Ecosyste.ms: Papers

10.1371/journal.pcbi.1007337

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets
Cited by: 15
Author(s): M. Vijayabaskar, Debbie K. Goode, Nadine Obier, Monika Lichtinger, Amber M.L. Emmett, Fatin N Zainul Abidin, Nisar Ahmed Shar, Rebecca Hannah, Salam A. Assi, Michael Lie-A-Ling, Berthold Göttgens, Georges Lacaud, Valérie Kouskoff, Constanze Bonifer, David R. Westhead
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-68879-2

Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins
Cited by: 2
Author(s): S. Yu. Funikov, Alexander P. Rezvykh, Д. А. Куликова, E. S. Zelentsova, Lyudmila A. Protsenko, Lyubov N. Chuvakova, Venera Tyukmaeva, Irina R. Arkhipova, Michael B. Evgen’ev
Software Mentions: 6
Published: almost 4 years ago

10.1186/gb-2013-14-11-r124

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation
Cited by: 27
Author(s): Sarah Aldridge, Stephen Watt, Michael A. Quail, Tim Rayner, Margus Lukk, Michael F Bimson, Daniel J. Gaffney, Duncan T. Odom
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pbio.3000241

Islands of retroelements are major components of Drosophila centromeres
Cited by: 117
Author(s): Ching-Ho Chang, Ankita Chavan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-ting Wu, Amanda M. Larracuente, Barbara G. Mellone
Software Mentions: 6
Published: about 5 years ago

10.15252/msb.20156520

Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children
Cited by: 93
Author(s): Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan‐Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M. Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanné, Stefan Wiemann, Christina Geörg, Hendrik G. Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann
Software Mentions: 6
Published: about 8 years ago

10.1111/gtc.12058

<scp>DROMPA</scp>: easy‐to‐handle peak calling and visualization software for the computational analysis and validation of ChIP‐seq data
Cited by: 62
Author(s): Ryuichiro Nakato, Takehiko Itoh, Katsuhiko Shirahige
Software Mentions: 6
Published: about 11 years ago

10.1111/acel.12890

Cell‐free DNA as a biomarker of aging
Cited by: 68
Author(s): Yee Voan Teo, Miriam Capri, Cristina Morsiani, G Pizza, Ana Maria Caetano Faria, Claudio Franceschi, Nicola Neretti
Software Mentions: 6
Published: over 5 years ago

10.1186/gb-2011-12-8-r83

Cistrome: an integrative platform for transcriptional regulation studies
Cited by: 583
Author(s): Tao Liu, Jorge Ortíz, Len Taing, Clifford A. Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Suei Nee Wong, Jian Ma, Ying Lei, Utz Johann Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu
Software Mentions: 6
Published: over 13 years ago

10.1371/journal.pgen.1008531

ELF5 modulates the estrogen receptor cistrome in breast cancer
Cited by: 16
Author(s): Catherine Piggin, Daniel Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha Oakes, David Gallego‐Ortega, Susan J. Clark, Jason S. Carroll, Nenad Bartoniček, Christopher J. Ormandy
Software Mentions: 6
Published: over 4 years ago

10.1002/1878-0261.12491

A 17 gene panel for non‐small‐cell lung cancer prognosis identified through integrative epigenomic‐transcriptomic analyses of hypoxia‐induced epithelial–mesenchymal transition
Cited by: 21
Author(s): Yue‐Lei Chen, Yihe Zhang, Junwen Wang, Na Chen, Weiying Fang, Jianing Zhong, Yi Liu, Rui Qin, Xinxin Yu, Zhen Sun, Fei Gao
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2105-15-280

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
Cited by: 49
Author(s): Huihuang Yan, Jared M. Evans, Mike Kalmbach, Raymond M. Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Liu, Zhifu Sun, Xianfeng Chen, Jean-Pierre A. Kocher
Software Mentions: 5
Published: almost 10 years ago

10.1534/g3.115.019166

Genome-Wide Analysis of<i>Drosophila</i>RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis
Cited by: 15
Author(s): Yiliang Wei, Shamba S. Mondal, Rima Mouawad, Bartek Wilczyński, R. William Henry, David N. Arnosti
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-15-1072

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column
Cited by: 18
Author(s): Satadal Chatterjee, V. Sivakamasundari, Sook Peng Yap, Petra Kraus, Vibhor Kumar, Xing Xing, Siew Lan Lim, Joel Sng, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 5
Published: over 9 years ago

10.1534/g3.116.028712

Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes
Cited by: 6
Author(s): Silvia N. Kariuki, John Blischak, Shigeki Nakagome, David B. Witonsky, Anna Di Rienzo
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0011471

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection
Cited by: 263
Author(s): Elizabeth G. Wilbanks, Marc T. Facciotti
Software Mentions: 5
Published: almost 14 years ago

10.18632/oncotarget.8192

Integrated analysis of long non-coding RNAs in human colorectal cancer
Cited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: about 8 years ago

10.18632/oncotarget.20405

Cancer cell line specific co-factors modulate the FOXM1 cistrome
Cited by: 8
Author(s): Yue Wang, Matthew Ung, Tian Xia, Wenqing Cheng, Chao Cheng
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2105-14-169

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data
Cited by: 21
Author(s): Yanchun Bao, Veronica Vinciotti, Ernst Wit, Peter A C ‘t Hoen
Software Mentions: 5
Published: almost 11 years ago

10.7554/eLife.07103

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
Cited by: 103
Author(s): Irene Gallego Romero, Bryan J. Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C. Ward, Nicholas E. Banovich, Courtney L Kagan, Jonathan E. Burnett, Constance H Huang, Amy Mitrano, Claudia Chavarria, Inbar Friedrich Ben-Nun, Yingchun Li, Karen Sabatini, Trevor R. Leonardo, Mana M. Parast, Tomàs Marquès‐Bonet, Louise C. Laurent, Jeanne F. Loring, Yoav Gilad
Software Mentions: 5
Published: almost 9 years ago

10.7554/eLife.30862

Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation
Cited by: 54
Author(s): Angela Halstead, Chiraag D Kapadia, Jennifer K. Bolzenius, Clarence E Chu, Andrew E. Schriefer, Lukas D. Wartman, Gregory R. Bowman, Vivek Arora
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-016-1248-6

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
Cited by: 11
Author(s): Lydia Müller, Daniel Gerighausen, Mariam R. Farman, Dirk Zeckzer
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.02024

MOF-associated complexes ensure stem cell identity and Xist repression
Cited by: 73
Author(s): Tomasz Chelmicki, Friederike Dündar, Matthew James Turley, Tasneem Khanam, Tuğçe Aktaş, Fidel Ramírez, Anne-Valérie Gendrel, Patrick R. Wright, Pavankumar Videm, Rolf Backofen, Edith Heard, Thomas Manke, Asifa Akhtar
Software Mentions: 5
Published: about 10 years ago

10.18699/VJ21.002

Application of alternative &lt;i&gt;de novo&lt;/i&gt; motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites
Cited by: 3
Author(s): Anton Vitalievich Tsukanov, Victor G. Levitsky, Т. И. Меркулова
Software Mentions: 5
Published: about 3 years ago

10.1534/g3.119.400986

Adaptation to Industrial Stressors Through Genomic and Transcriptional Plasticity in a Bioethanol Producing Fission Yeast Isolate
Cited by: 1
Author(s): Dane Vassiliadis, Koon Ho Wong, Jo Anne Blinco, Geoff Dumsday, Alex Andrianopoulos, Brendon J. Monahan
Software Mentions: 5
Published: about 4 years ago

10.15252/msb.156172

Comprehensive assembly of novel transcripts from unmapped human RNA‐Seq data and their association with cancer
Cited by: 17
Author(s): Majid Kazemian, Min Ren, Jian-Xin Lin, Wei Liao, Rosanne Spolski, Warren J. Leonard
Software Mentions: 5
Published: almost 9 years ago

10.7554/eLife.63093

MITF reprograms the extracellular matrix and focal adhesion in melanoma
Cited by: 42
Author(s): Ramile Dilshat, Valerie Fock, Colin Kenny, Ilse Gerritsen, Romain Lasseur, Jana Trávníčková, Ossia M. Eichhoff, Philipp Cerny, Katrín Möller, Sara Sigurbjörnsdóttir, Kritika Kirty, Berglind O. Einarsdottir, Phil F. Cheng, Mitchell P. Levesque, Robert A. Cornell, E. Elizabeth Patton, Lionel Larue, Marie de Tayrac, Erna Magnúsdóttir, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms19020593

Luminal lncRNAs Regulation by ERα-Controlled Enhancers in a Ligand-Independent Manner in Breast Cancer Cells
Cited by: 13
Author(s): Valentina Miano, Giulio Ferrero, Valentina Rosti, Eleonora Manitta, Jamal Elhasnaoui, Giulia Basile, Michele De Bortoli
Software Mentions: 5
Published: over 6 years ago

10.15252/emmm.202012105

Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease
Cited by: 23
Author(s): Rafael Alcalá-Vida, Marta Garcia‐Forn, Carla Castany‐Pladevall, Jordi Creus-Muncunill, Yoko Itō, Enrique Blanco, Arantxa Golbano, Kilian Crespí-Vázquez, Aled Parry, Guy Slater, Shamith A. Samarajiwa, Sandra Peiró, Luciano Di Croce, Masashi Narita, Esther Pérez‐Navarro
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-016-0902-3

NEAT: a framework for building fully automated NGS pipelines and analyses
Cited by: 7
Author(s): Patrick Schorderet
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.51373

PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells
Cited by: 18
Author(s): Payal Jain, Cecilia Ballaré, Enrique Blanco, Pedro Vizán, Luciano Di Croce
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cited by: 36
Author(s): Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xinwei Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd C. Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.25125

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression
Cited by: 111
Author(s): Daniel Andergassen, Christoph P. Dotter, D. Wenzel, Verena Sigl, Philipp C. Bammer, Markus Muckenhuber, Daniela Mayer, Tomasz M. Kuliński, Hans-Christian Theussl, Josef Penninger, Christoph Bock, Denise P. Barlow, Florian M. Pauler, Quanah J. Hudson
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.00675

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis
Cited by: 344
Author(s): Katherine Noelani Chang, Shan Zhong, Matthew T. Weirauch, Gary C. Hon, Mattia Pelizzola, Hai Li, S. Huang, Robert J. Schmitz, Mark A. Urich, Dwight Kuo, Joseph R. Nery, Hong Qiao, Ally Yang, Abdullah Jamali, Huaming Chen, Trey Ideker, Bing Ren, Ziv Bar‐Joseph, Timothy R. Hughes, Joseph R. Ecker
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12864-016-3135-y

A comparative study of ChIP-seq sequencing library preparation methods
Cited by: 21
Author(s): Arvind Sundaram, Timothy R. Hughes, Shea Biondi, Nathalie Bolduc, Sarah K. Bowman, Andrew Camilli, Yap Ching Chew, Catherine Couture, Andrew Farmer, John P. Jerome, David W. Lazinski, Andrew McUsic, Peng Xu, Kamran Shazand, Feng Xu, Robert Lyle, Gregor D. Gilfillan
Software Mentions: 5
Published: over 7 years ago

10.1038/onc.2016.382

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer
Cited by: 125
Author(s): Alison Harrod, Janet S. Fulton, Van Nguyen, Manikandan Periyasamy, L Ramos-Garcia, C-F Lai, Gergana Metodieva, Alex de Giorgio, Richard Williams, Delfran Batista dos Santos, Pablo Gómez, M-L Lin, Metodi V. Metodiev, Justin Stebbing, Leandro Castellano, Luca Magnani, R. Charles Coombes, Laki Buluwela, Simak Ali
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pgen.1005698

Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans
Cited by: 43
Author(s): Maxwell Kramer, Anna Lena Kranz, Amanda Su, Lara Winterkorn, Sarah Elizabeth Albritton, Sevinç Ercan
Software Mentions: 5
Published: over 8 years ago

10.1128/mBio.01457-20

Kaposi’s Sarcoma-Associated Herpesvirus Drives a Super-Enhancer-Mediated Survival Gene Expression Program in Primary Effusion Lymphoma
Cited by: 13
Author(s): Mark Manzano, Thomas Guenther, Honglyoul Ju, John Nicholas, Elizabeth T. Bartom, Adam Grundhoff, Eva Gottwein
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.03549

Zinc finger protein Zfp335 is required for the formation of the naïve T cell compartment
Cited by: 21
Author(s): Brenda Y. Han, Shuang Wu, Chuan-Sheng Foo, Robert M. Horton, Craig N. Jenne, Susan R. Watson, Belinda Whittle, Christopher C. Goodnow, Jason G. Cyster
Software Mentions: 5
Published: over 9 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-021-01799-7

Genomic insights into the host specific adaptation of the Pneumocystis genus
Cited by: 16
Author(s): Ousmane Cissé, Liang Ma, John P. Dekker, Pavel P. Khil, Jung Ho Youn, Jason M. Brenchley, Robert V Blair, Bapi Pahar, Magali Chabé, Koen K. A. Van Rompay, Rebekah I. Keesler, Antti Sukura, Vanessa M. Hirsch, Geetha Kutty, Yueqin Liu, Peng Li, Jie Chen, Jun Song, Christiane Weissenbacher‐Lang, Jie Xu, Nathan S. Upham, Jason E. Stajich, Christina A. Cuomo, Melanie T. Cushion, Joseph A. Kovacs
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-021-93297-3

Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs
Cited by: 7
Author(s): Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Software Mentions: 5
Published: almost 3 years ago

10.26508/lsa.202000709

Myeloid transformation by <i>MLL</i>-<i>ENL</i> depends strictly on C/EBP
Cited by: 4
Author(s): Radosław Wesołowski, Elisabeth Kowenz‐Leutz, Karin Zimmermann, Dorothea Dörr, Maria Hofstätter, Robert K. Slany, Alexander Mildner, Achim Leutz
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-021-01716-y

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Cited by: 28
Author(s): Jianbo Yuan, Xiaojun Zhang, Min Wang, Yamin Sun, Xianhui Qin, Shihao Li, Yang Yu, Yi Gao, Fei Liu, Jie Kong, Guangyi Fan, Chengsong Zhang, Lu Feng, Jianhai Xiang, Fuhua Li
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-019-40867-1

Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development
Cited by: 17
Author(s): Naomi D. Chrispijn, Dei M. Elurbe, Michaela Mickoleit, Marco Aben, Dennis E. M. de Bakker, Karolina M. Andralojc, Jan Huisken, Jeroen Bakkers, Leonie M. Kamminga
Software Mentions: 5
Published: about 5 years ago

10.1016/j.ccell.2020.03.001

Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation
Cited by: 84
Author(s): Zeda Zhang, Chuanli Zhou, Xiaoling Li, Spencer Barnes, Su Deng, Elizabeth Hoover, Chi Chao Chen, Young Sun Lee, Yanxiao Zhang, Choushi Wang, Lauren Metang, Chao Wu, Carla Rodriguez Tirado, Nickolas A. Johnson, John Wongvipat, Kristina Navrazhina, Zhen Cao, Danielle Choi, Chen‐Hung Huang, Eliot Linton, Xiaoping Chen, Yupu Liang, Christopher E. Mason, Elisa de Stanchina, Wassim Abida, Amaia Lujambio, Sheng Li, Scott W. Lowe, Joshua T. Mendell, Venkat S. Malladi, Charles L. Sawyers, Ping Mu
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pgen.1005693

Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome
Cited by: 24
Author(s): Luke Isbel, Richa Srivastava, Harald Oey, Alex Spurling, Lucia Daxinger, Hamsa Puthalakath, Emma Whitelaw
Software Mentions: 5
Published: over 8 years ago

10.1016/j.csbj.2020.06.010

Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics
Cited by: 33
Author(s): Lian Liu, Bowen Song, Jiani Ma, Yi Song, Song-Yao Zhang, Yujiao Tang, Xiangyu Wu, Zhen Wei, Kunqi Chen, Jionglong Su, Rong Rong, Zhi-Liang Lu, João Pedro de Magalhães, Daniel J. Rigden, Lin Zhang, Shaowu Zhang, Yufei Huang, Xiujuan Lei, Hui Liu, Jia Meng
Software Mentions: 5
Published: over 4 years ago

10.1016/j.stem.2017.10.013

Constitutively Active SMAD2/3 Are Broad-Scope Potentiators of Transcription-Factor-Mediated Cellular Reprogramming
Cited by: 34
Author(s): Tyson Joel Ruetz, Ulrich Pfisterer, Bruno Di Stefano, James Ashmore, Meryam Beniazza, Tian V. Tian, Daniel F. Kaemena, Luca Tosti, Wenfang Tan, Jonathan Manning, Eleni Chantzoura, Daniella Rylander Ottosson, Samuel Collombet, Anna Johnsson, Erez Cohen, Kosuke Yusa, Sten Linnarsson, Thomas Graf, Malin Parmar, Keisuke Kaji
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-017-14942-4

Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression
Cited by: 6
Author(s): Yusuke Morita, Mikiko Ohno, Kiyoto Nishi, Yutaka Hiraoka, Sayaka Saijo, Shintaro Matsuda, Toru Kita, Takeshi Kimura, Eiichiro Nishi
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.23645

Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation
Cited by: 27
Author(s): Sarah Elizabeth Albritton, Anna Lena Kranz, Lara Winterkorn, Lena Annika Street, Sevinç Ercan
Software Mentions: 5
Published: almost 7 years ago

10.1016/j.cmet.2021.01.004

Polycystic ovary syndrome is transmitted via a transgenerational epigenetic process
Cited by: 100
Author(s): Nour El Houda Mimouni, Isabel Paiva, Anne‐Laure Barbotin, Fatima Ezzahra Timzoura, Damien Plassard, Stéphanie Le Gras, Gaëtan Ternier, Pascal Pigny, Sophie Catteau-Jonard, Virginie Simon, Vincent Prévot, Anne‐Laurence Boutillier, Paolo Giacobini
Software Mentions: 5
Published: about 3 years ago

10.1155/2020/3817573

Diet Modifies Pioglitazone’s Influence on Hepatic PPAR<i>γ</i>-Regulated Mitochondrial Gene Expression
Cited by: 5
Author(s): Sakil Kulkarni, Jiansheng Huang, Eric Tycksen, Paul Cliften, David A. Rudnick
Software Mentions: 5
Published: over 3 years ago

10.1038/srep25668

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
Cited by: 76
Author(s): Konrad J. Dębski, Asla Pitkänen, Noora Puhakka, Anna Bot, Ishant Khurana, K N Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El‐Osta, Katarzyna Łukasiuk, Katja Kobow
Software Mentions: 5
Published: about 8 years ago

10.1083/jcb.201711097

Control of mitotic chromosome condensation by the fission yeast transcription factor Zas1
Cited by: 3
Author(s): Christoph Schiklenk, Boryana Petrova, Marc Kschonsak, Markus Hassler, Carlo Klein, Toby J. Gibson, Christian H. Haering
Software Mentions: 5
Published: about 6 years ago

10.1002/hep4.1749

Meta‐analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions
Cited by: 4
Author(s): Emilian Jungwirth, Katrin Panzitt, Hanns‐Ulrich Marschall, Gerhard Thallinger, Martin Wagner
Software Mentions: 5
Published: almost 3 years ago

10.1186/s12859-019-3100-2

RACS: rapid analysis of ChIP-Seq data for contig based genomes
Cited by: 4
Author(s): Marcelo Ponce, Alejandro Saettone, Syed Nabeel‐Shah, Jeffrey Fillingham
Software Mentions: 5
Published: over 4 years ago

10.1038/s41438-021-00529-8

Chromatin accessibility and translational landscapes of tea plants under chilling stress
Cited by: 21
Author(s): Pengjie Wang, Shan Jin, Xuejin Chen, Lihua Wu, Yuanrun Zheng, Chuan Yue, Yan Guo, Xingtan Zhang, Jing Yang, Naixing Ye
Software Mentions: 5
Published: about 3 years ago

10.1038/sdata.2016.4

DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing
Cited by: 10
Author(s): Anneleen Decock, Maté Ongenaert, Wim Van Criekinge, Franki Speleman, Jo Vandesompele
Software Mentions: 5
Published: over 8 years ago

10.1038/srep29647

Tracking Cancer Genetic Evolution using OncoTrack
Cited by: 4
Author(s): Asoke K. Talukder, Mahima Agarwal, Kenneth H. Buetow, Patrice Denèfle
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pcbi.1002638

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
Cited by: 255
Author(s): Yuchun Guo, Shaun Mahony, David K. Gifford
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pcbi.1004751

metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns
Cited by: 11
Author(s): Charles Joly Beauparlant, Fabien C. Lamaze, Astrid Deschênes, Rawane Samb, Audrey Lemaçon, Pascal Belleau, Steve Bilodeau, Arnaud Droit
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13073-020-00760-3

ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer
Cited by: 32
Author(s): Aileen P. Szczepanski, Zibo Zhao, Victoria Sosnowski, Young Ah Goo, Elizabeth T. Bartom, Lu Wang
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41419-021-03739-z

WNT/β-catenin-suppressed FTO expression increases m6A of c-Myc mRNA to promote tumor cell glycolysis and tumorigenesis
Cited by: 61
Author(s): Xueying Yang, Fei Shao, Dong Guo, Wei Wang, Juhong Wang, Rongxuan Zhu, Yibo Gao, Jie He, Zhimin Lu
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pcbi.1002887

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Cited by: 46
Author(s): S. Huang, David Clarke, Sara J.C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
Software Mentions: 5
Published: over 11 years ago

10.1186/s12864-017-3673-y

Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Cited by: 95
Author(s): Jenna Kropp Schmidt, José A. Carrillo, Hadjer Namous, Daniels Alyssa, Sana M. Salih, Jiuzhou Song, Hasan Khatib
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-021-02376-1

A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks
Cited by: 15
Author(s): Chongze Yuan, Haojie Chen, Shiqi Tu, Hsin Yi Huang, Yunjian Pan, Xiuqi Gui, Muyu Kuang, Xuxia Shen, Qiang Zheng, Yang Zhang, Chao Cheng, Hui Hong, Xiaoting Tao, Yizhou Peng, Xingxin Yao, Fei-Long Meng, Hongbin Ji, Zongshu Shao, Yihua Sun
Software Mentions: 5
Published: about 3 years ago

10.1186/s13073-021-00863-5

Microglial PGC-1α protects against ischemic brain injury by suppressing neuroinflammation
Cited by: 69
Author(s): Bin Han, Wei Jiang, Pan Cui, Kai Zheng, Chun Dang, Junjie Wang, He Li, Lin Chen, Rongxin Zhang, Qing Mei Wang, Zhenyu Ju, Junwei Hao
Software Mentions: 5
Published: about 3 years ago

10.1186/s13059-018-1489-y

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells
Cited by: 25
Author(s): Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jérémy Denizot, Raquel Manzano García, Steven Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip T. Hawkins, Len R. Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E. Corcoran, Patrick Varga‐Weisz
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0083506

Widespread Misinterpretable ChIP-seq Bias in Yeast
Cited by: 128
Author(s): Daechan Park, Yaelim Lee, Gurvani Bhupindersingh, Vishwanath R. Iyer
Software Mentions: 5
Published: over 10 years ago

10.1186/s12864-016-3288-8

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
Cited by: 24
Author(s): Giovanna Ambrosini, René Dreos, Sunil Kumar, Philipp Bücher
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-016-0991-z

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains
Cited by: 29
Author(s): Joshua Starmer, Terry Magnuson
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pgen.1006587

Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease
Cited by: 38
Author(s): Katrina Soderquest, Arnulf Hertweck, Claudia Giambartolomei, Stephen Henderson, Mohamed Rosmawati, Rimma Goldberg, Esperanza Perucha, Lude Franke, Javier Herrero, Vincent Plagnol, Richard G. Jenner, Graham M. Lord
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-015-0597-1

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis
Cited by: 127
Author(s): Julieta L. Mateos, Pedro Madrigal, Kazuhiko Tsuda, Vimal Rawat, René Richter, Maida Romera-Branchat, Fabio Fornara, Korbinian Schneeberger, Paweł Krajewski, George Coupland
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pbio.2006347

Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation
Cited by: 33
Author(s): Mingming Zhao, Jaimy Joy, Weiqiang Zhou, Supriyo De, William H. Wood, Kevin G. Becker, Hongkai Ji, Ranjan Sen
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-014-0494-z

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach
Cited by: 31
Author(s): Daniel Wong, Wanseon Lee, Peter Humburg, Seiko Makino, Evelyn Lau, Vivek Naranbhai, Benjamin P. Fairfax, Kenneth Chan, Katharine Plant, Julian C. Knight
Software Mentions: 5
Published: over 9 years ago

10.1186/s13059-015-0840-9

A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63
Cited by: 126
Author(s): Xiaomin Bao, Adam J. Rubin, Kun Qu, Jiajing Zhang, Paul G. Giresi, Howard Y. Chang, Paul A. Khavari
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0226435

The acute myeloid leukemia associated AML1-ETO fusion protein alters the transcriptome and cellular progression in a single-oncogene expressing in vitro induced pluripotent stem cell based granulocyte differentiation model
Cited by: 15
Author(s): Esther Tijchon, Guoqiang Yi, Amit Mandoli, Jos G. A. Smits, Francesco Ferrari, Branco M. H. Heuts, Falco Wijnen, Bowon Kim, Eva M. Janssen-Megens, Jan Jacob Schuringa, Joost H.A. Martens
Software Mentions: 5
Published: over 4 years ago

10.1186/gb-2012-13-10-r95

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers
Cited by: 60
Author(s): Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H. Schulte, Rosa Noguera, Raymond Stallings, An Van Damme, Geneviève Laureys, Joëlle Vermeulen, Tom Van Maerken, Frank Speleman, Jo Vandesompele
Software Mentions: 5
Published: over 12 years ago

10.1186/gb-2013-14-10-r112

Genome-wide analysis of condensin binding in Caenorhabditis elegans
Cited by: 74
Author(s): Anna-Lena Kranz, Chenyu Jiao, Lara Winterkorn, Sarah Elizabeth Albritton, Maxwell Kramer, Sevinç Ercan
Software Mentions: 5
Published: over 11 years ago

10.1016/j.cell.2016.09.006

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Cited by: 349
Author(s): Angelo Amabile, Alessandro Migliara, Paola Capasso, Mauro Biffi, Davide Cittaro, Luigi Naldini, Angelo Lombardo
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0225180

Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation
Cited by: 10
Author(s): Aisling M. Redmond, Soleilmane Omarjee, Igor Chernukhin, Muriel Le Romancer, Jason S. Carroll
Software Mentions: 5
Published: over 4 years ago

10.1186/gb-2014-15-3-r41

Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
Cited by: 205
Author(s): Alice Pajoro, Pedro Madrigal, Jose M. Muiño, José Tomás Matus, Jiaxin Jin, Martín A. Mecchia, Juan M. Debernardi, Javier F. Palatnik, Salma Balazadeh, Muhammad Arif, Diarmuid S. Ó’Maoiléidigh, Frank Wellmer, Paweł Krajewski, José Luis Riechmann, Gerco C. Angenent, Kerstin Kaufmann
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0098404

Deep Sequencing Reveals New Aspects of Progesterone Receptor Signaling in Breast Cancer Cells
Cited by: 12
Author(s): Anastasia Kougioumtzi, Panayiotis Tsaparas, Angeliki Magklara
Software Mentions: 4
Published: almost 10 years ago

10.1186/1471-2105-8-62

Blast sampling for structural and functional analyses
Cited by: 9
Author(s): Anne Friedrich, Raymond Ripp, Nicolas Garnier, Emmanuel Bettler, Gilbert Deléage, Olivier Poch, Luc Moulinier
Software Mentions: 4
Published: about 17 years ago

10.1371/journal.pone.0029021

Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells
Cited by: 72
Author(s): Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antònia Navarro, Diana Monsivais, John S. Coon, Julie Kim, Yang Dai, Serdar E. Bulun
Software Mentions: 4
Published: over 12 years ago

10.3389/fpls.2021.715820

Genome-Wide Identification of the ARF Gene Family and ARF3 Target Genes Regulating Ovary Initiation in Hazel via ChIP Sequencing
Cited by: 8
Author(s): Wei Heng, Yufei Cheng, Ying Sun, Xingzheng Zhang, Hailong He, Jianfeng Liu
Software Mentions: 4
Published: almost 3 years ago

10.3389/fnins.2021.605654

Alteration of N6 -Methyladenosine mRNA Methylation in a Rat Model of Cerebral Ischemia–Reperfusion Injury
Cited by: 34
Author(s): Dazhuang Yi, Qunhui Wang, Yuhao Zhao, Shuhui Yu, Hong You, Jian Wang, Renjie Liu, Shi Zhong-qiang, Xuan Chen, Qi Luo
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-015-0460-0

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
Cited by: 20
Author(s): Wuming Gong, Naoko Koyano-Nakagawa, Tongbin Li, Daniel J. Garry
Software Mentions: 4
Published: about 9 years ago

10.3390/plants10071405

Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil
Cited by: 4
Author(s): Oussama Badad, Naoufal Lakhssassi, Nabil Zaïd, Abdelhalim El Baze, Younes Zaid, Jonas Meksem, David A. Lightfoot, Hüseyin Tombuloğlu, El Houcine Zaid, Turgay Ünver, Khalid Meksem
Software Mentions: 4
Published: almost 3 years ago

10.3389/fonc.2020.556497

Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
Cited by: 19
Author(s): Xing Niu, Jun Xu, Jinwen Liu, Lijie Chen, Xue Qin, Ming Zhong
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-12-139

PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Cited by: 146
Author(s): Xin Feng, Robert L. Grossman, Lincoln Stein
Software Mentions: 4
Published: about 13 years ago

10.3389/fgene.2015.00331

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
Cited by: 12
Author(s): Marina Lizio, Yuri Ishizu, Masayoshi Itoh, Timo Lassmann, Akira Hasegawa, Atsutaka Kubosaki, Jessica Severin, Hideya Kawaji, Yukio Nakamura, Harukazu Suzuki, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest
Software Mentions: 4
Published: over 8 years ago

10.3389/fgene.2014.00329

A comparison of control samples for ChIP-seq of histone modifications
Cited by: 24
Author(s): Christoffer Flensburg, Sarah Kinkel, Andrew Keniry, Marnie E. Blewitt, Alicia Oshlack
Software Mentions: 4
Published: over 9 years ago

10.3389/fcell.2021.615950

The Novel Non-coding Transcriptional Regulator Gm18840 Drives Cardiomyocyte Apoptosis in Myocardial Infarction Post Ischemia/Reperfusion
Cited by: 1
Author(s): Changjun Luo, Si Xiong, Yiteng Huang, Ming Deng, Jing Zhang, Jianlin Chen, Rongfeng Yang, Xiaoyan Ke
Software Mentions: 4
Published: almost 3 years ago

10.1186/1471-2164-14-S8-S3

QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions
Cited by: 28
Author(s): Bin Liu, Jimmy Yi, Aishwarya Sv, Xun Lan, Yiyi Ma, Tim H.M. Huang, Gustavo Leone, Victor X. Jin
Software Mentions: 4
Published: over 10 years ago

10.3389/fgene.2019.00306

Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress
Cited by: 13
Author(s): Hengyu Yan, Yue Liu, Kang Zhang, Jakyoung Song, Wenying Xu, Zhen Su
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0239367

Mining a human transcriptome database for chemical modulators of NRF2
Cited by: 18
Author(s): John P. Rooney, Brian N. Chorley, Steven Hiemstra, Steven Wink, Xuting Wang, Douglas A. Bell, Bob van de Water, J. Christopher Corton
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0186435

Identification of cis-regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response
Cited by: 14
Author(s): Bernardo Pérez-Zamorano, Sandra Rosas‐Madrigal, Oscar Arturo Migueles Lozano, Manuel Castillo Méndez, Verónica Valverde-Garduño
Software Mentions: 4
Published: over 6 years ago

10.3390/epigenomes3020011

Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors
Cited by: 11
Author(s): Diana L. Gerrard, Joseph R. Boyd, Gary S. Stein, Victor X. Jin, Seth Frietze
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-15-539

ChIPseek, a web-based analysis tool for ChIP data
Cited by: 59
Author(s): Ting-Wen Chen, Hsin Pai Li, Chi-Ching Lee, Ruei Chi Gan, Po-Jung Huang, Timothy Wu, Cheng Yang Lee, Ian Yi‐Feng Chang, Petrus Tang
Software Mentions: 4
Published: almost 10 years ago