pypi: MACS2 | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1007991

Sumoylation of DNA-bound transcription factor Sko1 prevents its association with nontarget promoters
Cited by: 12
Author(s): Veroni S. Sri Theivakadadcham, Benjamin G. Bergey, Emanuel Rosonina
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-019-1642-2

Identification of transcription factor binding sites using ATAC-seq
Cited by: 284
Author(s): Li Z, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke, Ivan G. Costa
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-019-1694-3

Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery
Cited by: 77
Author(s): Bo Hu, Nan Wang, Xiuli Bi, Ezgi Süheyla Karaaslan, Anna-Lena Weber, Weiren Zhu, Kenneth W. Berendzen, Chang Liu
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-019-0543-y

The role of chromatin dynamics under global warming response in the symbiotic coral model Aiptasia
Cited by: 23
Author(s): Eviatar Weizman, Oren Levy
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1007969

Transcription-driven chromatin repression of Intragenic transcription start sites
Cited by: 66
Author(s): Mathias Nielsen, Ryan Ard, Xueyuan Leng, Maxim Ivanov, Peter Kindgren, Vicent Pelechano, Sebastian Marquardt
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13072-016-0097-x

An H4K16 histone acetyltransferase mediates decondensation of the X chromosome in C. elegans males
Cited by: 15
Author(s): Alyssa C. Lau, Kevin P. Zhu, Elizabeth A. Brouhard, Mary Ellen Davis, Györgyi Csankovszki
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-020-07268-5

ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus
Cited by: 9
Author(s): Dayle Johnston, JaeWoo Kim, Jeremy F. Taylor, Bernadette Earley, Matthew S. McCabe, Ken Lemon, Catherine Duffy, Michael McMenamy, S. L. Cosby, Sinéad M. Waters
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1009542

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

10.3390/cancers12092551

Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells
Cited by: 12
Author(s): Michał Marczyk, Gauri A. Patwardhan, Jun Zhao, Rihao Qu, Xiaotong Li, Vikram B. Wali, Abhishek Kumar Gupta, Manoj M. Pillai, Yuval Kluger, Qin Yan, Christos Hatzis, Lajos Pusztai, Vignesh Gunasekharan
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-019-2708-6

Predicting enhancers in mammalian genomes using supervised hidden Markov models
Cited by: 11
Author(s): Tobias Zehnder, Philipp Benner, Martin Vingron
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.49314

Kinetics of cytokine receptor trafficking determine signaling and functional selectivity
Cited by: 31
Author(s): Jonathan Martínez-Fábregas, Stephan Wilmes, Luopin Wang, Maximillian Hafer, Elizabeth Pöhler, Juliane Lokau, Christoph Garbers, Adeline Cozzani, Paul K. Fyfe, Jacob Piehler, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.17361

Satb2 determines miRNA expression and long-term memory in the adult central nervous system
Cited by: 64
Author(s): Clemens Jaitner, Chethan Reddy, Andreas Abentung, Nigel Whittle, Dietmar Rieder, Andrea Delekate, Martin Körte, Gaurav Jain, André Fischer, Farahnaz Sananbenesi, Isabella Cera, Nicolas Singewald, Georg Dechant, Galina Apostolova
Software Mentions: 3
Published: almost 8 years ago

10.3390/ijms22168574

Comparison of Histone H3K4me3 between IVF and ICSI Technologies and between Boy and Girl Offspring
Cited by: 6
Author(s): Huixia Yang, Zhi Ma, Peng Lin, Christina Kühn, Martina Rahmeh, Sven Mahner, Udo Jeschke, Viktoria von Schönfeldt
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-019-1877-y

Chromatin interactome mapping at 139 independent breast cancer risk signals
Cited by: 22
Author(s): Jonathan Beesley, Haran Sivakumaran, Mahdi Moradi Marjaneh, Luize Gonçalves Lima, Kristine M. Hillman, Susanne Kaufmann, Natasha Tuano, Nehal Hussein, Sunyoung Ham, Pamela Mukhopadhyay, Stephen H. Kazakoff, Jason S. Lee, Kyriaki Michailidou, Daniel R. Barnes, Antonis C. Antoniou, Laura Fachal, Alison M. Dunning, Douglas F. Easton, Nicola Waddell, Joseph Rosenbluh, Andreas Möller, Georgia Chenevix-Trench, Juliet D. French, Stacey L. Edwards
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1009710

DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress
Cited by: 18
Author(s): Kohei Nozawa, Jiani Chen, Jingchao Jiang, Sarah M. Leichter, Masataka Yamada, Takamasa Suzuki, Fengquan Liu, Hidetaka Ito, Xuehua Zhong
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1007999

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

10.1371/journal.pgen.1008476

Photodamage repair pathways contribute to the accurate maintenance of the DNA methylome landscape upon UV exposure
Cited by: 15
Author(s): Stéfanie Graindorge, Valérie Cognat, Philippe Johann to Berens, Jérôme Mutterer, Jean Molinier
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-020-01984-7

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

10.1186/s12859-020-3510-1

A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks
Cited by: 3
Author(s): Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva, Riccardo Bellazzi
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1007823

Nucleosome positions establish an extended mutation signature in melanoma
Cited by: 30
Author(s): Alexander Brown, Peng Mao, Michael J. Smerdon, John J. Wyrick, Steven A. Roberts
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.00312

Age-Dependent Changes in Transcription Factor FOXO Targeting in Female Drosophila
Cited by: 28
Author(s): Allison Birnbaum, Xiaofen Wu, Marc Tatar, Nan Liu, Hua Bai
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1004290

Copy Number Variation Is a Fundamental Aspect of the Placental Genome
Cited by: 55
Author(s): Roberta L. Hannibal, Edward B. Chuong, Juan Carlos Rivera-Mulia, David M. Gilbert, Anton Valouev, Julie C. Baker
Software Mentions: 3
Published: over 10 years ago

10.1186/s13072-021-00405-8

Altered hypothalamic DNA methylation and stress-induced hyperactivity following early life stress
Cited by: 5
Author(s): Eamon Fitzgerald, Matthew C. Sinton, Sara Wernig-Zorc, Nicholas M. Morton, Megan C. Holmes, James P. Boardman, Amanda J. Drake
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009708

Ras/ERK and PI3K/AKT signaling differentially regulate oncogenic ERG mediated transcription in prostate cells
Cited by: 6
Author(s): Brady G. Strittmatter, Travis J. Jerde, Peter C. Hollenhorst
Software Mentions: 3
Published: over 3 years ago

10.18632/oncotarget.20098

Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets
Cited by: 60
Author(s): Michaela C. Baldauf, Martin F. Orth, Marlene Dallmayer, Aruna Marchetto, Julia S. Gerke, Rebeca Alba Rubío, Merve Meryem Kıran, Julian Musa, Max Knott, Shunya Ohmura, Jing Li, Nusret Akpolat, Ayşe Nur Akatlı, Özlem Özen, Uta Dirksen, Wolfgang Hartmann, Enrique de Álava, Daniel Baumhoer, Giuseppina Sannino, Thomas Kirchner, Thomas G.P. Grünewald
Software Mentions: 3
Published: over 7 years ago

10.1186/s12967-021-02754-0

FOXO1 mitigates the SMAD3/FOXL2C134W transcriptomic effect in a model of human adult granulosa cell tumor
Cited by: 5
Author(s): Christian Secchi, Paola Benaglio, Francesca Mulas, Martina Belli, Dwayne G. Stupack, Shunichi Shimasaki
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009044

NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation
Cited by: 18
Author(s): Yuta Hiraike, Hironori Waki, Kana Miyake, Takahito Wada, Misato Oguchi, Kaede Saito, Sadami Tsutsumi, Hiroyuki Aburatani, Toshimasa Yamauchi, Takashi Kadowaki
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1006571

Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis
Cited by: 25
Author(s): Lijuan Feng, Zhen Shi, Xin Chen
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13072-015-0049-x

Roles of cofactors and chromatin accessibility in Hox protein target specificity
Cited by: 46
Author(s): Ching Yew Beh, Sherif El‐Sharnouby, Aikaterini Chatzipli, Steven Russell, Siew Woh Choo, Robert A. White
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1008002

Deletion of Cdkn1b in ACI rats leads to increased proliferation and pregnancy-associated changes in the mammary gland due to perturbed systemic endocrine environment
Cited by: 10
Author(s): Ling Ding, Lauren B. Shunkwiler, Nicholas W. Harper, Yang Zhao, Kunihiko Hinohara, Sung Jin Huh, Muhammad B. Ekram, Jan Guz, Michael J. Kern, Alexander Awgulewitsch, James D. Shull, Bart M. G. Smits, Kornélia Polyák
Software Mentions: 3
Published: over 5 years ago

10.1186/s13072-019-0306-5

Early-life DNA methylation profiles are indicative of age-related transcriptome changes
Cited by: 17
Author(s): Niran Hadad, Dustin R. Masser, Laura Blanco-Berdugo, David R. Stanford, Willard M. Freeman
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.55361

Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors
Cited by: 33
Author(s): Shiri Kult, Tsviya Olender, Marco Osterwalder, Svetalana Markman, Dena Leshkowitz, Sharon Krief, Ronnie Blecher‐Gonen, Shani Ben‐Moshe, Lydia Farack, Hadas Keren‐Shaul, Tomer-Meir Salame, Terence D. Capellini, Shalev Itzkovitz, Ido Amit, Axel Visel, Elazar Zelzer
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-020-07078-9

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Cited by: 36
Author(s): Michelle M. Halstead, Colin Kern, Perot Saelao, Ying Wang, Ganrea Chanthavixay, Juan F. Medrano, Alison L. Van Eenennaam, Ian F Korf, Christopher K. Tuggle, Catherine W. Ernst, Huaijun Zhou, Pablo J. Ross
Software Mentions: 3
Published: about 4 years ago

10.1038/s42003-019-0718-6

Monocytes undergo multi-step differentiation in mice during oral infection by Toxoplasma gondii
Cited by: 8
Author(s): Aurélie Detavernier, Abdulkader Azouz, Hussein Shehade, Marion Splittgerber, Laurye Van Maele, Muriel Nguyen, Séverine Thomas, Younès Achouri, David Švec, Emilie Calonne, François Fuks, Guillaume Oldenhove, Stanislas Goriely
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1007884

Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi
Cited by: 12
Author(s): Valentina del Olmo Toledo, Robert Puccinelli, Polly M. Fordyce, J. Christian Pérez
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13059-020-02152-7

Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation
Cited by: 57
Author(s): Celestia Fang, Zhenjia Wang, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman, Valentina Serafin, Giuseppe Basso, Kyle P. Eagen, Alexandre Gaspar-Maia, María E. Figueroa, Benjamin D. Singer, Aakrosh Ratan, Panagiotis Ntziachristos, Chongzhi Zang
Software Mentions: 3
Published: about 4 years ago

10.1038/celldisc.2016.10

Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing
Cited by: 161
Author(s): Wenqiang Liu, Xiaoyu Liu, Chenfei Wang, Yawei Gao, Rui Gao, Xiaochen Kou, Yanhong Zhao, Jingyi Li, You Wu, Wenchao Xiu, Su Wang, Jie Yin, Wei Liu, Tao Cai, Hong Wang, Yong Zhang, Shaorong Gao
Software Mentions: 3
Published: over 8 years ago

10.1186/s13072-016-0065-5

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells
Cited by: 19
Author(s): Christopher L. Frank, Dinesh Manandhar, Raluca Gordân, Gregory E. Crawford
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-020-02201-1

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Cited by: 28
Author(s): Yue Feng, Yao Wang, Xiangnan Wang, Xiaohong He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie, Hanhui Ma
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13072-019-0280-y

p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes
Cited by: 22
Author(s): Jing Qu, Guoqiang Yi, Huiqing Zhou
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.65884

Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation
Cited by: 7
Author(s): Teresa Romeo Luperchio, Leandros Boukas, Li Zhang, Genay Pilarowski, Jenny Jiang, Allison Kalinousky, Kasper D. Hansen, Hans T. Björnsson
Software Mentions: 3
Published: about 3 years ago

10.1186/s13072-018-0212-2

CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites
Cited by: 31
Author(s): Philip A. Ruzycki, Xiaodong Zhang, Shiming Chen
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1008540

MED19 alters AR occupancy and gene expression in prostate cancer cells, driving MAOA expression and growth under low androgen
Cited by: 8
Author(s): Hannah Weber, Rachel Ruoff, Michael J. Garabedian
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-020-02253-3

SPIN reveals genome-wide landscape of nuclear compartmentalization
Cited by: 52
Author(s): Yuchuan Wang, Yang Zhang, Ruochi Zhang, Tom van Schaik, Liguo Zhang, Takayo Sasaki, Daniel Peric-Hupkes, Yu Chen, David M. Gilbert, Bas van Steensel, Andrew S. Belmont, Jian Ma
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-021-02209-8

Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes
Cited by: 4
Author(s): Hong Wang, Aiping Duan, Jing Zhang, Qi Wang, Yufei Xing, Zhaohui S. Qin, Zhihong Liu, Jingping Yang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0182528

Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish
Cited by: 29
Author(s): Yunru Chen, Shiyang Zeng, Ruikun Hu, Xiangxiu Wang, Wenyan Huang, Jiangfang Liu, Luying Wang, Guifen Liu, Ying Cao, Yong Zhang
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-021-02270-w

simATAC: a single-cell ATAC-seq simulation framework
Cited by: 12
Author(s): Zeinab Navidi, Lin Zhang, Bo Wang
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009318

Ush regulates hemocyte-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis
Cited by: 10
Author(s): Jonathan Lenz, Robert Liefke, Julianne Funk, Samuel Shoup, Andrea Nist, Thorsten Stiewe, Robert A. Schulz, Yumiko Tokusumi, Lea Albert, Hartmann Raifer, Klaus Förstemann, Olalla Vázquez, Tsuyoshi Tokusumi, Nancy Fossett, Alexander Brehm
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13059-021-02323-0

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Cited by: 46
Author(s): Gareth Benjamin Gillard, Lars Grønvold, Line Lieblein Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, J. Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen Rød Sandve, Torgeir R. Hvidsten
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0243332

Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data
Cited by: 0
Author(s): Ruslan N. Sharipov, Yury V. Kondrakhin, Anna S. Ryabova, Ivan S. Yevshin, Fedor A. Kolpakov
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1007681

Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk
Cited by: 37
Author(s): Dharini Iyer, Quanyi Zhao, Robert Wirka, Ameay V. Naravane, Trieu Nguyen, Boxiang Liu, Manabu Nagao, Paul Cheng, Clint L. Miller, Juyong Brian Kim, Milos Pjanic, Thomas Quertermous
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-018-2577-4

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

10.1371/journal.pone.0089110

Otx2 ChIP-seq Reveals Unique and Redundant Functions in the Mature Mouse Retina
Cited by: 53
Author(s): Alexander Samuel, Michael Housset, Bruno Fant, Thomas Lamonerie
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13072-020-00348-6

HiCoP, a simple and robust method for detecting interactions of regulatory regions
Cited by: 8
Author(s): Yan Zhang, Zhaoqiang Li, Shasha Bian, Hao Zhao, Delong Feng, Yanhong Chen, Yuhe Hou, Qifa Liu, Bingtao Hao
Software Mentions: 3
Published: over 4 years ago

10.1038/s42003-019-0665-2

Transcription factor Znf2 coordinates with the chromatin remodeling SWI/SNF complex to regulate cryptococcal cellular differentiation
Cited by: 18
Author(s): Jianfeng Lin, Youbao Zhao, Aileen R Ferraro, Ence Yang, Zachary A. Lewis, Xiaorong Lin
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-021-02456-2

Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index
Cited by: 18
Author(s): Minglei Shi, Kaiqiang You, Taoyu Chen, Chao Hou, Zhengyu Liang, Mingwei Liu, Jifeng Wang, Taotao Wei, Jun Qin, Yang Chen, Michael Q. Zhang, Tingting Li
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-021-07795-9

A functional map of genomic HIF1α-DNA complexes in the eye lens revealed through multiomics analysis
Cited by: 5
Author(s): Joshua Disatham, Lisa A. Brennan, Daniel Chauss, Jason Kantorow, Behdad Afzali, Marc Kantorow
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.37344

Chromatin accessibility dynamics across C. elegans development and ageing
Cited by: 66
Author(s): Jürgen Jänes, Dong Yan, Michael Schoof, Jacques Serizay, Alex Appert, Chiara Cerrato, Carson Woodbury, Chen Ron, Carolina Gemma, Ni Huang, Djem U. Kissiov, Przemyslaw Stempor, Annette Steward, Eva Zeiser, Sascha Sauer, Julie Ahringer
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.64444

A β-catenin-driven switch in TCF/LEF transcription factor binding to DNA target sites promotes commitment of mammalian nephron progenitor cells
Cited by: 27
Author(s): Qiuyu Guo, Albert D. Kim, Bin Li, Andrew Ransick, Helena Bugacov, Xi Chen, Nils O. Lindström, Aaron C. Brown, Leif Oxburgh, Bing Ren, Andrew P. McMahon
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.57519

The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth
Cited by: 20
Author(s): Baisakhi Mondal, Hong Jin, Satish Kallappagoudar, Yurii Sedkov, Tanner Martinez, Monica F. Sentmanat, Greg J Poet, Chunliang Li, Yiping Fan, Shondra M. Pruett-Miller, Hans‐Martin Herz
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-021-02465-1

NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
Cited by: 5
Author(s): Kun Fang, Tianbao Li, Yufei Huang, Victor X. Jin
Software Mentions: 3
Published: about 3 years ago

10.7554/eLife.50670

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling
Cited by: 29
Author(s): Rachel K. Lex, Zhicheng Ji, Kristin N. Falkenstein, Weiqiang Zhou, Joanna L Henry, Hongkai Ji, Steven A. Vokes
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.52712

Hair follicle stem cells regulate retinoid metabolism to maintain the self-renewal niche for melanocyte stem cells
Cited by: 23
Author(s): Zhiwei Lü, Yuhua Xie, Huanwei Huang, Kaiju Jiang, Bin Zhou, Fengchao Wang, Ting Chen
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13072-018-0243-8

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs
Cited by: 51
Author(s): Derek H. Janssens, Steven J. Wu, Jay F. Sarthy, Michael P. Meers, Carrie Myers, James M. Olson, Kami Ahmad, Steven Henikoff
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41419-020-2228-3

Two faces of bivalent domain regulate VEGFA responsiveness and angiogenesis
Cited by: 10
Author(s): Jiahuan Chen, Xiaodong Liang, Shasha Zhang, Shiyan Wang, Sara P. Garcia, Pengyi Yan, Huijing Yu, Zixuan Li, Li Liu, Fang Zhang, Weiting Wei, Le Han, Yan Zhang, Guo‐Cheng Yuan, Sun Chen, Yingwei Chen, Sun Kim, William T. Pu, Bing Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-16-S13-S10

Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data
Cited by: 18
Author(s): Mikhail G. Dozmorov, Indra Adrianto, Cory B. Giles, Edmund Glass, Stuart B. Glenn, Courtney G. Montgomery, Kathy L. Sivils, Lorin E. Olson, Tomoaki Iwayama, Willard M. Freeman, Christopher J. Lessard, Jonathan D. Wren
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13072-016-0087-z

Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers
Cited by: 23
Author(s): Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen‐Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery‐Padan, David Shechter, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: about 8 years ago

10.1186/s13072-017-0132-6

The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo
Cited by: 24
Author(s): David Latrasse, Natalia Yaneth Rodriguez-Granados, Alaguraj Veluchamy, Kadarkaraisamy Mariappan, Claudia Bevilacqua, Nicolas Crapart, Carlos Camps, Vivien Sommard, Cécile Raynaud, Catherine Dogimont, Adnane Boualem, Moussa Benhamed, Abdelhafid Bendahmane
Software Mentions: 2
Published: over 7 years ago

10.1186/s13072-018-0195-z

Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points
Cited by: 39
Author(s): Elisabeth F. Heuston, Cheryl A. Keller, Jens Lichtenberg, Belinda Giardine, Stacie M. Anderson, Ross C. Hardison, David M. Bodine
Software Mentions: 2
Published: over 6 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

10.1038/cddis.2017.345

The cohesin complex prevents Myc-induced replication stress
Cited by: 10
Author(s): Sara Rohban, Aurora Cerutti, Marco J. Morelli, Fabrizio d’Adda di Fagagna, Stefano Campaner
Software Mentions: 2
Published: over 7 years ago

10.1186/s13072-019-0318-1

Reduced H3K27me3 leads to abnormal Hox gene expression in neural tube defects
Cited by: 25
Author(s): Jianhua Yu, Lei Wang, Pei Pei, Xue Li, Jianxin Wu, Zhiyong Qiu, Juan Zhang, Ruifang Ao, Shan Wang, Ting Zhang, Jun Xie
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13072-019-0272-y

Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways
Cited by: 32
Author(s): Yilin Zhao, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: over 5 years ago

10.1038/s41419-018-0668-9

Transcriptional and epigenetic modulation of autophagy promotes EBV oncoprotein EBNA3C induced B-cell survival
Cited by: 33
Author(s): Shaoni Bhattacharjee, Priyanka Bose, Krishna Patel, Shatadru Ghosh Roy, Chandrima Gain, Harsha Gowda, Erle S. Robertson, Abhik Saha
Software Mentions: 2
Published: over 6 years ago

10.1186/s13072-018-0229-6

The methylome of the marbled crayfish links gene body methylation to stable expression of poorly accessible genes
Cited by: 54
Author(s): Fanny Gatzmann, Cassandra Falckenhayn, Julian Gutekunst, Katharina Hanna, Günter Raddatz, Vitor Coutinho Carneiro, Frank Lyko
Software Mentions: 2
Published: about 6 years ago

10.1186/s13072-019-0291-8

Identification of a pituitary ERα-activated enhancer triggering the expression of Nr5a1, the earliest gonadotrope lineage-specific transcription factor
Cited by: 12
Author(s): Vincent Pacini, Florence Petit, Bruno Quérat, Jean-Noël Laverrière, Joëlle Cohen‐Tannoudji, David L’Hôte
Software Mentions: 2
Published: over 5 years ago

10.1186/s13072-020-00335-x

Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes
Cited by: 12
Author(s): Iyer Aditya Mahadevan, Sanjeev Kumar, Rao M
Software Mentions: 2
Published: over 4 years ago

10.12688/f1000research.17956.1

Detection and analysis of RNA methylation
Cited by: 33
Author(s): Nigel P. Mongan, Richard D. Emes, Nathan Archer
Software Mentions: 2
Published: over 5 years ago

10.1016/j.cell.2017.11.042

Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner
Cited by: 497
Author(s): Morgane Sonia Thion, Donovan Low, Aymeric Silvin, Jinmiao Chen, Pauline Grisel, Jonas Schulte-Schrepping, Ronnie Blecher‐Gonen, Thomas Ulas, Paola Squarzoni, Guillaume Hoeffel, Fanny Coulpier, Eleni Siopi, Friederike S. David, Claus‐Jürgen Scholz, Shihui Foo, Josephine Lum, Arlaine Anne Amoyo, Anis Larbi, Michael Poidinger, Anne Buttgereit, Pierre-Marie Lledo, Melanie Greter, Jerry Kok Yen Chan, Ido Amit, Marc Beyer, Joachim L. Schultze, Andreas Schlitzer, Sven Pettersson, Florent Ginhoux, Sonia Garel
Software Mentions: 2
Published: almost 7 years ago

10.3389/fcell.2019.00372

Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos
Cited by: 7
Author(s): Marta Silvia Magri, Sandra Jiménez-Gancedo, Stéphanie Bertrand, Alicia Madgwick, Héctor Escrivà, Patrick Lemaire, José Luis Gómez-Skármeta
Software Mentions: 2
Published: almost 5 years ago

10.3389/fcell.2021.682593

Epigenetic Reprogramming Mediated by Maternal Diet Rich in Omega-3 Fatty Acids Protects From Breast Cancer Development in F1 Offspring
Cited by: 13
Author(s): Ata Abbas, Theodore R. Witte, William L. Patterson, Johannes F. Fahrmann, Kai Guo, Junguk Hur, W. Elaine Hardman, Philippe Georgel
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2020.00196

Dynamics of the Transcriptome and Accessible Chromatin Landscapes During Early Goose Ovarian Development
Cited by: 12
Author(s): Shiyan Hu, Shuang Yang, Yao Lu, Yan Deng, Li Li, Jiaran Zhu, Yuan Zhang, Bo Hu, Jiwei Hu, Lu Xia, Hua He, Chunchun Han, Hehe Liu, Bo Kang, Liang Li, Jiwen Wang
Software Mentions: 2
Published: over 4 years ago

10.3389/fcell.2021.686737

JFK Is a Hypoxia-Inducible Gene That Functions to Promote Breast Carcinogenesis
Cited by: 1
Author(s): Ziran Yang, Xuehong Zhou, Enrun Zheng, Yizhou Wang, Xinhua Liu, Yue Wang, Yiguang Wang, Zhaofei Liu, Fei Pei, Yue Zhang, Jie Ren, Yunchao Huang, Xianping Lu, Sudun Guan, Sen Qin, Feiya Suo, Jie Shi, Lijing Wang, Lin He, Luyang Sun
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers13040739

Metformin Reduces Histone H3K4me3 at the Promoter Regions of Positive Cell Cycle Regulatory Genes in Lung Cancer Cells
Cited by: 13
Author(s): Dongho Kim, Yujin Kim, Bo Bin Lee, Eun Yoon Cho, Joungho Han, Young Mog Shim, Duk-Hwan Kim
Software Mentions: 2
Published: almost 4 years ago

10.3390/cancers13153801

Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development
Cited by: 3
Author(s): Tabea L. Bauer, Katrin Collmar, Till Kaltofen, Ann-Katrin Loeffler, Lorena Decker, Jan Mueller, Sabine Pinter, Stephan A. Eisler, Sven Mahner, Patricia Fraungruber, Stefan Kommoss, Annette Staebler, Lewis Francis, R. Steven Conlan, Johannes Zuber, Udo Jeschke, Fabian Trillsch, Philipp Rathert
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2020.00289

H3K4me1 Distribution Predicts Transcription State and Poising at Promoters
Cited by: 55
Author(s): Sunhee Bae, Bluma J. Lesch
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers10010021

IRF4 Mediates the Oncogenic Effects of STAT3 in Anaplastic Large Cell Lymphomas
Cited by: 26
Author(s): Cecilia Bandini, Aldi Pupuleku, Elisa Spaccarotella, Elisa Pellegrino, Rui Wang, Nicoletta Vitale, Carlotta Duval, Daniela Cantarella, Andrea Rinaldi, Paolo Provero, Ferdinando Di Cunto, Enzo Medico, Francesco Bertoni, Giorgio Inghirami, Roberto Piva
Software Mentions: 2
Published: almost 7 years ago

10.3389/fendo.2018.00034

Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
Cited by: 14
Author(s): Frederique Ruf-Zamojski, Miguel Fribourg, Yongchao Ge, Venugopalan D. Nair, Hanna Pinças, Elena Zaslavsky, German Nudelman, Stephanie Tuminello, Hideo Watanabe, Judith L Turgeon, Stuart C. Sealfon
Software Mentions: 2
Published: almost 7 years ago

10.3389/fgene.2020.00230

Effect for Human Genomic Variation During the BMP4-Induced Conversion From Pluripotent Stem Cells to Trophoblast
Cited by: 5
Author(s): Haitao Li, Yajun Li, Hongde Liu, Xiao Sun
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2021.649959

“Adopt-a-Tissue” Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare
Cited by: 7
Author(s): Nicole B. Kingsley, Natasha A. Hamilton, Gabriella Lindgren, Ludovic Orlando, Ernest Bailey, Samantha A. Brooks, Molly E. McCue, Theodore S. Kalbfleisch, James N. MacLeod, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.651604

The Chromatin Accessibility Landscape of Adult Rat
Cited by: 1
Author(s): Yue Yuan, Qiuting Deng, Xiaoyü Wei, Yang Liu, Qing Lan, Yu Jiang, Yeya Yu, Pengcheng Guo, Jiangshan Xu, Yu Sheng Cong, Lei Han, Mengnan Cheng, Peng Wu, Xiao Zhang, Yiwei Lai, Giacomo Volpe, Miguel A. Esteban, Huanming Yang, Chuanyu Liu, Longqi Liu
Software Mentions: 2
Published: over 3 years ago

10.3390/cancers12082137

Epigenetic Targeting of Mcl-1 Is Synthetically Lethal with Bcl-xL/Bcl-2 Inhibition in Model Systems of Glioblastoma
Cited by: 14
Author(s): Enyuan Shang, Trang Nguyen, Chang Shu, Mike‐Andrew Westhoff, Georg Karpel‐Massler, Markus D. Siegelin
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2020.00269

MASQC: Next Generation Sequencing Assists Third Generation Sequencing for Quality Control in N6-Methyladenine DNA Identification
Cited by: 25
Author(s): Siqian Yang, Yaoxin Wang, Ying Chen, Qi Dai
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2020.612031

Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages
Cited by: 9
Author(s): Alisha T. Massa, Michelle R. Mousel, Maria K. Herndon, David R. Herndon, Brenda M. Murdoch, Stephen N. White
Software Mentions: 2
Published: almost 4 years ago

10.3390/cancers13092171

Pparγ1 Facilitates ErbB2-Mammary Adenocarcinoma in Mice
Cited by: 4
Author(s): Xuanmao Jiao, Lifeng Tian, Zhao Zhang, Joanna Balcerek, Andrew V. Kossenkov, Mathew C. Casimiro, Chenguang Wang, Yichuan Liu, Adam Ertel, Raymond E. Soccio, Eric R. Chen, Qin Liu, Anthony W. Ashton, Wei Tong, Richard G. Pestell
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2021.628849

Characterizing Genetic Regulatory Elements in Ovine Tissues
Cited by: 6
Author(s): Kimberly M Davenport, Alisha T. Massa, Suraj Bhattarai, Stephanie McKay, Michelle R. Mousel, Maria K. Herndon, Stephen N. White, Noelle E. Cockett, Timothy P. L. Smith, Brenda M. Murdoch
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-0957-1

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
Cited by: 4
Author(s): Qi Zhang, Xin Zeng, Samuel G. Younkin, Trupti Kawli, M Snyder, Sündüz Keleş
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2021.642807

Stable Epigenetic Programming of Effector and Central Memory CD4 T Cells Occurs Within 7 Days of Antigen Exposure In Vivo
Cited by: 3
Author(s): Sarah L Bevington, Rémi Fiancette, Dominika W Gajdasik, Peter Keane, Jake K Soley, Claire Willis, Dan Coleman, David R. Withers, Peter N. Cockerill
Software Mentions: 2
Published: over 3 years ago

10.3389/fimmu.2020.01322

PIK3AP1 and SPON2 Genes Are Differentially Methylated in Patients With Periodic Fever, Aphthous Stomatitis, Pharyngitis, and Adenitis (PFAPA) Syndrome
Cited by: 7
Author(s): Ema Lovšin, Jernej Kovač, Tine Tesovnik, Nataša Toplak, Denis Perko, Tomaž Rozmarič, Maruša Debeljak, Tadej Avčin
Software Mentions: 2
Published: over 4 years ago

10.3389/fimmu.2020.00579

NCOR1 Orchestrates Transcriptional Landscapes and Effector Functions of CD4+ T Cells
Cited by: 10
Author(s): Daniela Hainberger, Valentina Stolz, Ci Zhu, Michael Schuster, Lena Müller, Patricia Hamminger, Ramona Rica, Darina Waltenberger, Marlis Alteneder, Thomas Krausgruber, Anastasiya Hladik, Sylvia Knapp, Christoph Bock, Michael Trauner, Michael A. Farrar, Wilfried Ellmeier
Software Mentions: 2
Published: over 4 years ago

Projects: pypi: MACS2

Papers Mentioning MACS2 1,203