Ecosyste.ms: Papers

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

10.1093/biostatistics/kxy084

MACPET: model-based analysis for ChIA-PET
Cited by: 0
Author(s): Ioannis Vardaxis, Finn Drabløs, Morten Rye, Bo Henry Lindqvist
Software Mentions: 4
Published: over 5 years ago

10.1186/s13072-017-0160-2

Ubiquitin C-terminal hydrolase isozyme L1 is associated with shelterin complex at interstitial telomeric sites
Cited by: 6
Author(s): Aleksandar Ilić, Sumin Lu, Vikram Bhatia, Farhana Begum, Thomas Klonisch, Prasoon Agarwal, Wayne Xu, James R. Davie
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: over 9 years ago

10.1155/2017/8932583

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos
Cited by: 9
Author(s): Wenqing Jean Lee, Satadal Chatterjee, Sook Peng Yap, Siew Lan Lim, Xing Xing, Petra Kraus, Wenjie Sun, Xiaoming Hu, V. Sivakamasundari, Hsiao Yun Chan, Prasanna R. Kolatkar, Shyam Prabhakar, Thomas Lufkin
Software Mentions: 4
Published: over 7 years ago

10.1155/2020/9031723

Identification and Analysis of Estrogen Receptor <i>α</i> Promoting Tamoxifen Resistance-Related lncRNAs
Cited by: 11
Author(s): Xiulei Zhang, Shanjun Gao, Zhen Li, Wei Wang, Guangzhi Liu
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.21221

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice
Cited by: 45
Author(s): Jeroen Overman, Frank Fontaine, Mehdi Moustaqil, Deepak Mittal, Emma Sierecki, Natalia Sacilotto, Johannes Zuegg, Avril A. B. Robertson, Kelly A. Holmes, Angela A. Salim, Sreeman K. Mamidyala, Mark S. Butler, Ashley Robinson, Emmanuelle Lesieur, Wayne A. Johnston, Kirill Alexandrov, Brian L. Black, Benjamin M. Hogan, Sarah De Val, Robert J. Capon, Jason S. Carroll, Timothy L. Bailey, Peter Koopman, Ralf Jauch, Mark J. Smyth, Matthew A. Cooper, Yann Gambin, Mathias François
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.36435

Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters
Cited by: 8
Author(s): Ryo Nabeshima, Osamu Nishimura, Takako Maeda, Nobujiro Shimizu, Takahiro Ide, Kenta Yashiro, Yasuo Sakai, Chikara Meno, Mitsutaka Kadota, Hidetaka Shiratori, Shigehiro Kuraku, Hiroshi Hamada
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40478-021-01135-4

C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation
Cited by: 14
Author(s): Tatsuya Ozawa, Syuzo Kaneko, Frank Szulzewsky, Zhiwei Qiao, Mutsumi Takadera, Yoshitaka Narita, Tadashi Kondo, Eric C. Holland, Ryuji Hamamoto, Koichi Ichimura
Software Mentions: 4
Published: about 3 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

10.4049/jimmunol.1602033

Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells
Cited by: 45
Author(s): Ruth Brignall, Pierre Cauchy, Sarah L Bevington, Bethany Gorman, Angela Oliveira Pisco, James Bagnall, Christopher Boddington, William Rowe, Hazel England, Kevin Rich, Lorraine Schmidt, Nigel P. Dyer, Mark A. Travis, Sascha Ott, Dean A. Jackson, Peter N. Cockerill, Pawel Paszek
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5779-x

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function
Cited by: 39
Author(s): Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka, John A. Capra
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-020-00973-8

5-Hydroxymethylcytosine profiles of cfDNA are highly predictive of R-CHOP treatment response in diffuse large B cell lymphoma patients
Cited by: 9
Author(s): Hangyu Chen, Weilong Zhang, Lei Zhang, Ping Yang, Fang Li, Zeruo Yang, Jing Wang, Pei Meng, Yun Hong, Changjian Yan, Wei Li, Jia Liu, Nuo Xu, Long Chen, Xiu-Bing Xiao, Yan Qin, Xiaohong He, Hui Liu, Haichuan Zhu, Chuan He, Jian Lin, Hongmei Jing
Software Mentions: 4
Published: over 3 years ago

10.1016/j.ydbio.2015.04.010

Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern
Cited by: 7
Author(s): Tomasz M. Kuliński, M. Rita T. Casari, Philipp M. Guenzl, D. Wenzel, Daniel Andergassen, Anastasiya Hladik, Paul Datlinger, Matthias Farlik, Hans-Christian Theussl, Josef Penninger, Sylvia Knapp, Christoph Bock, Denise P. Barlow, Quanah J. Hudson
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.08007

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome
Cited by: 129
Author(s): Yoong Wearn Lim, Lionel A. Sanz, Xiaoqin Xu, Stella R. Hartono, Frédéric Chédin
Software Mentions: 4
Published: almost 9 years ago

10.7150/thno.47830

LncRNA DSCAM-AS1 interacts with YBX1 to promote cancer progression by forming a positive feedback loop that activates FOXA1 transcription network
Cited by: 68
Author(s): Yin Zhang, Yong-Xin Huang, Dan-Lan Wang, Bing Yang, Haiyan Yan, Lehang Lin, Yun Li, Jie Chen, Lisha Xie, Yongsheng Huang, Jian-You Liao, Kaishun Hu, Jun He, Phei Er Saw, Xiaoding Xu, Yin Ding
Software Mentions: 4
Published: over 4 years ago

10.1016/j.celrep.2019.11.093

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

10.1038/s42003-021-02097-y

Multi Locus View: an extensible web-based tool for the analysis of genomic data.
Cited by: 3
Author(s): Martin J. Sergeant, Jim R. Hughes, Lance D. Hentges, Gerton Lunter, Damien J. Downes, Stephen Taylor
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0238546

MITF and TFEB cross-regulation in melanoma cells
Cited by: 12
Author(s): Josué Ballesteros‐Álvarez, Ramile Dilshat, Valerie Fock, Katrín Möller, Ludwig Karl, Lionel Larue, Margrét H. Ögmundsdóttir, Eirı́kur Steingrı́msson
Software Mentions: 4
Published: over 3 years ago

10.1016/j.celrep.2013.08.012

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency
Cited by: 95
Author(s): George E. Gentsch, Nick Owens, Stephen R. Martin, Paul Piccinelli, Tiago Faial, Matthew Trotter, Michael J. Gilchrist, James C. Smith
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-018-31371-z

Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440
Cited by: 37
Author(s): Esther Blanco-Romero, Miguel Redondo‐Nieto, Francisco Martínez‐Granero, Daniel Garrido‐Sanz, Marı́a Isabel Ramos-González, Marta Martín, Rafael Rivilla
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1004890

Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation
Cited by: 41
Author(s): Jacob C. Ulirsch, Jessica Lacy, Xiuli An, Narla Mohandas, Tarjei S. Mikkelsen, Vijay G. Sankaran
Software Mentions: 4
Published: over 9 years ago

10.1016/j.celrep.2018.07.026

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

10.1186/1756-8935-7-26

Protection of CpG islands against de novo DNA methylation during oogenesis is associated with the recognition site of E2f1 and E2f2
Cited by: 23
Author(s): Heba Saadeh, Reiner Schulz
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1003748

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression
Cited by: 91
Author(s): Mathilde Paris, Tommy Kaplan, Xiao Yong Li, Jacqueline E. Villalta, Susan E. Lott, Michael B. Eisen
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pgen.1004595

The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription
Cited by: 26
Author(s): Aamna K Kaul, Eugene F. Schuster, Barbara Jennings
Software Mentions: 4
Published: over 9 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pgen.1002658

Dynamic Deposition of Histone Variant H3.3 Accompanies Developmental Remodeling of the Arabidopsis Transcriptome
Cited by: 113
Author(s): Heike Wollmann, Sarah Holec, Keith Alden, Neil D. Clarke, Pierre-Étienne Jacques, Frédéric Berger
Software Mentions: 4
Published: about 12 years ago

10.1016/j.devcel.2016.08.013

Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis
Cited by: 61
Author(s): Stefano Bencivenga, Antonio Serrano-Mislata, Maxwell S. Bush, Samantha Fox, Robert Sablowski
Software Mentions: 4
Published: over 7 years ago

10.1084/jem.20150907

Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells
Cited by: 76
Author(s): Alejandro V. Villarino, Giuseppe Sciumè, Fred P. Davis, S. Iwata, Beatrice Zitti, Gertraud W. Robinson, Lothar Hennighausen, Yuka Kanno, John J. O’Shea
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.21697

Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ
Cited by: 43
Author(s): Lorenzo Rinaldi, Alexandra Avgustinova, Mercé Martı́n, Debayan Datta, Guiomar Solanas, Neus Prats, Salvador Aznar Benitah
Software Mentions: 4
Published: about 7 years ago

10.1038/s41421-018-0027-0

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

10.1038/celldisc.2015.45

Mapping gene regulatory circuitry of Pax6 during neurogenesis
Cited by: 56
Author(s): Sudhir Thakurela, Neha Tiwari, Sandra Schick, Angela Garding, Robert Ivánek, Benedikt Berninger, Vijay Tiwari
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-00267-9

Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis
Cited by: 12
Author(s): Anthony R. Soltis, Shmulik Motola, Santiago Vérnia, Christopher Ng, Norman J. Kennedy, Simona Dalin, Bryan J. Matthews, Roger J. Davis, Ernest Fraenkel
Software Mentions: 4
Published: about 7 years ago

10.1186/s12920-015-0139-4

Genome-wide DNA methylome reveals the dysfunction of intronic microRNAs in major psychosis
Cited by: 27
Author(s): Hongying Zhao, Jiu Hua Xu, Lin Pang, Yunpeng Zhang, Huihui Fan, Ling Liu, Tingting Liu, Fulong Yu, Guanxiong Zhang, Yujia Lan, Jing Bai, Xia Li, Yun Xiao
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-019-5709-y

Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data
Cited by: 53
Author(s): Hamid Beiki, Haibo Li, Jinrong Huang, Nancy Manchanda, D. Nonneman, Timothy P. L. Smith, James M. Reecy, Christopher K. Tuggle
Software Mentions: 4
Published: about 5 years ago

10.26508/lsa.202000944

In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord blood
Cited by: 6
Author(s): Louis Legoff, Shereen Cynthia D’Cruz, Katia Bouchekhchoukha, Christine Monfort, Christian Jaulin, Luc Multigner, Fátima Smagulova
Software Mentions: 4
Published: about 3 years ago

10.1038/s41419-018-0841-1

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

10.1038/s41598-017-03665-1

Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem
Cited by: 20
Author(s): Steven G. Hussey, Mattheus Theodor Loots, Karen Van der Merwe, Eshchar Mizrachi, Alexander Andrew Myburg
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41419-021-03826-1

Gata2-L359V impairs primitive and definitive hematopoiesis and blocks cell differentiation in murine chronic myelogenous leukemia model
Cited by: 7
Author(s): Yanbin Fu, Yun Tan, Baichang Wu, Yuting Dai, Xiaoguang Xu, Mengmeng Pan, Zhiwei Chen, Na Qiao, Jing Wu, Lu Jiang, Jing Lu, Bing Chen, Avigail Rein, Shai Izraeli, Xiao Jian Sun, Jinyan Huang, Qiu-Hua Huang, Zhu Chen, Sai‐Juan Chen
Software Mentions: 4
Published: almost 3 years ago

10.1186/1471-2164-16-S7-S13

MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures
Cited by: 6
Author(s): Yizhe Zhang, Yiping He, Guangyong Zheng, Chaochun Wei
Software Mentions: 4
Published: almost 9 years ago

10.1038/srep09027

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

10.1186/s12859-015-0834-3

MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis
Cited by: 1
Author(s): Sini Rautio, Harri Lähdesmäki
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-07757-w

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Cited by: 63
Author(s): Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.cell.2013.03.012

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3
Cited by: 288
Author(s): Joerg Betschinger, Jennifer Nichols, Sabine Dietmann, Philip Corrin, Patrick J. Paddison, Austin Smith
Software Mentions: 4
Published: about 11 years ago

10.1126/sciadv.abe3516

Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor
Cited by: 37
Author(s): Kang Wang, Honghong Wang, Conghui Li, Zhenggang Yin, Ran Xiao, Qiuzi Li, Xiaofang Ying, Wen Wang, Jian Huang, Liang Chen, Pingping Fang, Kaiwei Liang
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pgen.1007123

Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish
Cited by: 4
Author(s): Napo K. M. Cheung, Ryohei Nakamura, Ayako Uno, Masahiko Kumagai, Harumi Fukushima, Shinichi Morishita, Hiroyuki Takeda
Software Mentions: 4
Published: over 6 years ago

10.1126/sciadv.abf7346

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

10.1371/journal.pgen.1002676

LINT, a Novel dL(3)mbt-Containing Complex, Represses Malignant Brain Tumour Signature Genes
Cited by: 30
Author(s): Karin Meier, Eve-Lyne Mathieu, Florian Finkernagel, L. Maximilian Reuter, Maren Scharfe, Gunther Doehlemann, Michael Jarek, Alexander Brehm
Software Mentions: 4
Published: about 12 years ago

10.3390/cancers11101533

17β-Estradiol Activates HSF1 via MAPK Signaling in ERα-Positive Breast Cancer Cells
Cited by: 22
Author(s): Natalia Vydra, Patryk Janus, Agnieszka Toma-Jonik, Tomasz Stokowy, Katarzyna Mrowiec, Joanna Korfanty, Anna Długajczyk, Bartosz Wojtaś, Bartłomiej Gielniewski, Wiesława Widłak
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0094164

From Human Monocytes to Genome-Wide Binding Sites - A Protocol for Small Amounts of Blood: Monocyte Isolation/ChIP-Protocol/Library Amplification/Genome Wide Computational Data Analysis
Cited by: 4
Author(s): Sebastian Weiterer, Florian Uhle, Sabin Bhuju, Michael Jarek, Markus A. Weigand, Marek Bartkuhn
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pgen.1006828

p63 exerts spatio-temporal control of palatal epithelial cell fate to prevent cleft palate
Cited by: 34
Author(s): Rose Richardson, Karen S. Mitchell, Nigel L. Hammond, Maria Rosaria Mollo, Evelyn N. Kouwenhoven, Niki Wyatt, Ian J. Donaldson, Leo Zeef, Tim Burgis, Rognvald Blance, Simon J. van Heeringen, Hendrik G. Stunnenberg, Huiqing Zhou, Caterina Missero, Rose Anne Romano, Satrajit Sinha, Michael J. Dixon, Jill Dixon
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0065598

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
Cited by: 292
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J. Nestler
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pgen.1005457

Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration
Cited by: 65
Author(s): Kfir Baruch Umansky, Yael Gruenbaum-Cohen, Michael Tsoory, Ester Feldmesser, Dalia Goldenberg, Ori Brenner, Yoram Groner
Software Mentions: 4
Published: almost 9 years ago

10.3390/cancers12030709

Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia
Cited by: 30
Author(s): Elise Aasebø, Frode S. Berven, Sushma Bartaula-Brevik, Tomasz Stokowy, Randi Hovland, Marc Vaudel, Stein Ove Døskeland, Emmet McCormack, Tanveer S. Batth, Jesper V. Olsen, Øystein Bruserud, Frode Selheim, Maria Hernandez-Valladares
Software Mentions: 4
Published: about 4 years ago

10.1093/gigascience/giy080

A workflow for simplified analysis of ATAC-cap-seq data in R
Cited by: 5
Author(s): Ram Krishna Shrestha, Pingtao Ding, Jonathan D. G. Jones, Dan MacLean
Software Mentions: 4
Published: almost 6 years ago

10.1074/jbc.RA120.015896

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation
Cited by: 21
Author(s): Fabiana Passaro, Ilaria De Martino, Federico Zambelli, Giorgia Di Benedetto, Matteo Barbato, Anna Maria D’Erchia, Caterina Manzari, Graziano Pesole, Margherita Mutarelli, Davide Cacchiarelli, Dario Antonini, Silvia Parisi, Tommaso Russo
Software Mentions: 4
Published: over 3 years ago

10.1172/JCI96138

REVERBa couples the circadian clock to hepatic glucocorticoid action
Cited by: 69
Author(s): Giorgio Caratti, Mudassar Iqbal, Louise Hunter, Dong Hwan Kim, Ping Wang, Ryan Vonslow, Nicola Begley, Abigail J. Tetley, Joanna Woodburn, Marie Pariollaud, Robert Maidstone, Ian J. Donaldson, Zhenguang Zhang, Louise Ince, Gareth Kitchen, Matthew Baxter, Toryn Poolman, Dion A. Daniels, David R. Stirling, Chad Brocker, Frank J. Gonzalez, A. S. I. Loudon, David A. Bechtold, Magnus Rattray, Laura Matthews, David Ray
Software Mentions: 4
Published: over 5 years ago

10.1126/sciadv.abf9808

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

10.1371/journal.pcbi.1003246

dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
Cited by: 13
Author(s): Dongjun Chung, Dan Park, Kevin S. Myers, Jeffrey A. Grass, Patricia J. Kiley, Robert Landick, Sündüz Keleş
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2105-14-188

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking
Cited by: 14
Author(s): George Y. Wu, Hongkai Ji
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13059-021-02390-3

Transcription shapes DNA replication initiation to preserve genome integrity
Cited by: 17
Author(s): Yang Liu, Chen Ai, Tingting Gan, Jinchun Wu, Yongpeng Jiang, Xuhao Liu, Ru-Sen Lu, Ning Gao, Qing Li, Ji Xiong, Jiazhi Hu
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0067134

Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia
Cited by: 57
Author(s): Carolyn Glass, Charles A. Wuertzer, Xiaohui Cui, Yingtao Bi, Ramana V. Davuluri, Ying Yi Xiao, Michael P. Wilson, Kristina M. Owens, Yi Zhang, Archibald S. Perkins
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13059-020-01973-w

Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9
Cited by: 27
Author(s): Xin Liu, Yong Chen, Yuannyu Zhang, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang, Jian Xu
Software Mentions: 4
Published: about 4 years ago

10.1186/s13059-015-0617-1

CopywriteR: DNA copy number detection from off-target sequence data
Cited by: 169
Author(s): Thomas Kuilman, Arno Velds, Kristel Kemper, Marco Ranzani, Lorenzo Bombardelli, Marlous Hoogstraat, Ekaterina Nevedomskaya, Guotai Xu, Julian de Ruiter, Martijn P. Lolkema, Bauke Ylstra, Jos Jonkers, Sven Rottenberg, Lodewyk F.A. Wessels, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
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

10.1371/journal.pone.0221760

Population size estimation for quality control of ChIP-Seq datasets
Cited by: 4
Author(s): Semyon Kolmykov, Yury V. Kondrakhin, Ivan S. Yevshin, Ruslan N. Sharipov, Anna S. Ryabova, Fedor A. Kolpakov
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-017-1159-5

RNF40 regulates gene expression in an epigenetic context-dependent manner
Cited by: 38
Author(s): Wanhua Xie, Sankari Nagarajan, Simon J. Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri, Steven A. Johnsen
Software Mentions: 4
Published: over 7 years ago

10.1186/s12915-018-0569-5

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance
Cited by: 16
Author(s): Jessica M Stringer, Samuel C. Forster, Zhibo Qu, Lexie Prokopuk, Moira K O'Bryan, David K. Gardner, Stefan J. White, David L. Adelson, Patrick Western
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-6687-9

Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties
Cited by: 2
Author(s): Jing Jin, Ximiao He, Elena M. Silva
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1003326

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Cited by: 228
Author(s): Timonthy Bailey, Paweł Krajewski, István Ladunga, Céline Lefèbvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-014-0536-6

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning
Cited by: 41
Author(s): Sarah D. Diermeier, Petros Kolovos, Leonhard Heizinger, Uwe Schwartz, Theodore Georgomanolis, Anne Zirkel, Gero Wedemann, Frank Grosveld, Tobias Knoch, Rainer Merkl, Peter R. Cook, Gernot Längst, Argyris Papantonis
Software Mentions: 4
Published: over 9 years ago

10.1111/acel.12479

Characterization of the direct targets of <scp>FOXO</scp> transcription factors throughout evolution
Cited by: 158
Author(s): Ashley E. Webb, Anshul Kundaje, Anne Brunet
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-019-1894-x

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Cited by: 76
Author(s): Elissavet Kentepozidou, Sarah J. Aitken, Christine Feig, Klara Stefflova, Ximena Ibarra-Soria, Duncan T. Odom, Maša Roller, Paul Flicek
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-017-1698-5

NaviSE: superenhancer navigator integrating epigenomics signal algebra
Cited by: 5
Author(s): Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J. Araúzo-Bravo
Software Mentions: 4
Published: almost 7 years ago

10.1186/gb-2014-15-2-r32

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: over 10 years ago

10.1590/1678-4685-GMB-2017-0164

Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells
Cited by: 5
Author(s): Zhizhong Gong, Jianyun Liu, Xin Xie, Xiaoyuan Xu, Ping Wu, Huimin Li, Yaqin Wang, Weidong Li, Jianjun Xiong
Software Mentions: 4
Published: almost 6 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

10.1186/s12915-020-00793-5

Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns
Cited by: 28
Author(s): Yang Zhou, Shuli Liu, Yan Hu, Lingzhao Fang, Yahui Gao, Han Xia, Steven G. Schroeder, Benjamin D. Rosen, Erin E. Connor, Congjun Li, R.L. Baldwin, John B. Cole, Curtis P. Van Tassell, Liguo Yang, Li Ma, George E. Liu
Software Mentions: 4
Published: almost 4 years ago

10.1186/gb-2013-14-12-r147

Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties
Cited by: 77
Author(s): Aurélien A. Sérandour, Gordon D. Brown, Joshua D. Cohen, Jason S. Carroll
Software Mentions: 4
Published: over 11 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

10.3389/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

10.1371/journal.pone.0093873

CMT: A Constrained Multi-Level Thresholding Approach for ChIP-Seq Data Analysis
Cited by: 3
Author(s): Iman Rezaeian, Luis Rueda
Software Mentions: 4
Published: about 10 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

10.1371/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

10.1186/1471-2105-13-176

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding
Cited by: 9
Author(s): Karl Kornacker, Morten Rye, Tony Håndstad, Finn Drabløs
Software Mentions: 4
Published: almost 12 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

10.1186/s12915-018-0585-5

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions
Cited by: 8
Author(s): Xinyi Yang, Martin Vingron
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0095875

The DNA Methylome and Transcriptome of Different Brain Regions in Schizophrenia and Bipolar Disorder
Cited by: 70
Author(s): Yun Xiao, Cynthia Camarillo, Yanyan Ping, Tania Bedard Arana, Hongying Zhao, Peter M. Thompson, Chaohan Xu, Bai-Horng Su, Huihui Fan, Javier Ordoñez, Li Wang, Chunxiang Mao, Yunpeng Zhang, Dianne A. Cruz, Michael Escamilla, Xia Li, Xu Chun
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0130379

A FOXM1 Dependent Mesenchymal-Epithelial Transition in Retinal Pigment Epithelium Cells
Cited by: 13
Author(s): Parul Choudhary, Benjamin T Dodsworth, Ben S. Sidders, Alex Gutteridge, Christos Michaelides, Joshua K. Duckworth, Paul J. Whiting, Caroline Benn
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pbio.2004986

Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids
Cited by: 10
Author(s): Ewa M. Michalak, Michael J. G. Milevskiy, Rachel Joyce, Johanna F. Dekkers, Paul Jamieson, Bhupinder Pal, Caleb A. Dawson, Yifang Hu, Stuart H. Orkin, Warren S. Alexander, Geoffrey J. Lindeman, Gordon K. Smyth, Jane E. Visvader
Software Mentions: 4
Published: almost 6 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/gb-2014-15-3-r52

Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis
Cited by: 120
Author(s): Hai Wu, Troy W. Whitfield, Jonathan A. R. Gordon, Jason R. Dobson, Phillip W. L. Tai, André J. van Wijnen, Janet L. Stein, Jane B. Lian
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.pgen.1006879

Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma
Cited by: 40
Author(s): Edward Britton, Connor Rogerson, Shaveta Mehta, Yaoyong Li, Xiaodun Li, Rebecca C. Fitzgerald, Yeng Ang, Andrew D Sharrocks
Software Mentions: 4
Published: over 6 years ago

10.1186/s13072-018-0252-7

Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia
Cited by: 14
Author(s): Sara Wernig-Zorc, Mukesh Yadav, Pradeep Kumar Kopparapu, Mats Bemark, Hallgerður Lind Kristjánsdóttir, Per‐Ola Andersson, Chandrasekhar Kanduri, Meena Kanduri
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-015-0671-8

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Cited by: 76
Author(s): Alaguraj Veluchamy, Achal Rastogi, Xin Lin, Bérangère Lombard, Omer Murik, Y. Thomas, Florent Dingli, Máximo Rivarola, Sandra Ott, Xinyue Liu, Yan Sun, Pablo D. Rabinowicz, James S. McCarthy, Andrew E. Allen, Damarys Loew, Chris Bowler, Leïla Tirichine
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pbio.3000153

Time-dependent Pax3-mediated chromatin remodeling and cooperation with Six4 and Tead2 specify the skeletal myogenic lineage in developing mesoderm
Cited by: 17
Author(s): Alessandro Magli, June Baik, Lauren J. Mills, Il-Youp Kwak, Bridget S. Dillon, Ricardo Mondragón-González, David Stafford, Scott Swanson, Ron Stewart, James A. Thomson, Daniel J. Garry, Brian David Dynlacht, Rita C.R. Perlingeiro
Software Mentions: 4
Published: about 5 years ago

10.1186/s13072-015-0040-6

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships
Cited by: 127
Author(s): Julie Nadel, Rodoniki Athanasiadou, Christophe Lemetre, N. Ari Wijetunga, Pilib Ó Broin, Hanae Sato, Zhengdong Zhang, Jeffrey A. Jeddeloh, Cristina Montagna, Aaron Golden, Cathal Seoighe, John M. Greally
Software Mentions: 4
Published: over 8 years ago