigenomic Analysis of Transcriptional Regulation of Human CircRNAs
Cited by: 3
Author(s): Xuecang Li, Zhidong Tang, Li Peng, Yanyu Li, Fengcui Qian, Jian Zhao, Ling-Wen Ding, Xiaojuan Du, Meng Li, Jian Zhang, Xuefeng Bai, Jiang Zhu, Chenchen Feng, Qiuyu Wang, Jian Pan, Chunquan Li
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2019.00220

The DNA Methylation Status of Wnt and Tgfβ Signals Is a Key Factor on Functional Regulation of Skeletal Muscle Satellite Cell Development
Cited by: 13
Author(s): Weiya Zhang, Saixian Zhang, Yongming Xu, Yunlong Ma, Dingxiao Zhang, Xinyun Li, Shuhong Zhao
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-2169-x

Genome-wide mapping of Hif-1α binding sites in zebrafish
Cited by: 29
Author(s): David Greenald, Justin Jeyakani, Bernd Pelster, Ian Sealy, Sinnakaruppan Mathavan, Fredericus J. van Eeden
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0187891

ChIP-Seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts
Cited by: 11
Author(s): Atilla Biçer, Serena Orlando, Abul B.M.M.K. Islam, Edurne Gallastegui, Arnaud Besson, Rosa Aligué, Oriol Bachs, María Jesús Pujol
Software Mentions: 3
Published: about 7 years ago

10.3389/fcell.2021.637873

Kinome-Wide RNAi Screen Uncovers Role of Ballchen in Maintenance of Gene Activation by Trithorax Group in Drosophila
Cited by: 2
Author(s): Muhammad Haider Farooq Khan, Junaid Akhtar, Zain Umer, Najma Shaheen, Ammad Shaukat, Muhammad Shahbaz Munir, Aziz Mithani, Saeed Anwar, Muhammad Tariq
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-021-04221-5

Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models
Cited by: 2
Author(s): Arnaud Liehrmann, Guillem Rigaill, Toby Dylan Hocking
Software Mentions: 3
Published: over 3 years ago