Ecosyste.ms: Papers

10.1016/j.celrep.2018.07.026

Fine-Tuning Mybl2 Is Required for Proper Mesenchymal-to-Epithelial Transition during Somatic Reprogramming
Cited by: 16
Author(s): Carl Ward, Giacomo Volpe, Pierre Cauchy, Anetta Ptasińska, Ruba Almaghrabi, Daniel Blakemore, Monica Nafria, Doris Kestner, Jon Frampton, George J. Murphy, Yosef Buganim, Keisuke Kaji, Paloma García
Software Mentions: 4
Published: over 6 years ago

10.1016/j.celrep.2019.11.093

Dysregulation of RNA Splicing in Tauopathies
Cited by: 49
Author(s): Daniel J. Apicco, Cheng Zhang, Brandon F. Maziuk, Lulu Jiang, Heather Ballance, Samantha Boudeau, Choong Yong Ung, Hu Li, Benjamin Wolozin
Software Mentions: 4
Published: almost 5 years ago

10.1126/sciadv.abf9808

Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4
Cited by: 23
Author(s): Marten A. Hoeksema, Zeyang Shen, Inge R. Holtman, An Zheng, Nathan Spann, Isidoro Cobo, Melissa Gymrek, Christopher K. Glass
Software Mentions: 4
Published: over 3 years ago

10.1038/srep09027

Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma
Cited by: 28
Author(s): Ali Rihani, Alan Van Goethem, Maté Ongenaert, Sara De Brouwer, Pieter-Jan Volders, Saurabh Agarwal, Katleen De Preter, Pieter Mestdagh, Jason M. Shohet, Franki Speleman, Jo Vandesompele, Tom Van Maerken
Software Mentions: 4
Published: over 9 years ago

10.1038/s41421-018-0027-0

Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity
Cited by: 38
Author(s): Chih Chao Hsu, Dan Zhao, Jiejun Shi, Danni Peng, Haipeng Guan, Yuanyuan Li, Yaling Huang, Hong Wen, Wei Li, Haitao Li, Xiaobing Shi
Software Mentions: 4
Published: over 6 years ago

10.1038/celldisc.2015.45

Mapping gene regulatory circuitry of Pax6 during neurogenesis
Cited by: 56
Author(s): Sudhir Thakurela, Neha Tiwari, Sandra Schick, Angela Garding, Robert Ivánek, Benedikt Berninger, Vijay Tiwari
Software Mentions: 4
Published: almost 9 years ago

10.1126/sciadv.abe3516

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor
Cited by: 37
Author(s): Kang Wang, Honghong Wang, Conghui Li, Zhenggang Yin, Ran Xiao, Qiuzi Li, Xiaofang Ying, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Software Mentions: 4
Published: almost 4 years ago

10.1128/MCB.00668-17

The <i>Caenorhabditis elegans</i> Ortholog of TDP-43 Regulates the Chromatin Localization of the Heterochromatin Protein 1 Homolog HPL-2
Cited by: 12
Author(s): Tassa Saldi, Patrick Gonzales, Alfonso Garrido-Lecca, Vishantie Dostal, Christine M. Roberts, Leonard Petrucelli, Christopher D. Link
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-14-349

NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data
Cited by: 3
Author(s): Nak-Kyeong Kim, Rasika V Jayatillake, John L. Spouge
Software Mentions: 4
Published: almost 12 years ago

10.1038/s41419-018-0841-1

The detrimental effects of glucocorticoids exposure during pregnancy on offspring’s cardiac functions mediated by hypermethylation of bone morphogenetic protein-4
Cited by: 13
Author(s): Jun Peng, Yuhao Zhou, Zhiyu Zhang, Zhiming Wang, Ling-Tong Gao, Xiao Zhang, Fang Zhou, Guangyao Li, Huaiyan Chen, Hongxing Yang, Lu Gao
Software Mentions: 4
Published: over 6 years ago

10.1126/sciadv.abf7346

Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome
Cited by: 4
Author(s): Seung Kyoon Kim, Xihui Liu, Jong-Min Park, Dahun Um, Gokhul Kilaru, Cheng Ming Chiang, Min-Hee Kang, Kimberly M. Huber, Keunsoo Kang, Tae Kyung Kim
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.60681

SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans
Cited by: 6
Author(s): Charlotte P Choi, Rebecca J Tay, Margaret R. Starostik, Suhua Feng, James J. Moresco, Brooke E. E. Montgomery, Emily Xu, Maya A Hammonds, Michael C. Schatz, Taiowa A. Montgomery, John R. Yates, Steven E. Jacobsen, John K. Kim
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.molcel.2020.01.008

Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription
Cited by: 33
Author(s): Giacomo Cossa, Isabelle Roeschert, Florian Prinz, Apoorva Baluapuri, Raphael Silveira Vidal, Christina Schülein-Völk, Yun-Chien Chang, Carsten P. Ade, Guido Mastrobuoni, Cyrille Girard, Amit Kumar, Lars Wortmann, Susanne Walz, Reinhard Lührmann, Stefan Kempa, Bernhard Küster, Elmar Wolf, Dominik Mumberg, Martin Eilers
Software Mentions: 3
Published: over 4 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

10.1038/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

10.1111/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/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

10.1038/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

10.1186/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

10.1007/s11033-018-4247-z

HIRA directly targets the enhancers of selected cardiac transcription factors during in vitro differentiation of mouse embryonic stem cells
Cited by: 4
Author(s): Rasha N.M. Saleh, Daniel Dilg, Abla Ahmed Abou Zeid, Doaa Hashad, Peter Scambler, Ariane Chapgier
Software Mentions: 3
Published: over 6 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/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

10.1186/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

10.1371/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

10.1186/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

10.3390/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

10.1186/1471-2164-14-826

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets
Cited by: 29
Author(s): Gabriele Schweikert, Botond Cseke, Thomas Clouaire, Adrian Bird, Guido Sanguinetti
Software Mentions: 3
Published: almost 12 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

10.18632/aging.202439

A short deletion in the DNA-binding domain of STAT3 suppresses growth and progression of colon cancer cells
Cited by: 3
Author(s): Yijia Xiong, Dongyang Liu, Rongrong Shen, Yanbao Xiong
Software Mentions: 3
Published: almost 4 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

10.1186/1471-2164-14-337

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver
Cited by: 48
Author(s): Logan J. Everett, John Le Lay, Sabina Lukovac, Diana Bernstein, David J. Steger, Mitchell A. Lazar, Klaus H. Kaestner
Software Mentions: 3
Published: over 11 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

10.1242/bio.014308

Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells
Cited by: 40
Author(s): Catriona Manville, Kayleigh A. Smith, Zbysław Sońdka, Holly Ashlene Rance, Simon Cockell, Ian G. Cowell, Ka Cheong Lee, Nicholas J. Morris, Kay Padget, Graham Jackson, Caroline A. Austin
Software Mentions: 3
Published: about 9 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

10.1371/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

10.1093/bioinformatics/btw672

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning
Cited by: 25
Author(s): Toby Dylan Hocking, Patricia Goerner-Potvin, Andréanne Morin, Xiaojian Shao, Tomi Pastinen, Guillaume Bourque
Software Mentions: 3
Published: about 8 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/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

10.1186/1752-0509-7-S2-S9

Identifying novel glioma associated pathways based on systems biology level meta-analysis
Cited by: 10
Author(s): Yangfan Hu, Jinquan Li, Wenying Yan, Jiajia Chen, Yin Li, Guang Hu, Bairong Shen
Software Mentions: 3
Published: almost 12 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.pgen.1004613

Targeted H3R26 Deimination Specifically Facilitates Estrogen Receptor Binding by Modifying Nucleosome Structure
Cited by: 43
Author(s): Michael J. Guertin, Xuesen Zhang, Lynne J. Anguish, Sohyoung Kim, Lyuba Varticovski, John T. Lis, Gordon L. Hager, Scott A. Coonrod
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-016-3006-6

Genome-wide recruitment profiling of transcription factor Crz1 in response to high pH stress
Cited by: 24
Author(s): Alicia Roque, Silvia Petrezsélyová, Albert Serra-Cardona, Joaquı́n Ariño
Software Mentions: 3
Published: over 8 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

10.1186/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

10.1371/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

10.1534/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.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

10.1186/1471-2164-14-493

Suppression of genetic recombination in the pseudoautosomal region and at subtelomeres in mice with a hypomorphic Spo11 allele
Cited by: 19
Author(s): Fátima Smagulova, Kevin Brick, Yongmei Pu, Uttara Sengupta, R. Daniel Camerini‐Otero, Galina V. Petukhova
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-15-35

Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals
Cited by: 91
Author(s): Masahiro Uesaka, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1001114

Chromatin Landscape Dictates HSF Binding to Target DNA Elements
Cited by: 193
Author(s): Michael J. Guertin, John T. Lis
Software Mentions: 3
Published: about 14 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

10.1371/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/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/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

10.3389/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.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

10.3389/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

10.1371/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/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/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

10.3389/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

10.3389/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

10.3389/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.2019.00936

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

10.1371/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

10.3389/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

10.1371/journal.pone.0083723

Function of GATA Factors in the Adult Mouse Liver
Cited by: 39
Author(s): Rena Zheng, Boris Rebolledo‐Jaramillo, Yiwei Zong, Liqing Wang, Pierre Russo, Wayne W. Hancock, Ben Z. Stanger, Ross C. Hardison, Gerd A. Blobel
Software Mentions: 3
Published: almost 11 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

10.1371/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

10.1371/journal.pone.0102968

Role of Polycomb Group Proteins in the DNA Damage Response – A Reassessment
Cited by: 12
Author(s): Hollie Chandler, Harshil Patel, Richard D. Palermo, Sharon Brookes, Nik Matthews, Gordon Peters
Software Mentions: 3
Published: over 10 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

10.3389/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/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

10.3389/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/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

10.1371/journal.pone.0180583

Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data
Cited by: 24
Author(s): Chengchen Zhao, Shengen Hu, Xiao Huo, Yong Zhang
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2020.00293

ALKBH4 Functions as a Suppressor of Colorectal Cancer Metastasis via Competitively Binding to WDR5
Cited by: 9
Author(s): Chaoqin Shen, Tingting Yan, Ting Tong, Debin Shi, Linlin Ren, Youwei Zhang, Xinyu Zhang, Yingying Cao, Yuqing Yan, Yanru Ma, Xiaoqiang Zhu, Xianglong Tian, Jing‐Yuan Fang, Haoyan Chen, Linhua Ji, Jie Hong, Baoqin Xuan
Software Mentions: 3
Published: over 4 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.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

10.1371/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

10.1371/journal.pone.0118453

Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes
Cited by: 25
Author(s): I-Hsuan Lin, Dow-Tien Chen, Yi-Feng Chang, Yu-Ling Lee, Chia-Hsin Su, Ching Wei Cheng, Yi-Chien Tsai, Swee-Chuan Ng, Hsiao-Tan Chen, Mei‐Chen Lee, Hongwei Chen, Shih-Hui Suen, Yu‐Cheng Chen, Tze-Tze Liu, Chuan-Hsiung Chang, Ming Hsu
Software Mentions: 3
Published: over 9 years ago

10.3389/fcvm.2020.594325

The Regulatory Role of Histone Modification on Gene Expression in the Early Stage of Myocardial Infarction
Cited by: 5
Author(s): Jinyu Wang, Bo Lin, Yanping Zhang, Le Ni, Lingjie Hu, Jian Yang, Liang Xu, Dan Shi, Yihan Chen
Software Mentions: 3
Published: almost 4 years ago

10.3389/fcell.2021.642697

Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord
Cited by: 3
Author(s): Filipe Almeida Monteiro, Rafael Mendes Miranda, Marta C Samina, Ana Cristina Dias, Alexandre A.S.F. Raposo, Patrícia Oliveira, Carlos Reguenga, Diogo S. Castro, Deolinda Lima
Software Mentions: 3
Published: over 3 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

10.1371/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

10.1371/journal.pgen.1009090

A genetic variant controls interferon-β gene expression in human myeloid cells by preventing C/EBP-β binding on a conserved enhancer
Cited by: 2
Author(s): Anaïs Assouvie, Maxime Rotival, Juliette Hamroune, Didier Busso, Paul-Henri Roméo, Lluís Quintana‐Murci, Germain Rousselet
Software Mentions: 3
Published: about 4 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

10.1371/journal.pone.0079909

Genome-Wide Identification of Regulatory Elements and Reconstruction of Gene Regulatory Networks of the Green Alga Chlamydomonas reinhardtii under Carbon Deprivation
Cited by: 14
Author(s): Flávia Vischi Winck, Samuel Arvidsson, Diego Mauricio Riaño-Pachón, Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, David Gomez, Jens Rupprecht, Bernd Mueller‐Roeber
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0120020

Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers
Cited by: 34
Author(s): Ignacio Blanco, Karoline Kuchenbaecker, Daniel Cuadras, Xianshu Wang, Daniel Barrowdale, Gorka Ruíz de Garibay, Pablo Librado, Alejandro Sánchez-Gracia, Julio Rozas, Núria Bonifaci, Lesley McGuffog, V. Shane Pankratz, Abul B.M.M.K. Islam, Francesca Mateo, Antoni Berenguer, Audrey Petit, Isabel Catalá, Joan Brunet, Lídia Feliubadaló, Eva Tornero, Javier Benı́tez, Ana Osorio, Teresa Ramón, Cajal Teresa, Heli Nevanlinna, Kristiina Aittomäki, Banu K. Arun, Amanda E. Toland, Beth Y. Karlan, Christine Walsh, Jenny Lester, Mark H. Greene, L. Phuong, Robert L. Nussbaum, Irene L. Andrulis, Susan M. Domchek, Katherine L. Nathanson, Timothy R. Rebbeck, Rósa B. Barkardóttir, Anna Jakubowska, Jan Lubiński, Katarzyna Durda, Katarzyna Jaworska–Bieniek, Kathleen Claes, Tom Van Maerken, Orland Dı́ez, Thomas V.O. Hansen, Lars Jønson, Anne–Marie Gerdes, Bent Ejlertsen, Miguel de la Hoya, Trinidad Caldés, Alison M. Dunning, Clare Oliver, Elena Fineberg, Margaret Cook, Susan Peock, Emma McCann, Alex Murray, Chris Jacobs, Gabriella Pichert, Fiona Lalloo, Carol Chu, Huw Dorkins, Joan Paterson, Kai Ren Ong, Manuel R. Teixeira, Thais Bonfim Teixeira, Frans B.L. Hogervorst, Annemarie H. van der Hout, Caroline Seynaeve, Rob B. van der Luijt, Marjolijn J. L. Ligtenberg, Peter Devilee, Juul T. Wijnen, Matti A. Rookus, Hanne Meijers-Heijboer, Marinus J. Blok, Ans M.W. van den Ouweland, Cora M. Aalfs, Gustavo C. Rodriguez, Kelly‐Anne Phillips, Marion Piedmonte, Stacy Nerenstone, Victoria Bae‐Jump, David M. O’Malley, Elena Ratner, Rita K. Schmutzler, Barbara Wappenschmidt, Kerstin Rhiem, Christoph Engel, Alfons Meindl, Nina Ditsch, Norbert Arnold, Hansjoerg Plendl, Dieter Niederacher, Christian Sutter, Shan Wang-Gohrke, Doris Steinemann, Sabine Preisler-Adams, Karin Kast, Raymonda Varon-Mateeva, Andrea Gehrig, Anders Bojesen, Inge Søkilde Pedersen, Lone Sunde, Uffe Birk Jensen, Mads Thomassen, Torben A. Kruse, Lenka Foretová, Paolo Peterlongo, Loris Bernard, Bernard Peissel, Giulietta Scuvera, Siranoush Manoukian, Paolo Radice, Laura Ottini, Marco Montagna, Simona Agata, Christine M. Maugard, Jacques Simard, Penny Soucy, Andreas Berger, A. Fink-Retter, Christian F. Singer, Christine Rappaport, Daphne Geschwantler-Kaulich, Muy Kheng Tea, Georg Pfeiler, Esther M. John, Alexander Miron, Susan L. Neuhausen, Mary Beth Terry, Wendy K. Chung, Mary B. Daly, David E. Goldgar, Ramūnas Janavičius, Cecilia M. Dorfling, Elizabeth J. van Rensburg, Florentia Fostira, Irene Konstantopoulou, Judy E. Garber, Andrew K. Godwin, Edith Olàh, Steven A. Narod, Gad Rennert, Shani Shimon Paluch, Yael Laitman, Eitan Friedman, Annelie Liljegren, Johanna Rantala, Marie Stenmark-Askmalm, Niklas Loman, Evgeny N. Imyanitov, Ute Hamann, Amanda B. Spurdle, Sue Healey, Jeffrey N. Weitzel, Josef Herzog, David A. Margileth, Chiara Gorrini, Manel Esteller, Antonio Gómez, Sergi Sayols, Enrique Vidal, Holger Heyn, Dominique Stoppa‐Lyonnet, Mélanie Léone, Laure Barjhoux, Marion Fassy-Colcombet, Antoine de Pauw, Christine Lasset, Sandra Fert Ferrer, Laurent Castéra, Pascaline Berthet, François Cornélis, Yves Jean Bignon, Francesca Damiola, Sylvie Mazoyer, Olga M. Sinilnikova, Christopher A. Maxwell, Joseph Vijai, Mark E. Robson, Noah D. Kauff, Marina Corines, Danylko Villano, Julie M. Cunningham, Adam F. Lee, Noralane M. Lindor, Conxi Lázaro, Douglas F. Easton, Kenneth Offit, Georgia Chenevix-Trench, Fergus J. Couch, Antonis C. Antoniou, Miguel Ángel Pujana
Software Mentions: 3
Published: over 9 years ago

10.1111/acel.13348

NELF‐A controls <i>Drosophila</i> healthspan by regulating heat‐shock protein‐mediated cellular protection and heterochromatin maintenance
Cited by: 5
Author(s): Zhen‐Kai Ngian, Wei‐Qi Lin, Chin‐Tong Ong
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1002688

YY1 Regulates Melanocyte Development and Function by Cooperating with MITF
Cited by: 42
Author(s): Juying Li, Jun S. Song, Robert J.A. Bell, Thanh Nga Tran, Rizwan Haq, Huifei Liu, Kevin T. Love, Robert Langer, Daniel G. Anderson, Lionel Larue, David E. Fisher
Software Mentions: 3
Published: over 12 years ago

10.1186/s13072-018-0177-1

Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells
Cited by: 36
Author(s): Andrea Coluccio, Gabriela Ecco, Julien Duc, Sandra Offner, Priscilla Turelli, Didier Trono
Software Mentions: 3
Published: over 6 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

10.1371/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

10.1186/1471-2164-14-666

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

10.1371/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