pypi: MACS2 | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0236666

Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq
Cited by: 1
Author(s): Yong Chen, Yunfei Wang, Xin Liu, Jian Xu, Michael Q. Zhang
Software Mentions: 2
Published: over 4 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

10.3389/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/fimmu.2017.01038

Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response
Cited by: 44
Author(s): Benoı̂t Roux, James A. Heward, Louise E. Donnelly, Simon W. Jones, Mark A. Lindsay
Software Mentions: 2
Published: about 7 years ago

10.3389/fimmu.2017.00383

Genome-Wide Identification of Target Genes for the Key B Cell Transcription Factor Ets1
Cited by: 15
Author(s): Prontip Saelee, Alyssa Kearly, Stephen L. Nutt, Lee Ann Garrett‐Sinha
Software Mentions: 2
Published: over 7 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

10.1371/journal.pone.0176190

Pax7 remodels the chromatin landscape in skeletal muscle stem cells
Cited by: 35
Author(s): Karin Lilja, Nan Zhang, Alessandro Magli, Volkan Gündüz, Christopher J. Bowman, Robert W. Arpke, Radbod Darabi, Michael Kyba, Rita Perlingeiro, Brian David Dynlacht
Software Mentions: 2
Published: over 7 years ago

10.3389/fnmol.2021.651355

Single-Nucleus Chromatin Accessibility Landscape Reveals Diversity in Regulatory Regions Across Distinct Adult Rat Cortex
Cited by: 7
Author(s): Yeya Yu, Xiaoyü Wei, Qiuting Deng, Qing Lan, Yiping Guo, Lei Han, Yue Yuan, Peng Fan, Peng Wu, Shuncheng Shangguan, Yang Liu, Yiwei Lai, Giacomo Volpe, Miguel A. Esteban, Chuanyu Liu, Yong Hou, Longqi Liu
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-019-2646-3

A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin loops
Cited by: 12
Author(s): Jayoung Ryu, Hyunwoong Kim, Dongchan Yang, Andrew Lee, Inkyung Jung
Software Mentions: 2
Published: over 5 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

10.1534/g3.116.035402

Alternative Oxidase Transcription Factors AOD2 and AOD5 ofNeurospora crassaControl the Expression of Genes Involved in Energy Production and Metabolism
Cited by: 6
Author(s): Zhigang Qi, Kristina M. Smith, Erin L. Bredeweg, Natasa Bosnjak, Michael Freitag, Frank E. Nargang
Software Mentions: 2
Published: almost 8 years ago

10.1534/g3.117.039586

The Saccharomyces cerevisiae Cdk8 Mediator Represses AQY1 Transcription by Inhibiting Set1p-Dependent Histone Methylation
Cited by: 5
Author(s): Michael J. Law, Michael A Finger
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.117.040907

Retrotransposons Are the Major Contributors to the Expansion of theDrosophila ananassaeMuller F Element
Cited by: 22
Author(s): Wilson Leung, C. Shaffer, Elizabeth J Chen, Thomas J Quisenberry, Kevin Ko, John M. Braverman, Thomas C. Giarla, Nathan T. Mortimer, Laura K. Reed, Sheryl T. Smith, Srebrenka Robic, Shannon R. McCartha, Danielle R Perry, Lindsay M Prescod, Zenyth A Sheppard, Ken Saville, Allison E. McClish, Emily A Morlock, Victoria R Sochor, Brittney Stanton, Isaac C Veysey-White, Dennis Revie, Luis A. Jiménez, Jennifer J Palomino, Melissa D. Patao, Shane M. Patao, Edward Himelblau, Jaclyn D Campbell, Alexandra L Hertz, Maddison F McEvilly, Allison R Wagner, James Youngblom, Baljit Bedi, Jeffery Bettincourt, Erin Duso, Maiye Her, William A. Hilton, Samantha House, Masud Karimi, Kevin Kumimoto, Rebekah Lee, Darryl Lopez, George Odisho, Ricky Prasad, Holly Lyn Robbins, Tanveer Sandhu, Tracy Selfridge, Kara Tsukashima, Hani Yosif, Nighat P. Kokan, Latia Britt, Alycia Zoellner, Eric P. Spana, Ben Chlebina, Insun Chong, Harrison Friedman, Danny Mammo, Chun L. Ng, Vinayak Nikam, Nicholas U. Schwartz, Thomas Q. Xu, Martin G. Burg, Spencer M Batten, Lindsay M Corbeill, Erica Enoch, Jesse J Ensign, Mary E Franks, Breanna Haiker, Judith Ingles, Lyndsay D Kirkland, Joshua M. Lorenz-Guertin, Jordan E. Matthews, Cody M Mittig, Nicholaus Monsma, Katherine J Olson, Guillermo Perez-Aragon, Alen Ramic, Jordan R Ramirez, Christopher Scheiber, P A Schneider, Devon E Schultz, Matthew Simon, Eric Spencer, Adam C Wernette, Maxine E Wykle, Elizabeth Zavala-Arellano, Mitchell McDonald, Kristine Ostby, Peter Wendland, Justin R. DiAngelo, Alexis M Ceasrine, Amanda H. Cox, James E. B. Docherty, Robert M Gingras, Stephanie M Grieb, Michael J. Pavia, Casey L Personius, Grzegorz Polak, Dale L. Beach, Heaven L Cerritos, Edward A Horansky, Karim A. Sharif, Ryan Moran, Susan Parrish, Kirsten Bickford, Jennifer Bland, Juliana Broussard, Kerry S. Campbell, Katelynn E Deibel, Richard Forka, Monika C Lemke, Marlee B Nelson, Catherine O’Keeffe, S Mariel Ramey, Luke M. Schmidt, Paola Villegas, Christopher J. Jones, Stephanie L Christ, Sami Mamari, Adam S Rinaldi, Ghazal Stity, Amy T. Hark, Mark Scheuerman, State Key, Briana D McRae, Adam Haberman, Sam Asinof, Harriette Carrington, Kelly Drumm, Terrance Embry, Richard McGuire, Drew Miller-Foreman, Stella Rosen, Nadia Safa, Darrin T. Schultz, Matt Segal, Yakov Shevin, Petros Svoronos, Tam D. Vuong, Gary R. Skuse, Don Paetkau, Rachael K Bridgman, Charlotte M. Brown, Alicia R Carroll, Francesca M Gifford, Julie Beth Gillespie, Susan E Herman, Krystal L Holtcamp, Misha A Host, Gabrielle Hussey, Danielle M Kramer, Joan Q Lawrence, Madeline M Martin, Ellen N Niemiec, Ashleigh P O'Reilly, Olivia A Pahl, Guadalupe Quintana, Elizabeth A S Rettie, Torie L Richardson, Arianne E. Rodriguez, Mona O Rodriguez, Laura K Schiraldi, Joanna J Smith, Kelsey F Sugrue, Lindsey J Suriano, Kaitlyn E Takach, Arielle M Vasquez, Ximena Vélez, Elizabeth J Villafuerte, Laura Vives, Victoria R. Zellmer, Jeanette Hauke, Charles R. Hauser, Karolyn Barker, Laurie Cannon, Perouza Parsamian, Samantha Parsons, Zachariah Wichman, Christopher Bazinet, Diana Johnson, Abubakarr Bangura, Jordan A Black, Victoria Chevée, Sarah A Einsteen, Sarah K Hilton, Max Kollmer, Rahul Nadendla, Joyce Stamm, Antoinette E. Fafara-Thompson, Amber M. Gygi, Emmy E. Ogawa, Matt Van Camp, Zuzana Kocsisova, Judith L. Leatherman, Cassandra M. Modahl, Michael R. Rubin, Susana S Apiz-Saab, Suzette M. Arias‐Mejias, Carlos F Carrion-Ortiz, Patricia Claudio-Vázquez, Debbie M Espada-Green, Marium Feliciano-Camacho, Karina M Gonzalez-Bonilla, Mariela Taboas-Arroyo, Dorianmarie Vargas‐Franco, Raquel Montañez-Gonzalez, Joseph Perez-Otero, Myrielis Rivera-Burgos, Francisco J Rivera-Rosario, Heather L. Eisler, Jackie Alexander, Samatha K Begley, Deana Gabbard, Robert J. Allen, Wint Yan Aung, William D. Barshop, Amanda Boozalis, Vanessa P Chu, Jeremy S Davis, Ryan N Duggal, Robert R. Franklin, Katherine Gavinski, Heran Gebreyesus, Henry Gong, Rachel Greenstein, Averill D Guo, Casey Hanson, Kaitlin E Homa, Simon Hsu, Yi Huang, Lucy Huo, Sarah Jacobs, Sasha Jia, Kyle L. Jung, Sarah Wai-Chee Kong, Matthew Kroll, Brandon M Lee, Paul F Lee, Kevin M. Levine, Amy S Li, Chengyu Liu, Max Mian Liu, Adam Lousararian, Peter B Lowery, Allyson P Mallya, Joseph E Marcus, Patrick Ng, Hien P. Nguyen, R. Patel, Hashini Precht, Suchita Rastogi, Jonathan M Sarezky, Adam Schefkind, Michael Schultz, Delia Shen, Tara Skorupa, Nicholas C. Spies, Gabriel Stancu, Hiu Man Vivian Tsang, Alice Turski, Rohit Venkat, Leah E Waldman, Kaidi Wang, Tracy Wang, Jeffrey W Wei, Dennis Y. Wu, David D. Xiong, Jack Y. Yu, Karen Zhou, Gerard P. McNeil, Robert W. Fernandez, Patrick Gomez Menzies, Tingting Gu, Jeremy Buhler, Elaine R. Mardis, Sarah C. R. Elgin
Software Mentions: 2
Published: over 7 years ago

10.1534/g3.117.300138

Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources
Cited by: 12
Author(s): Xiaoqing Rong-Mullins, Michael C. Ayers, Mahmoud Summers, Jennifer E. G. Gallagher
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes5041115

Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential
Cited by: 18
Author(s): Y. Kurihara, Yuko Makita, Mika Kawashima, Hidefumi Hamasaki, Yoshiharu Y. Yamamoto, Minami Matsui
Software Mentions: 2
Published: almost 10 years ago

10.3390/genes7010001

Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex
Cited by: 22
Author(s): Dovilė Strepetkaitė, Gediminas Alzbutas, Eimantas Astromskas, Aru̅nas Lagunavičius, Rasa Sabaliauskaitė, Кęstutis Arbačiauskas, Juozas R. Lazutka
Software Mentions: 2
Published: almost 9 years ago

10.3390/genes12081182

Set1 Targets Genes with Essential Identity and Tumor-Suppressing Functions in Planarian Stem Cells
Cited by: 2
Author(s): Prince Verma, Courtney K. M. Waterbury, Elizabeth M. Duncan
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0166575

5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation
Cited by: 13
Author(s): David K. Kranzhöfer, Ralf Gilsbach, Björn Grüning, Rolf Backofen, Thomas Nührenberg, Lutz Hein
Software Mentions: 2
Published: about 8 years ago

10.1186/gb-2014-15-1-r18

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis
Cited by: 85
Author(s): Beibei Chen, Jonghyun Yun, Min Soo Kim, Joshua T. Mendell, Yang Xie
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13059-015-0771-5

The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages
Cited by: 52
Author(s): Shruthi S. Vembar, Cameron Ross MacPherson, Odile Sismeiro, Jean‐Yves Coppée, Artur Scherf
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-016-0948-6

Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations
Cited by: 55
Author(s): Alice M. Walsh, John W. Whitaker, Chaohua Huang, Yauheniya Cherkas, S. Lamberth, Carrie Brodmerkel, Mark Curran, Radu Dobrin
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0223554

An integrated epigenome and transcriptome analysis identifies PAX2 as a master regulator of drug resistance in high grade pancreatic ductal adenocarcinoma
Cited by: 7
Author(s): Imlimaong Aier, Rahul Semwal, Aiindrila Dhara, Nirmalya Sen, Pritish Kumar Varadwaj
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2105-15-269

Study of cell differentiation by phylogenetic analysis using histone modification data
Cited by: 13
Author(s): Nishanth Ulhas Nair, Yongjun Lin, Ana Manasovska, Jelena Antić, Paulina Grnarova, Avinash Sahu, Philipp Bücher, Bernard M. E. Moret
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-017-1187-1

Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism
Cited by: 162
Author(s): Oliver Hahn, Sebastian Grönke, Thomas M. Stubbs, Gabriella Ficz, Oliver Hendrich, Felix Krueger, Simon Andrews, Zuo‐Feng Zhang, Michael J.O. Wakelam, Andreas Beyer, Wolf Reik, Linda Partridge
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0173421

mRNA N6-methyladenosine methylation of postnatal liver development in pig
Cited by: 44
Author(s): He Shen, Hong Wang, Rui Li, Mengnan He, Tiandong Che, Long Jin, Lüe Deng, Shilin Tian, Yán Li, Hongfeng Lü, Xuewei Li, Zhi Jiang, Diyan Li, Mingzhou Li
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04320-3

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes
Cited by: 6
Author(s): Lélia Polit, Gwenneg Kerdivel, Sebastian Gregoricchio, Michela Esposito, Christel Guillouf, Valentina Boeva
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0237248

Assessment of STAT5 as a potential therapy target in enzalutamide-resistant prostate cancer
Cited by: 11
Author(s): Holger H.H. Erb, Julia Bodenbender, Florian Handle, Tamara Diehl, Lukas Donix, Igor Tsaur, Martin Gleave, Axel Haferkamp, Johannes Huber, Susanne Fuessel, Eva Juengel, Zoran Čulig, Christian Thomas
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-017-1345-5

Functional assessment of human enhancer activities using whole-genome STARR-sequencing
Cited by: 85
Author(s): Yuwen Liu, Shan Yu, Vineet K. Dhiman, Tonya M. Brunetti, Heather Eckart, Kevin P. White
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0222435

PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma
Cited by: 4
Author(s): Haridha Shivram, Steven V. Le, Vishwanath R. Iyer
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0074513

Genome-Wide Analysis Reveals Coating of the Mitochondrial Genome by TFAM
Cited by: 46
Author(s): Yun E. Wang, Georgi K. Marinov, B Wold, David C. Chan
Software Mentions: 2
Published: about 11 years ago

10.1186/s40478-018-0573-6

Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA
Cited by: 15
Author(s): Jorge Mata-Garrido, Olga Tapia, Íñigo Casafont, Marı́a T. Berciano, Ana Cuadrado, Miguel Lafarga
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-019-1749-5

Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene
Cited by: 25
Author(s): Simon Lalonde, Valérie-Anne Codina-Fauteux, Sébastian Méric de Bellefon, F. Leblanc, Mélissa Beaudoin, Simon Maguire, Rola Dali, Tony Kwan, Ken Sin Lo, Tomi Pastinen, Guillaume Lettre
Software Mentions: 2
Published: over 5 years ago

10.1186/s13059-019-1853-6

EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation
Cited by: 27
Author(s): Priscillia Lhoumaud, Gunjan Sethia, Franco Izzo, Theodore Sakellaropoulos, Valentina Snetkova, Simon E. Vidal, Sana Badri, MacIntosh Cornwell, Dafne Campigli Di Giammartino, Kyu‐Tae Kim, Effie Apostolou, Matthias Stadtfeld, Dan A. Landau, Jane A. Skok
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1006741

Differential gene expression along the animal-vegetal axis in the ascidian embryo is maintained by a dual functional protein Foxd
Cited by: 14
Author(s): Shin Ichi Tokuhiro, Miki Tokuoka, Kenji Kobayashi, Atsushi Kubo, Izumi Oda-Ishii, Yutaka Satou
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04108-5

ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach
Cited by: 0
Author(s): Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi‐Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1007109

SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells
Cited by: 49
Author(s): Sabine Jägle, Hauke Busch, Vivien Freihen, Sven Beyes, Monika Schrempp, Melanie Boerries, Andreas Hecht
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1008796

Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2
Cited by: 33
Author(s): Dana Lau-Corona, Woo Kyun Bae, Lothar Hennighausen, David J. Waxman
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1007367

Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo
Cited by: 39
Author(s): Jenna E. Haines, Michael B. Eisen
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1003897

Ash1l Methylates Lys36 of Histone H3 Independently of Transcriptional Elongation to Counteract Polycomb Silencing
Cited by: 68
Author(s): Hiroyuki Miyazaki, Ken Higashimoto, Yukari Yada, Takaho A. Endo, Jafar Sharif, Toshiharu Komori, Masashi Matsushima, Haruhiko Koseki, Manabu Nakayama, Hidenobu Soejima, Hiroshi Handa, Susumu Hirose, Kusuki Nishioka
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1007375

Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution
Cited by: 36
Author(s): Sebastian Kittelmann, Alexandra D. Buffry, Franziska Anni Franke, Isabel Almudí, Marianne Yoth, Gonzalo Sabarís, Juan Pablo Couso, Maria D. S. Nunes, Nicolás Frankel, José Luis Gómez‐Skarmeta, José Ignacio Pueyo, Saad Arif, Alistair P. McGregor
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-020-02194-x

STARRPeaker: uniform processing and accurate identification of STARR-seq active regions
Cited by: 31
Author(s): Dong‐Hoon Lee, Manman Shi, Jennifer R. Moran, Martha L Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P. White, Mark Gerstein
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1008397

Chromatin dynamics enable transcriptional rhythms in the cnidarian Nematostella vectensis
Cited by: 9
Author(s): Eviatar Weizman, Miriam Tannenbaum, Ann M. Tarrant, Ofir Hakim, Oren Levy
Software Mentions: 2
Published: about 5 years ago

10.1186/s13059-020-02213-x

An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes
Cited by: 10
Author(s): Saba Ghaffari, Casey Hanson, Remington E. Schmidt, Kelly J. Bouchonville, Steven M. Offer, Saurabh Sinha
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1006353

A Multistate Toggle Switch Defines Fungal Cell Fates and Is Regulated by Synergistic Genetic Cues
Cited by: 24
Author(s): Matthew Anderson, Allison M. Porman, Na Wang, Eugenio Mancera, Denis Huang, Christina A. Cuomo, Richard J. Bennett
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1008339

A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure
Cited by: 5
Author(s): Mingguang Li, Ryan D. Fine, Manikarna Dinda, Stefan Bekiranov, Jeffrey S. Smith
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1003461

The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3
Cited by: 109
Author(s): Mareike Albert, Sandra U. Schmitz, Susanne M. Kooistra, Martina Malatesta, Cristina Morales Torres, Jens C. Rekling, Jens Vilstrup Johansen, Iratxe Abarrategui, Kristian Helin
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1008724

Integrative and quantitative view of the CtrA regulatory network in a stalked budding bacterium
Cited by: 6
Author(s): Oliver Leicht, Muriel C. F. van Teeseling, Gaël Panis, Celine Reif, Heiko Wendt, Patrick H. Viollier, Martin Thanbichler
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-021-04097-5

A flexible ChIP-sequencing simulation toolkit
Cited by: 4
Author(s): An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren, Melissa Gymrek
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1009282

Discovering differential genome sequence activity with interpretable and efficient deep learning
Cited by: 8
Author(s): Jennifer Hammelman, David K. Gifford
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pbio.3000664

YTHDF2 promotes mitotic entry and is regulated by cell cycle mediators
Cited by: 40
Author(s): Qili Fei, Zhongyu Zou, Ian A. Roundtree, Hui‐Lung Sun, Chuan He
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-021-02432-w

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
Cited by: 10
Author(s): Giancarlo Bonora, Vijay Ramani, Ritambhara Singh, Fang He, Dana L. Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William Stafford Noble, Christine M. Distèche
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pbio.3000747

High-fidelity SaCas9 identified by directional screening in human cells
Cited by: 35
Author(s): Haihua Xie, Xianglian Ge, Fayu Yang, Bang Wang, Shuang Li, Jinzhi Duan, Xiujuan Lv, Congsheng Cheng, Zongming Song, Changbao Liu, Junzhao Zhao, Yu Zhang, Jinyu Wu, Caixia Gao, Jinwei Zhang, Feng Gu
Software Mentions: 2
Published: over 4 years ago

10.1093/gbe/evz103

The Role of Chromatin Accessibility in cis-Regulatory Evolution
Cited by: 14
Author(s): Pei-Chen Peng, Pierre Khoueiry, Charles Girardot, James P. Reddington, David Garfield, Eileen E. M. Furlong, Saurabh Sinha
Software Mentions: 2
Published: over 5 years ago

10.1093/gbe/evz134

Comparative Analyses of Chromatin Landscape in White Adipose Tissue Suggest Humans May Have Less Beigeing Potential than Other Primates
Cited by: 21
Author(s): Devjanee Swain-Lenz, Alejandro Berrío, Alexias Safi, Gregory E. Crawford, Gregory A. Wray
Software Mentions: 2
Published: over 5 years ago

10.1186/s13073-018-0538-1

Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing
Cited by: 28
Author(s): Tianbao Li, Qi Liu, Nick Garza, Steven M. Kornblau, Victor X. Jin
Software Mentions: 2
Published: over 6 years ago

10.3390/plants9060674

Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis
Cited by: 3
Author(s): Tomoko Yamaguchi, Y. Kurihara, Yuko Makita, Emiko Okubo-Kurihara, Ami Kageyama, Emi Osada, Setsuko Shimada, Hiroko Tsuchida, Hiroaki Shimada, Minami Matsui
Software Mentions: 2
Published: over 4 years ago

10.1186/s13073-021-00871-5

PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling
Cited by: 42
Author(s): Bing Yao, Tao Gui, Xiangwei Zeng, Yexuan Deng, Zhi Wang, Ying Wang, Dezhi Yang, Qi-Xiang Li, Peipei Xu, Ruifeng Hu, Xinyu Li, Bing Chen, Jin Wang, Ke Zen, Haitao Li, Melissa J. Davis, Marco J. Herold, Huafeng Pan, Zhiwei Jiang, David C.S. Huang, Ming Liu, Junyi Ju, Quan Zhao
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.63299

HDAC1 SUMOylation promotes Argonaute-directed transcriptional silencing in C. elegans
Cited by: 14
Author(s): Hee-Sun Kim, Yue-He Ding, Gangming Zhang, Yan Ya, Darryl Conte, Meng‐Qiu Dong, Craig C. Mello
Software Mentions: 2
Published: over 3 years ago

10.1093/gigascience/giy035

m6ASNP: a tool for annotating genetic variants by m6A function
Cited by: 32
Author(s): Shuai Jiang, Yubin Xie, Zhan He, Zhang Ya, Yuli Zhao, Li Chen, Yueyuan Zheng, Yanyan Miao, Zhixiang Zuo, Jian Ren
Software Mentions: 2
Published: over 6 years ago

10.1186/s13007-018-0381-9

Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq
Cited by: 32
Author(s): Miriam Tannenbaum, Avital Sarusi-Portuguez, Ronen Krispil, Michal Schwartz, Olga Loza, Jennifer I. C. Benichou, Assaf Mosquna, Ofir Hakim
Software Mentions: 2
Published: almost 6 years ago

10.1093/gigascience/giz084

CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language
Cited by: 40
Author(s): Michael Kotliar, Andrey V. Kartashov, Artem Barski
Software Mentions: 2
Published: over 5 years ago

10.1186/s41065-021-00172-2

PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map
Cited by: 2
Author(s): Ronald J. Nowling, Susanta K. Behura, Marc S. Halfon, Scott J. Emrich, Molly Duman-Scheel
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41438-020-00419-5

The apple DNA-binding one zinc-finger protein MdDof54 promotes drought resistance
Cited by: 23
Author(s): Pengxiang Chen, Minmin Yan, Lei Li, Jieqiang He, Shuangxi Zhou, Zhongxing Li, Chundong Niu, Chana Bao, Fang Zhi, Fengwang Ma, Qingmei Guan
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.40854

Genome-wide Estrogen Receptor-α activation is sustained, not cyclical
Cited by: 13
Author(s): Andrew N Holding, Amy E Cullen, Florian Markowetz
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.23654

Distinct histone modifications denote early stress-induced drug tolerance in cancer
Cited by: 51
Author(s): Abdullah Al Emran, Diego M. Marzese, Dinoop Ravindran Menon, Mitchell Stark, Joachim Torrano, Heinz Hammerlindl, Gao Zhang, Patricia Brafford, Matthew P. Salomon, Nellie Nelson, Sabrina Hammerlindl, Deepesh Gupta, Gordon B. Mills, Yiling Lu, Richard A. Sturm, Keith T. Flaherty, Dave S. B. Hoon, Brian Gabrielli, Meenhard Herlyn, Helmut Schaider
Software Mentions: 2
Published: almost 7 years ago

10.1186/s40104-020-00511-9

Time-restricted feeding downregulates cholesterol biosynthesis program via RORγ-mediated chromatin modification in porcine liver organoids
Cited by: 10
Author(s): Kexin Zhang, Hao Li, Zimeng Xin, Yanwei Li, Xiaolong Wang, Yun Hu, Haoyu Liu, Demin Cai
Software Mentions: 2
Published: about 4 years ago

10.1074/jbc.RA120.013649

Molecular basis for histone H3 “K4me3-K9me3/2” methylation pattern readout by Spindlin1
Cited by: 13
Author(s): Fan Zhao, Yunan Liu, Xuantao Su, Jieun Lee, Yinglin Song, Daliang Wang, Kai Ge, Juntao Gao, Michael Q. Zhang, Haitao Li
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.jbc.2021.100962

Transcriptional regulation of miR-30a by YAP impacts PTPN13 and KLF9 levels and Schwann cell proliferation
Cited by: 4
Author(s): Alyssa Shepard, Sany Hoxha, Scott Troutman, David Harbaugh, Michael S. Kareta, Joseph L. Kissil
Software Mentions: 2
Published: over 3 years ago

10.7150/jca.50293

BRD7 inhibits tumor progression by positively regulating the p53 pathway in hepatocellular carcinoma
Cited by: 7
Author(s): Changlong Chen, Huaqian Mo, Yanjun Jiang, Xiaohui Zhao, Shuang Ma, Kaiyun You, Yue Pan, Yimin Liu
Software Mentions: 2
Published: almost 4 years ago

10.1111/jcmm.16583

Krϋppel‐like factor 15 suppresses renal glomerular mesangial cell proliferation via enhancing P53 SUMO1 conjugation
Cited by: 2
Author(s): Lingling Wu, Li Ou, Fengge Zhu, Xu Wang, Pu Chen, Guangyan Cai, Xiangmei Chen, Quan Hong
Software Mentions: 2
Published: over 3 years ago

10.1093/jxb/eraa052

ZmIBH1-1 regulates plant architecture in maize
Cited by: 33
Author(s): Yingying Cao, Haixia Zeng, Lixia Ku, Zhenzhen Ren, Yun Han, Huihui Su, Deqiang Dou, Huafeng Liu, Yan Dong, Fangfang Zhu, Tianyi Li, Qiannan Zhao, Yanhui Chen
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.ppat.1007499

INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana
Cited by: 15
Author(s): Ronny Völz, Soon-Kap Kim, Jianing Mi, Anamika Rawat, Alaguraj Veluchamy, Kadarkaraisamy Mariappan, Naganand Rayapuram, Jean-Michel Davière, Patrick Achard, Ikram Blilou, Salim Al‐Babili, Moussa Benhamed, Heribert Hirt
Software Mentions: 2
Published: almost 6 years ago

10.1002/1878-0261.12354

A patient‐derived explant ( <scp>PDE</scp> ) model of hormone‐dependent cancer
Cited by: 81
Author(s): Margaret M. Centenera, Theresa E. Hickey, Shalini Jindal, Natalie K. Ryan, Preethi Ravindranathan, Hisham Mohammed, James C. Robinson, Matthew J. Schiewer, Shihong Ma, Payal Kapur, Peter Sutherland, Clive E. Hoffmann, Claus G. Roehrborn, Leonard G. Gomella, Jason S. Carroll, Stephen N. Birrell, Karen E. Knudsen, Ganesh V. Raj, Lisa M. Butler, Wayne D. Tilley
Software Mentions: 2
Published: over 6 years ago

10.1007/s00204-017-2022-x

Genome-wide mapping and analysis of aryl hydrocarbon receptor (AHR)- and aryl hydrocarbon receptor repressor (AHRR)-binding sites in human breast cancer cells
Cited by: 37
Author(s): S.Y. Cindy Yang, Shaimaa Ahmed, Somisetty V. Satheesh, Jason Matthews
Software Mentions: 2
Published: over 7 years ago

10.1002/1878-0261.12693

Darolutamide antagonizes androgen signaling by blocking enhancer and super‐enhancer activation
Cited by: 20
Author(s): Simon J. Baumgart, Ekaterina Nevedomskaya, Ralf Lesche, Richard Newman, Dominik Mumberg, Bernard Haendler
Software Mentions: 2
Published: over 4 years ago

10.1073/pnas.1722125115

Histone H3 lysine 4 methylation signature associated with human undernutrition
Cited by: 22
Author(s): Robin Uchiyama, Kristyna Kupkova, Savera J. Shetty, Alicia S. Linford, Marilyn G. Pray-Grant, Lisa E. Wagar, Mark M. Davis, Rashidul Haque, Alban Gaultier, Marty W. Mayo, Patrick A. Grant, William A. Petri, Stefan Bekiranov, David T. Auble
Software Mentions: 2
Published: about 6 years ago

10.1007/s13238-021-00837-8

Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos
Cited by: 73
Author(s): Chuan Chen, Wenqiang Liu, Jiayin Guo, Yuanyuan Liu, Xuelian Liu, Jun Liu, Xiaoyang Dou, Rongrong Le, Yixin Huang, Chong Li, Lingyue Yang, Xiaochen Kou, Yanhong Zhao, You Wu, Jiayu Chen, Hong Wang, Bin Shen, Yawei Gao, Shaorong Gao
Software Mentions: 2
Published: over 3 years ago

10.1186/s12931-021-01617-y

Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq
Cited by: 11
Author(s): Justyna A. Karolak, Tomasz Gambin, Przemysław Szafrański, Paweł Stankiewicz
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12284-019-0342-6

Genome-wide Profiling of Histone Lysine Butyrylation Reveals its Role in the Positive Regulation of Gene Transcription in Rice
Cited by: 11
Author(s): Shuai Liu, Guanqing Liu, Pei-Feng Cheng, Cong Xue, Guohua Liang, Chen Xu, Ye Lu, Qiao Zhang, Tao Zhang, Zhiyun Gong
Software Mentions: 2
Published: almost 5 years ago

10.1126/sciadv.abg0108

Linking the FTO obesity rs1421085 variant circuitry to cellular, metabolic, and organismal phenotypes in vivo
Cited by: 18
Author(s): Samantha Laber, Sara Forcisi, Liz Bentley, Julia Petzold, Franco Moritz, Kirill S. Smirnov, Loubna Al Sadat, Iain Williamson, Sophie Strobel, Thomas Agnew, Shahana Sengupta, T L Nicol, Harald Grallert, Margit Heier, Julius Honecker, Joffrey Mianné, Lydia Teboul, Rebecca Dumbell, Helen Long, Michelle Simon, Cecilia M. Lindgren, Wendy A. Bickmore, Hans Hauner, Philippe Schmitt‐Kopplin, Melina Claussnitzer, Roger D. Cox
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.25536

Prostate cancer susceptibility gene HIST1H1A is a modulator of androgen receptor signaling and epithelial to mesenchymal transition
Cited by: 6
Author(s): Kendra A. Williams, Minnkyong Lee, Jean M. Winter, Derek Gildea, Carla Calagua, Natasha Curry, Jens Lichtenberg, Huihui Ye, Nigel P.S. Crawford
Software Mentions: 2
Published: over 6 years ago

10.1038/srep16803

Mutant cohesin affects RNA polymerase II regulation in Cornelia de Lange syndrome
Cited by: 34
Author(s): Linda Mannini, Fabien C. Lamaze, Francesco Cucco, Clelia Amato, Valentina Quarantotti, Ilaria Maria Rizzo, Ian D. Krantz, Steve Bilodeau, Antonio Musio
Software Mentions: 2
Published: about 9 years ago

10.18632/oncotarget.25617

Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids
Cited by: 21
Author(s): Samaneh K. Sarvestani, Steven A. Signs, Véronique Lefebvre, Stephen C. Mack, Ying Ni, Andrew Morton, E. Ricky Chan, Xiaoxia Li, Paul L. Fox, Angela H. Ting, Matthew F. Kalady, Michael Cruise, Jean Ashburn, Jennifer Stiene, Lai Wei, Dávid Líška, Xiang Shao, Emina H. Huang
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.63512

Promoter-specific changes in initiation, elongation, and homeostasis of histone H3 acetylation during CBP/p300 inhibition
Cited by: 22
Author(s): Emily Hsu, Nathan R. Zemke, Arnold Berk
Software Mentions: 2
Published: over 3 years ago

10.1038/srep36699

Insights into a novel nuclear function for Fascin in the regulation of the amino-acid transporter SLC3A2
Cited by: 21
Author(s): Amine Saad, Krikor Bijian, Dinghong Qiu, Sabrina Daniela da Silva, Maud Marques, Chia-Hao Chang, Hassan Nassour, Dindial Ramotar, Sambasivarao Damaraju, John R. Mackey, Tarek A. Bismar, Michael Witcher, Moulay A. Alaoui‐Jamali
Software Mentions: 2
Published: about 8 years ago

10.1038/srep37942

Mitochondrial control through nutritionally regulated global histone H3 lysine-4 demethylation
Cited by: 14
Author(s): M. Soloveychik, Mengshu Xu, Olga Zaslaver, Kwanyin Lee, Ashrut Narula, River Jiang, Adam P. Rosebrock, Amy A. Caudy, Marc D. Meneghini
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep41598

Genome-wide Regulatory Roles of the C2H2-type Zinc Finger Protein ZNF764 on the Glucocorticoid Receptor
Cited by: 14
Author(s): Abeer A. Fadda, Najeeb Syed, Rafah Mackeh, Anna Papadopoulou, Shigeru Suzuki, Puthen V. Jithesh, Tomoshige Kino
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep42522

Myotonic dystrophy type 1 patient-derived iPSCs for the investigation of CTG repeat instability
Cited by: 33
Author(s): Junko Ueki, Mikihito Nakamori, Masahiro Nakamura, Misato Nishikawa, Yoshinori Yoshida, Azusa Tanaka, Asuka Morizane, Masayoshi Kamon, Toshiyuki Araki, Masanori Takahashi, Akira Watanabe, Nobuya Inagaki, Hiroyuki Sakurai
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep43184

Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors
Cited by: 65
Author(s): Andrew Hughes, Jennifer M. Enright, Connie A. Myers, Susan Q. Shen, Joseph C. Corbo
Software Mentions: 2
Published: over 7 years ago

10.1038/srep46567

Sirtuins in the phylum Basidiomycota: A role in virulence in Cryptococcus neoformans
Cited by: 15
Author(s): Samantha D. M. Arras, Jessica L. Chitty, Maha S.I. Wizrah, Paige E. Erpf, Benjamin L. Schulz, Miloš Tanurdžić, James A. Fraser
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-02257-3

Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions
Cited by: 68
Author(s): Fan Cao, Yiwen Fang, Hong Kee Tan, Yufen Goh, Jocelyn Yeen Hui Choy, Bryan T. H. Koh, Jiong Hao Tan, Nicolas Bertin, Aroul Ramadass, Ewan Hunter, Jayne Green, Matthew Salter, Alexandre Akoulitchev, Wilson Wang, Wee Joo Chng, Daniel G. Tenen
Software Mentions: 2
Published: over 7 years ago

10.1016/j.molcel.2019.10.002

R-Loops Promote Antisense Transcription across the Mammalian Genome
Cited by: 97
Author(s): Sue Mei Tan-Wong, Somdutta Dhir, Nick J. Proudfoot
Software Mentions: 2
Published: about 5 years ago

10.3390/antiox10081232

Pterostilbene Changes Epigenetic Marks at Enhancer Regions of Oncogenes in Breast Cancer Cells
Cited by: 3
Author(s): Sadaf Harandi‐Zadeh, Cayla Boycott, Megan Beetch, T.Y. Yang, Bernice M. Martin, Kevin Ren, Anna Kwasniak, John H. Dupuis, Katarzyna Lubecka, Rickey Y. Yada, LeAnn Howe, Barbara Stefańska
Software Mentions: 2
Published: over 3 years ago

10.1016/j.molcel.2020.05.025

Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution
Cited by: 34
Author(s): Pakavarin Louphrasitthiphol, Robert Siddaway, Alessia Loffreda, Vivian Pogenberg, Hans Friedrichsen, Alexander Schepsky, Zhiqiang Zeng, Min Lü, Thomas Strub, Rasmus Freter, Richard J. Lisle, Eda Suer, Benjamin Thomas, Benjamin Schuster-Böckler, P. Filippakopoulos, Mark R. Middleton, Xin Lü, E. Elizabeth Patton, Irwin Davidson, Jean-Philippe Lambert, Matthias Wilmanns, Eirı́kur Steingrı́msson, Davide Mazza, Colin R. Goding
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-018-24915-w

The transcription factor Spores Absent A is a PKA dependent inducer of Dictyostelium sporulation
Cited by: 11
Author(s): Yoko Yamada, Andrew Cassidy, Pauline Schaap
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-25963-y

Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells
Cited by: 18
Author(s): Junko Hasegawa, Takuya Sakamoto, Shinsaku Fujimoto, Tomoe Yamashita, Takamasa Suzuki, Sachihiro Matsunaga
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-23276-8

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction
Cited by: 1,223
Author(s): Ziad Al Bkhetan, Dariusz Plewczynski
Software Mentions: 2
Published: over 6 years ago

10.1016/j.molcel.2018.06.003

The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression
Cited by: 119
Author(s): Susanne Bornelöv, Nicola Reynolds, Maria Xenophontos, Sarah Gharbi, Ewan Johnstone, Robin Floyd, Markus Ralser, Jason Signolet, Remco Loos, Sabine Dietmann, Paul Bertone, Brian Hendrich
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-018-32106-w

Histone acetylation as a new mechanism for bilirubin-induced encephalopathy in the Gunn rat
Cited by: 15
Author(s): Eleonora Vianello, Stefania Zampieri, Thomas Marcuzzo, Fabio Tordini, Cristina Bottin, Andrea Dardis, Fabrizio Zanconati, Claudio Tiribelli, Silvia Gazzin
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.62387

Runx2-Twist1 interaction coordinates cranial neural crest guidance of soft palate myogenesis
Cited by: 21
Author(s): Xia Han, Jifan Feng, Tingwei Guo, Yong-Hwee Eddie Loh, Yuan Yuan, Thach-Vu Ho, Courtney Kyeong Cho, Jingyuan Li, Junjun Jing, Eva Janečková, Jinzhi He, Fei Pei, Jing Bi, Brian J. Song, Yang Chai
Software Mentions: 2
Published: almost 4 years ago

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203