pypi: MACS | Projects | Ecosyste.ms: Papers

10.1111/mmi.12345

The <scp>APSES</scp> transcription factor <scp>Efg</scp>1 is a global regulator that controls morphogenesis and biofilm formation in <i><scp>C</scp>andida parapsilosis</i>
Cited by: 42
Author(s): Leona A. Connolly, Alessandro Riccombeni, Zsuzsana Grózer, Linda Holland, Denise B. Lynch, David R. Andes, Attila Gácser, Geraldine Butler
Software Mentions: 3
Published: over 11 years ago

10.1016/j.celrep.2015.12.012

NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR
Cited by: 27
Author(s): Kobe Yuen, Baoshan Xu, Ian D. Krantz, Jennifer L. Gerton
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12915-018-0573-9

UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells
Cited by: 32
Author(s): Cong Xiong, Zengqi Wen, Juan Yu, Jun Chen, Chao-Pei Liu, Xiaodong Zhang, Ping Chen, Rui-Ming Xu, Guohong Li
Software Mentions: 3
Published: about 6 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/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/s13059-016-1023-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/s13059-015-0696-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

10.1016/j.mce.2020.111007

Hypoxia regulates GR function through multiple mechanisms involving microRNAs 103 and 107
Cited by: 11
Author(s): Nan Yang, Andrew Berry, Carolin M Sauer, Matthew Baxter, Ian J. Donaldson, Karen Forbes, Rachelle Donn, Laura Matthews, David Ray
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

10.1038/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

10.1038/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

10.1007/s00401-013-1168-8

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
Cited by: 162
Author(s): Katja Kobow, Antony Kaspi, K N Harikrishnan, K. Kiese, Mark Ziemann, Ishant Khurana, Ina Fritzsche, Jan Hauke, Eric Hahnen, Roland Coras, Angelika Mühlebner, Assam El‐Osta, Ingmar Blümcke
Software Mentions: 3
Published: about 11 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

10.1016/j.celrep.2019.08.040

RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction
Cited by: 23
Author(s): Anetta Ptasińska, Anna Pickin, Salam A. Assi, Paulynn Suyin Chin, Luke Ames, Roberto Avellino, Stephan Gröschel, Ruud Delwel, Peter N. Cockerill, Cameron S. Osborne, Constanze Bonifer
Software Mentions: 3
Published: about 5 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.0138030

msCentipede: Modeling Heterogeneity across Genomic Sites and Replicates Improves Accuracy in the Inference of Transcription Factor Binding
Cited by: 37
Author(s): Anil Raj, Heejung Shim, Yoav Gilad, Jonathan K. Pritchard, Matthew Stephens
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-016-2682-6

Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information
Cited by: 5
Author(s): Martin Nettling, Hendrik Treutler, Jesús Cerquides, Ivo Große
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0040399

Dynamic Changes in Ezh2 Gene Occupancy Underlie Its Involvement in Neural Stem Cell Self-Renewal and Differentiation towards Oligodendrocytes
Cited by: 56
Author(s): Falak Sher, Erik Boddeke, Marta Olah, Sjef Copray
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0039573

ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries
Cited by: 32
Author(s): Nishanth Ulhas Nair, Avinash Sahu, Philipp Bücher, Bernard M. E. Moret
Software Mentions: 2
Published: over 12 years ago

10.1016/j.molcel.2018.09.016

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci
Cited by: 123
Author(s): Adam Buckle, Chris A. Brackley, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-014-0412-0

Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
Cited by: 10
Author(s): Anagha Joshi
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0019470

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity
Cited by: 110
Author(s): Anja Nitzsche, Maciej Paszkowski‐Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, Ingrid de Vries, Li Ding, Norbert Huebner, Matthias Mann, Hendrik G. Stunnenberg, Frank Buchholz
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0026054

Next-Generation Sequencing of Apoptotic DNA Breakpoints Reveals Association with Actively Transcribed Genes and Gene Translocations
Cited by: 11
Author(s): Melissa J. Fullwood, Joanne Lee, Lei Lin, Guoliang Li, Mikael Huss, Patrick Ng, Wing-Kin Sung, Shirish Shenolikar
Software Mentions: 2
Published: about 13 years ago

10.1186/s13059-015-0740-z

Predicting chromatin organization using histone marks
Cited by: 100
Author(s): Jialiang Huang, Eugenio Marco, Luca Pinello, Guo Cheng Yuan
Software Mentions: 2
Published: over 9 years ago

10.1186/gb-2014-15-4-r65

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens
Cited by: 144
Author(s): Jian Feng, Matthew B. Wilkinson, Xiaochuan Liu, Immanuel Purushothaman, Deveroux Ferguson, Vincent Vialou, Ian Maze, Ning‐Yi Shao, Pamela J. Kennedy, Ja Wook Koo, Caroline Dias, Benjamin M. Laitman, Victoria Stockman, Quincey LaPlant, Michael E. Cahill, Eric J. Nestler, Li Shen
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0125156

Identifying TF-MiRNA Regulatory Relationships Using Multiple Features
Cited by: 3
Author(s): Mingyu Shao, Yanni Sun, Shuigeng Zhou
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-014-0576-y

Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems
Cited by: 132
Author(s): Colm E. Nestor, Raffaele Ottaviano, Diana Reinhardt, Hazel A Cruickshanks, Heidi K. Mjoseng, Rhoanne C. McPherson, Antonio Lentini, John P. Thomson, Donncha S. Dunican, Sari Pennings, Stephen M. Anderton, Mikael Benson, Richard R. Meehan
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-15-39

Integrated transcriptome analysis of mouse spermatogenesis
Cited by: 116
Author(s): Gennady Margolin, Pavel P. Khil, Joongbaek Kim, Marina A. Bellani, R. Daniel Camerini‐Otero
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13059-015-0756-4

De novo ChIP-seq analysis
Cited by: 8
Author(s): Xin He, A. Ercüment Çiçek, Yuhao Wang, Marcel H. Schulz, Hai-Son Le, Ziv Bar‐Joseph
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0141066

An Orthologous Epigenetic Gene Expression Signature Derived from Differentiating Embryonic Stem Cells Identifies Regulators of Cardiogenesis
Cited by: 5
Author(s): Brian W. Busser, Yongshun Lin, Yanqin Yang, Jun Zhu, Guokai Chen, Alan M. Michelson
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0061654

Genetic, Functional and Molecular Features of Glucocorticoid Receptor Binding
Cited by: 22
Author(s): Francesca Luca, Joseph C. Maranville, Allison L. Richards, David B. Witonsky, Matthew Stephens, Anna Di Rienzo
Software Mentions: 2
Published: over 11 years ago

10.1186/gb-2013-14-9-r106

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples
Cited by: 96
Author(s): Abel González-Pérez, Alba Jené-Sanz, Núria López‐Bigas
Software Mentions: 2
Published: almost 12 years ago

10.1186/2040-2392-4-3

MeCP2 modulates gene expression pathways in astrocytes
Cited by: 74
Author(s): Dag H. Yasui, Huichun Xu, Keith W. Dunaway, Janine M. LaSalle, Lee‐Way Jin, Izumi Maezawa
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2014-15-2-r23

Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts
Cited by: 46
Author(s): Helen Pemberton, Emma Anderton, Harshil Patel, Sharon Brookes, Hollie Chandler, Richard D. Palermo, Julie Stock, Marc Rodríguez‐Niedenführ, Tomáš Raček, Lucas de Breed, Aengus Stewart, Nik Matthews, Gordon Peters
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-015-2095-y

The epigenetic processes of meiosis in male mice are broadly affected by the widely used herbicide atrazine
Cited by: 48
Author(s): Aurore Gély-Pernot, Chunxiang Hao, E. Becker, Igor Stuparević, Christine Kervarrec, Frédéric Chalmel, Michael Primig, Bernard Jégou, Fátima Smagulova
Software Mentions: 2
Published: about 9 years ago

10.1186/gb-2013-14-8-r83

Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function
Cited by: 61
Author(s): Maxim Ivanov, Mart Kals, Marina Kacevska, Isabel Barragán, Kie Kasuga, Anders Rane, Andres Metspalu, Lili Milani, Magnus Ingelman‐Sundberg
Software Mentions: 2
Published: almost 12 years ago

10.1099/mgen.0.000081

The RegA regulon exhibits variability in response to altered growth conditions and differs markedly between Rhodobacter species
Cited by: 20
Author(s): Heidi S. Schindel, Carl E. Bauer
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0097849

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) Analysis Uncovers Broad Changes in Chromatin Structure Resulting from Hexavalent Chromium Exposure
Cited by: 9
Author(s): Jerald L. Ovesen, Yunxia Fan, Xiang Zhang, Jing Chen, Mario Medvedovic, Ying Xia, Alvaro Puga
Software Mentions: 2
Published: over 10 years ago

10.1186/gb-2013-14-1-r6

Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells
Cited by: 112
Author(s): Deborah A. Sanders, Caryn S. Ross-Innes, Dario Beraldi, Jason S. Carroll, Shankar Balasubramanian
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0045486

WaveSeq: A Novel Data-Driven Method of Detecting Histone Modification Enrichments Using Wavelets
Cited by: 10
Author(s): Apratim Mitra, Jiuzhou Song
Software Mentions: 2
Published: about 12 years ago

10.1186/gb-2013-14-1-r3

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion
Cited by: 53
Author(s): Henar Hernando, Claire Shannon-Lowe, Abul B.M.M.K. Islam, Fátima Al‐Shahrour, Javier Rodríguez-Ubreva, Virginia C. Rodríguez-Cortez, Biola M. Javierre, Cristina Mangas, Agustín F. Fernández, Maribel Parra, Henri Jacques Delecluse, Manel Esteller, Eduardo López‐Granados, Mario F. Fraga, Núria López‐Bigas, Esteban Ballestar
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-017-3640-7

The Krüppel-like factor 9 cistrome in mouse hippocampal neurons reveals predominant transcriptional repression via proximal promoter binding
Cited by: 31
Author(s): Joseph R. Knoedler, Arasakumar Subramani, Robert J. Denver
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-015-1258-1

Spatial features for Escherichia coli genome organization
Cited by: 19
Author(s): Ting Xie, Liang-Yu Fu, Qingyong Yang, Heng Xiong, H. Eric Xu, Bin-Guang Ma, Hongyu Zhang
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2012-13-9-r50

Functional analysis of transcription factor binding sites in human promoters
Cited by: 140
Author(s): Troy W. Whitfield, Jie Wang, Patrick J. Collins, E. Christopher Partridge, Shelley Force Aldred, Nathan D. Trinklein, R Myers, Zhiping Weng
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0054359

Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data
Cited by: 37
Author(s): Анна Герасимова, Lukas Chávez, Bin Li, Grégory Seumois, Jason A. Greenbaum, Anjana Rao, Pandurangan Vijayanand, Bjoern Peters
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13059-015-0819-6

P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis
Cited by: 57
Author(s): Chenghua Cui, Ying Gan, Lin Gu, James M. Wilson, Zhaojun Liu, Baozhen Zhang, Dajun Deng
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-016-1306-0

DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks
Cited by: 3
Author(s): Saulius Lukauskas, Roberto Visintainer, Guido Sanguinetti, Gabriele Schweikert
Software Mentions: 2
Published: almost 8 years ago

10.1186/gb-2008-9-9-r137

Model-based Analysis of ChIP-Seq (MACS)
Cited by: 12,473
Author(s): Yong Zhang, Tao Liu, Clifford A. Meyer, Jérôme Eeckhoute, D. S. Johnson, B Bernstein, Chad Nusbaum, R Myers, Myles Brown, Wei Li, X Shirley Liu
Software Mentions: 2
Published: about 16 years ago

10.1186/s12711-021-00631-4

A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations
Cited by: 7
Author(s): Zhongzi Wu, Haiming Gong, Mingpeng Zhang, Xinkai Tong, Huashui Ai, Shijun Xiao, Miguel Pérez‐Enciso, Bin Yang, Lusheng Huang
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0084182

Epigenetic Reprogramming in Mist1−/− Mice Predicts the Molecular Response to Cerulein-Induced Pancreatitis
Cited by: 12
Author(s): Rashid Mehmood, Gábor Varga, Sonali Q. Mohanty, Scott W. Laing, Yuefeng Lu, C. L. Johnson, Alexei Kharitonenkov, Christopher L. Pin
Software Mentions: 2
Published: almost 11 years ago

10.1186/gb-2011-12-1-r2

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
Cited by: 126
Author(s): Shaun Mahony, Esteban O. Mazzoni, Scott McCuine, Richard A. Young, Hynek Wichterle, David K. Gifford
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0028171

Dual Function of Histone H3 Lysine 36 Methyltransferase ASH1 in Regulation of Hox Gene Expression
Cited by: 43
Author(s): Yujiro Tanaka, Koji Kawahashi, Zen-ichiro Katagiri, Yasuhiro Nakayama, Milind Mahajan, Dimitris Kioussis
Software Mentions: 2
Published: almost 13 years ago

10.26508/lsa.201800117

CARM1 methylates MED12 to regulate its RNA-binding ability
Cited by: 39
Author(s): Donghang Cheng, Vidyasiri Vemulapalli, Yue Lu, Jianjun Shen, Sakae Aoyagi, Christopher J. Fry, Yanzhong Yang, Charles E. Foulds, Fabio Stossi, Lindsey S. Treviño, Michael A. Mancini, Bert W. O’Malley, Cheryl L. Walker, Thomas G. Boyer, Mark T. Bedford
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0165581

Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome
Cited by: 10
Author(s): Jason Lin, Kiriko Hiraoka, Tomohiro Watanabe, Tony Kuo, Yoshinao Shinozaki, Atsushi Takatori, Nobuko Koshikawa, Anandhakumar Chandran, Joe Otsuki, Hiroshi Sugiyama, Paul Horton, Hiroki Nagase
Software Mentions: 2
Published: about 8 years ago

10.3390/genes10100750

The H3K9 Methylation Writer SETDB1 and its Reader MPP8 Cooperate to Silence Satellite DNA Repeats in Mouse Embryonic Stem Cells
Cited by: 13
Author(s): Paola Cruz‐Tapias, Philippe Robin, Julien Pontis, Laurence Del Maestro, Slimane Ait‐Si‐Ali
Software Mentions: 2
Published: about 5 years ago

10.1093/g3journal/jkab101

Effects of sheared chromatin length on ChIP-seq quality and sensitivity
Cited by: 2
Author(s): Cheryl A. Keller, Alexander Q. Wixom, Elisabeth F. Heuston, Belinda Giardine, Chris C.-S. Hsiung, Maria Long, Amber Miller, Stacie M. Anderson, April Cockburn, Gerd A. Blobel, David M. Bodine, R Hardison
Software Mentions: 2
Published: over 3 years ago

10.3390/genes11111301

PURα Promotes the Transcriptional Activation of PCK2 in Oesophageal Squamous Cell Carcinoma Cells
Cited by: 6
Author(s): Yan Sun, Jiajia Gao, Zongpan Jing, Yan Zhao, Yulin Sun, Xiaohang Zhao
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2164-14-477

Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq
Cited by: 64
Author(s): Md. Shamimuzzaman, Lila O. Vodkin
Software Mentions: 2
Published: almost 12 years ago

10.1534/g3.115.023499

Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects
Cited by: 14
Author(s): Karl M. Glastad, Michael A. D. Goodisman, Soojin V. Yi, Brendan G. Hunt
Software Mentions: 2
Published: almost 9 years ago

10.1186/bcr3664

VAV3 mediates resistance to breast cancer endocrine therapy
Cited by: 27
Author(s): Helena Aguilar, Ander Urruticoechea, Pasi Halonen, Kazuma Kiyotani, Taisei Mushiroda, Xavier Barril, Jordi Serra-Musach, Abul B.M.M.K. Islam, Livia Caizzi, Luciano Di Croce, Ekaterina Nevedomskaya, Wilbert Zwart, Josefine Bostner, Elin Karlsson, Gizeh Pérez Tenorio, Tommy Fornander, Dennis Sgroi, Rafael Garcı́a-Mata, Maurice P.H.M. Jansen, Nadia García, Núria Bonifaci, Fina Climent, María Teresa Soler, Alejo Rodríguez‐Vida, Miguel Ángel Cobos Gil, Joan Brunet, Griselda Martrat, Laia Gómez-Baldó, Ana I. Extremera, Agnés Figueras, J. Balart, Robert Clarke, Kerry L. Burnstein, Kathryn E. Carlson, John A. Katzenellenbogen, Miguel Vizoso, Manel Esteller, Alberto Villanueva, Ana B. Rodríguez-Peña, Xosé R. Bustelo, Yusuke Nakamura, Hitoshi Zembutsu, Olle Stål, Roderick L. Beijersbergen, Miguel Ángel Pujana
Software Mentions: 2
Published: over 10 years ago

10.1534/g3.113.007229

Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing
Cited by: 67
Author(s): Justin T. Page, Mark D. Huynh, Zach S. Liechty, Kara Grupp, David M. Stelly, Amanda M. Hulse, Hamid Ashrafi, Allen Van Deynze, Jonathan F. Wendel, Joshua A. Udall
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0200004

Activation of Nrf2 in the liver is associated with stress resistance mediated by suppression of the growth hormone-regulated STAT5b transcription factor
Cited by: 36
Author(s): John P. Rooney, Keiyu Oshida, Naresh Vasani, Beena Vallanat, Natalia Ryan, Brian N. Chorley, Xuting Wang, Douglas A. Bell, Kai Wu, Lauren M. Aleksunes, Curtis D. Klaassen, Thomas W. Kensler, J. Christopher Corton
Software Mentions: 2
Published: over 6 years ago

10.1186/s13058-020-01306-6

Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer
Cited by: 6
Author(s): Laura A. Baker, Holly Holliday, Daniel Roden, Christoph Krisp, Sunny Z. Wu, Simon Junankar, Aurélien A. Sérandour, Hisham Mohammed, Radhika Nair, Geetha Sankaranarayanan, Andrew M. K. Law, Andrea McFarland, Peter T. Simpson, Sunil R. Lakhani, Eoin Dodson, Christina Selinger, Lyndal Anderson, Goli Samimi, Neville F. Hacker, Elgene Lim, Christopher J. Ormandy, Matthew J. Naylor, Kaylene J. Simpson, Iva Nikolić, Sandra A. O’Toole, Warren Kaplan, Mark J. Cowley, Jason S. Carroll, Mark P. Molloy, Alexander Swarbrick
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0031621

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
Cited by: 80
Author(s): Satish Sati, Vinay Singh Tanwar, Kalle Anand Kumar, Ashok Patowary, Vaibhav Jain, Sourav Ghosh, Shadab Ahmad, Meghna Singh, Sujatha Reddy, Giriraj Ratan Chandak, Manchala Raghunath, Sridhar Sivasubbu, Kausik Chakraborty, Vinod Scaria, Shantanu Sengupta
Software Mentions: 2
Published: almost 13 years ago

10.1038/s41416-019-0395-8

MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ breast cancer
Cited by: 28
Author(s): Michael J. G. Milevskiy, Udai Gujral, Carolina Marques, Andrew Stone, Korinne Northwood, Les J. Burke, Julia M. Gee, Kenneth P. Nephew, Susan J. Clark, Melissa A. Brown
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0117415

A Non-Parametric Peak Calling Algorithm for DamID-Seq
Cited by: 5
Author(s): Renhua Li, Leonie U. Hempel, Tingbo Jiang
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2021.687826

RNA N6-Methyladenosine Responds to Low-Temperature Stress in Tomato Anthers
Cited by: 17
Author(s): Dandan Yang, Huachao Xu, Yue Liu, Mengzhuo Li, Muhammad Ali, Xiangyang Xu, Gang Lü
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2017.00607

Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae
Cited by: 30
Author(s): Paweł Mikulski, Olga Komarynets, Fabio Fachinelli, Andreas P.M. Weber, Daniel Schubert
Software Mentions: 2
Published: over 7 years ago

10.1186/gb-2011-12-11-r113

Discovery of active enhancers through bidirectional expression of short transcripts
Cited by: 120
Author(s): Michael Melgar, Francis S. Collins, Praveen Sethupathy
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13059-015-0832-9

Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization
Cited by: 48
Author(s): Т. Н. Кузнецова, Shuang-Yin Wang, Nagesha A.S. Rao, Amit Mandoli, Joost H.A. Martens, Nils Rother, Aafke Aartse, Laszlo Groh, Eva M. Janssen-Megens, Guoliang Li, Yijun Ruan, Colin Logie, Hendrik G. Stunnenberg
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0023409

Systematic Clustering of Transcription Start Site Landscapes
Cited by: 58
Author(s): Xiaobei Zhao, Eivind Valen, Brian J. Parker, Albin Sandelin
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-15-231

An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation
Cited by: 12
Author(s): Mathieu Lajoie, Yu-Chih Hsu, Richard M. Gronostajski, Timothy L. Bailey
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0042761

A Novel Approach for Transcription Factor Analysis Using SELEX with High-Throughput Sequencing (TFAST)
Cited by: 14
Author(s): D. Reiss, Frederick M. Howard, Harry L. T. Mobley
Software Mentions: 2
Published: over 12 years ago

10.3389/fonc.2020.526866

IL-37 Confers Anti-Tumor Activity by Regulation of m6A Methylation
Cited by: 12
Author(s): Xiaofeng Mu, Qi Zhao, Wen Chen, Yuxiang Zhao, Qing Guo Yan, Rui Peng, Jie Zhu, Chunrui Yang, Ketao Lan, Xiaosong Gu, Ye Wang
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0085879

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis
Cited by: 92
Author(s): Fabrice David, Julien Delafontaine, Solenne Carat, Frederick J. Ross, Grégory Lefebvre, Yohan Jarosz, Lucas Sinclair, Daan Noordermeer, Jacques Rougemont, Marion Leleu
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-018-2516-4

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning
Cited by: 93
Author(s): Yiqian Zhang, Michiaki Hamada
Software Mentions: 2
Published: almost 6 years ago

10.3389/fnmol.2014.00087

Defining the nociceptor transcriptome
Cited by: 102
Author(s): Matthew Thakur, Megan Crow, Natalie Richards, Gareth I. J. Davey, Emma Levine, Jayne H. Kelleher, Chibeza C. Agley, Franziska Denk, Sdr Harridge, Stephen B. McMahon
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-6-74

Cited by: 7
Author(s): Aba-Sah Dadzie, Albert Burger
Software Mentions: 2
Published: almost 20 years ago

10.3389/fmicb.2021.667637

ChIP-seq Analysis of the Global Regulator Vfr Reveals Novel Insights Into the Biocontrol Agent Pseudomonas protegens FD6
Cited by: 2
Author(s): Qingxia Zhang, Chenglin Xing, Xiangwei Kong, Cheng Wang, Xijun Chen
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.591778

Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins
Cited by: 5
Author(s): Rishikesh Lotke, Ulrike Schneeweiß, Marcel Pietrek, Thomas Guenther, Adam Grundhoff, Magdalena Weidner-Glunde, Thomas F. Schulz
Software Mentions: 2
Published: about 4 years ago

10.3389/fnins.2017.00307

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex
Cited by: 23
Author(s): Akiko Sakai, Ryuichiro Nakato, Yiwei Ling, Xubin Hou, Norikazu Hara, Tomoya Iijima, Yuchio Yanagawa, Ryozo Kuwano, Shujiro Okuda, Katsuhiko Shirahige, Sayaka Sugiyama
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1007826

Downregulation of ERG and FLI1 expression in endothelial cells triggers endothelial-to-mesenchymal transition
Cited by: 50
Author(s): Naomi Nagai, Hiroto Ohguchi, Ryo Nakaki, Yoshihiro Matsumura, Yasuharu Kanki, Juro Sakai, Hiroyuki Aburatani, Takashi Minami
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1006650

SRC-2-mediated coactivation of anti-tumorigenic target genes suppresses MYC-induced liver cancer
Cited by: 15
Author(s): Shruthy Suresh, Deniz Durakoglugil, Xiaorong Zhou, Bokai Zhu, Sarah A. Comerford, Chao Xing, Xian Jin Xie, Brian York, Kathryn A. O’Donnell
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1005108

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters
Cited by: 87
Author(s): Nicholas J. Fuda, Michael J. Guertin, Sumeet K. Sharma, Charles G. Danko, André L. Martins, Adam Siepel, John T. Lis
Software Mentions: 2
Published: over 9 years ago

10.3389/fimmu.2017.01550

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination
Cited by: 24
Author(s): Louise S. Matheson, Daniel J. Bolland, Peter Chovanec, Felix Krueger, Simon Andrews, Hashem Koohy, Anne E. Corcoran
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1005992

Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression
Cited by: 47
Author(s): Yichi Xu, Weimin Guo, Ping Li, Yan Zhang, Meng Zhao, Zenghua Fan, Zhihu Zhao, Jun Yan
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1008764

UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize
Cited by: 27
Author(s): Yanfang Du, Lei Liu, Yong Peng, Manfei Li, Yunfu Li, Dan Liu, Xingwang Li, Zuxin Zhang
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-15-1022

Genome-wide mapping of matrix attachment regions in Drosophila melanogaster
Cited by: 27
Author(s): Rashmi U. Pathak, Arumugam Srinivasan, Rakesh K. Mishra
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pgen.1006754

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Cited by: 52
Author(s): Wareed Ahmed, Claudia Sala, Shubhada R. Hegde, Rajiv Kumar Jha, Stewart T. Cole, Valakunja Nagaraja
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04217-1

GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization
Cited by: 1
Author(s): Shiyang Zeng, Yuwei Hua, Yong Zhang, Guifen Liu, Chengchen Zhao
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00766

Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice
Cited by: 12
Author(s): Nannan Zhao, Kang Zhang, Chunchao Wang, Hengyu Yan, Yue Liu, Wenying Xu, Zhen Su
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btw336

Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control
Cited by: 12
Author(s): Pol Cuscó, Guillaume J. Filion
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2018.00425

Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci
Cited by: 24
Author(s): Salvatore Loguercio, E. Mauricio Barajas-Mora, Han-Yu Shih, Michael S. Krangel, Ann J. Feeney
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2016.02044

The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana
Cited by: 4
Author(s): Elena V. Zemlyanskaya, Victor G. Levitsky, Dmitry Oshchepkov, Ivo Große, В. В. Миронова
Software Mentions: 2
Published: almost 8 years ago

10.1093/bioinformatics/btab274

Resolving diverse protein–DNA footprints from exonuclease-based ChIP experiments
Cited by: 3
Author(s): Anushua Biswas, Leelavati Narlikar
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1002841

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression
Cited by: 279
Author(s): Claudia Kutter, Stephen Watt, Klara Stefflova, Michael D. Wilson, Ângela Gonçalves, Chris P. Ponting, Duncan T. Odom, Ana C. Marques
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-13-372

Cell-type specificity of ChIP-predicted transcription factor binding sites
Cited by: 16
Author(s): Tony Håndstad, Morten Rye, Rok Močnik, Finn Drabløs, Pål Sætrom
Software Mentions: 2
Published: over 12 years ago

10.3389/fcell.2021.651655

Histone Lysine Methyltransferase SETD2 Regulates Coronary Vascular Development in Embryonic Mouse Hearts
Cited by: 8
Author(s): Fengling Chen, Jiewen Chen, Hong Wang, Huayuan Tang, Lei Huang, Shijia Wang, Xinru Wang, Xi Fang, Jie Liu, Li Li, Kunfu Ouyang, Zhen Han
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1002972

Tethering of the Conserved piggyBac Transposase Fusion Protein CSB-PGBD3 to Chromosomal AP-1 Proteins Regulates Expression of Nearby Genes in Humans
Cited by: 30
Author(s): Lucas T. Gray, Kimberly K. Fong, Thomas Pavelitz, Alan M. Weiner
Software Mentions: 2
Published: about 12 years ago

Projects: pypi: MACS

Papers Mentioning MACS 1,233