cran: JASPAR | Projects | Ecosyste.ms: Papers

10.15252/msb.20209539

Predictive features of gene expression variation reveal mechanistic link with differential expression
Cited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: almost 4 years ago

10.1186/s13059-020-1929-3

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: over 4 years ago

10.12688/f1000research.18456.1

A step-by-step guide to analyzing CAGE data using R/Bioconductor
Cited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: almost 5 years ago

10.3389/fcell.2021.642724

Identification of Stemness-Related Genes for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma by Integrated Bioinformatics Analysis
Cited by: 5
Author(s): Hongjun Guo, Siqiao Wang, Min Kyung Ju, Penghui Yan, Weiwei Sun, Zhenyu Li, Siyu Wu, Ruoyi Lin, Shuyuan Xian, Daoke Yang, Jun Wang, Zongqiang Huang
Software Mentions: 15
Published: about 3 years ago

10.1136/jitc-2020-000705

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
Cited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: over 3 years ago

10.7554/eLife.07836

Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence
Cited by: 158
Author(s): Michael J. Steinbaugh, Sri Devi Narasimhan, Stacey Robida-Stubbs, Lorenza E Moronetti Mazzeo, Jonathan M. Dreyfuss, John M. Hourihan, Prashant Raghavan, Theresa N. Operaña, Reza Esmaillie, T. Keith Blackwell
Software Mentions: 13
Published: over 8 years ago

10.1186/s13059-021-02493-x

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish
Cited by: 7
Author(s): Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles Kaufman, Stephen L. Johnson, Ting Wang
Software Mentions: 12
Published: over 2 years ago

10.1186/s13059-020-02070-8

The regulatory landscape of early maize inflorescence development
Cited by: 28
Author(s): Rajiv Krishna Parvathaneni, Edoardo Bertolini, Md. Shamimuzzaman, Daniel Vera, Pei Yau Lung, Brian R. Rice, Jinfeng Zhang, Patrick J. Brown, Alexander E. Lipka, Hank W. Bass, Andrea L. Eveland
Software Mentions: 12
Published: almost 4 years ago

10.1371/journal.pone.0016432

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: about 13 years ago

10.1038/s41598-017-02464-y

UROPA: a tool for Universal RObust Peak Annotation
Cited by: 38
Author(s): Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
Software Mentions: 11
Published: almost 7 years ago

10.1186/1471-2164-9-419

Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse
Cited by: 74
Author(s): Paul C. Boutros, Rui Yan, Ivy D. Moffat, Raimo Pohjanvirta, Allan B. Okey
Software Mentions: 11
Published: over 16 years ago

10.12688/f1000research.17976.2

TFutils: Data structures for transcription factor bioinformatics
Cited by: 2
Author(s): Benjamin J. Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin A. Raby, Vincent J. Carey
Software Mentions: 10
Published: almost 5 years ago

10.1093/bioinformatics/btaa073

<i>Coolpup.py:</i> versatile pile-up analysis of Hi-C data
Cited by: 86
Author(s): Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pone.0018337

mRNA Levels in Control Rat Liver Display Strain-Specific, Hereditary, and AHR-Dependent Components
Cited by: 7
Author(s): Paul C. Boutros, Ivy D. Moffat, Allan B. Okey, Raimo Pohjanvirta
Software Mentions: 9
Published: almost 13 years ago

10.7554/eLife.54756

ATR expands embryonic stem cell fate potential in response to replication stress
Cited by: 34
Author(s): Sina Atashpaz, Sara Samadi Shams, Javier Martín‐González, Endre Sebestyén, Negar Arghavanifard, Andrea Gnocchi, Eliene Albers, Simone Minardi, Giovanni Fagà, Paolo Soffientini, E. Allievi, Valeria Cancila, Ángela Bachi, Óscar Fernández-Capetillo, Claudio Tripodo, Francesco Ferrari, Andrés J. López-Contreras, Vincenzo Costanzo
Software Mentions: 9
Published: about 4 years ago

10.26508/lsa.202000794

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
Cited by: 5
Author(s): Elisa Redl, Raheleh Sheibani-Tezerji, Crhistian de Jesus Cardona, Patricia Hamminger, Gerald Timelthaler, Melanie R. Hassler, Maša Zrimšek, Sabine Lagger, Thomas Dillinger, Lorena Hofbauer, Kristina Draganić, Andreas Tiefenbacher, Michael Kothmayer, C. Dietz, Bernard Ramsahoye, Lukas Kenner, Christoph Bock, Christian Seiser, Wilfried Ellmeier, Gabriele Schweikert, Gerda Egger
Software Mentions: 9
Published: over 3 years ago

10.26508/lsa.202000658

Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.39380

Intergenerational epigenetic inheritance of cancer susceptibility in mammals
Cited by: 38
Author(s): Bluma J. Lesch, Zuzana Tóthová, Elizabeth A. Morgan, Zhicong Liao, Roderick T. Bronson, Benjamin L. Ebert, David C. Page
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pgen.1006883

Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses
Cited by: 108
Author(s): Jumpei Ito, Ryota Sugimoto, Hirofumi Nakaoka, Shiro Yamada, Tetsuaki Kimura, Takahide Hayano, Ituro Inoue
Software Mentions: 8
Published: almost 7 years ago

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: over 3 years ago

10.1016/j.cell.2017.04.013

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension
Cited by: 607
Author(s): Judith H.I. Haarhuis, Robin H. van der Weide, Vincent A. Blomen, J. Omar Yáñez-Cuna, Mario Amendola, Marjon S. van Ruiten, Peter H.L. Krijger, Hans Teunissen, René H. Medema, Bas van Steensel, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Software Mentions: 8
Published: about 7 years ago

10.1016/j.celrep.2019.10.018

Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells
Cited by: 91
Author(s): Christopher Piper, Elizabeth C. Rosser, Kristīne Oļeiņika, Kiran Nistala, Thomas Krausgruber, André F. Rendeiro, Aggelos Banos, Ignat Drozdov, Matteo Villa, Scott Thomson, Georgina Xanthou, Christoph Bock, Brigitta Stockinger, Claudia Mauri
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.52690

Sphingosine 1-phosphate-regulated transcriptomes in heterogenous arterial and lymphatic endothelium of the aorta
Cited by: 28
Author(s): Eric Engelbrecht, Michel V. Levesque, Liqun He, Michael Vanlandewijck, Anja Nitzsche, Hira Niazi, Andrew Kuo, Sasha A Singh, Masamichi Aikawa, Kristina M. Holton, Richard L. Proia, Mari Kono, William T. Pu, Eric Camerer, Christer Betsholtz, Timothy Hla
Software Mentions: 8
Published: about 4 years ago

10.1186/s12864-021-07760-6

UniBind: maps of high-confidence direct TF-DNA interactions across nine species
Cited by: 31
Author(s): Rafael Riudavets Puig, Paul Boddie, Aziz Khan, Jaime A Castro-Mondragón, Anthony Mathelier
Software Mentions: 8
Published: almost 3 years ago

10.1038/srep38411

Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians
Cited by: 34
Author(s): Ming Zhao, Jian Qin, Hang Yin, Yixin Tan, Wei Liao, Qian Liu, Shuangyan Luo, Min He, Gongping Liang, Yajing Shi, Qing Zhang, Wenjun Cai, Guangliang Yin, Yin Zhou, Jing Wang, Mengying Li, Yi Huang, Aiyun Liu, Haijian Wu, Zhiyong Zhang, Qianjin Lu
Software Mentions: 8
Published: over 7 years ago

10.1093/database/baz046

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data
Cited by: 621
Author(s): Oscar Franzén, Li‐Ming Gan, Johan Björkegren
Software Mentions: 8
Published: over 5 years ago

10.1186/1471-2164-12-507

Chipster: user-friendly analysis software for microarray and other high-throughput data
Cited by: 294
Author(s): M Aleksi Kallio, Jarno Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, M.K. Koski, Janne Käki, Eija Korpelainen
Software Mentions: 8
Published: over 12 years ago

10.1186/s13059-020-02075-3

Single-cell ATAC-seq signal extraction and enhancement with SCATE
Cited by: 29
Author(s): Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji
Software Mentions: 8
Published: almost 4 years ago

10.1038/srep35903

Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia
Cited by: 59
Author(s): Zi Yi Wan, Jun Xia, Grace Lin, Le Wang, Valerie Chun Ling Lin, Gen Hua Yue
Software Mentions: 8
Published: over 7 years ago

10.1038/s41598-019-40503-y

Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions
Cited by: 23
Author(s): Quen J. Cheng, Faraz Behzadi, Supriya Sen, Sho Ohta, Roberto Spreafico, Rosane M. B. Teles, Robert L. Modlin, Alexander Hoffmann
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pgen.1006995

Environmental perturbations lead to extensive directional shifts in RNA processing
Cited by: 24
Author(s): Allison L. Richards, Donovan Watza, Anthony Findley, Adnan Alazizi, Xiaoquan Wen, Athma A. Pai, Roger Piqué-Regi, Francesca Luca
Software Mentions: 8
Published: over 6 years ago

10.1002/ctm2.422

Single‐cell analyses reveal suppressive tumor microenvironment of human colorectal cancer
Cited by: 37
Author(s): Mei Yan, Weiwei Xiao, Hao Hu, Guan-Ming Lu, Lingdan Chen, Zhun Sun, Mengdie Lü, Wenhui Ma, Ting Jiang, Yuanhong Gao, LiRen Li, Gong Chen, Zifeng Wang, Hanjie Li, Duojiao Wu, Ping‐Hong Zhou, Qibin Leng, Guangshuai Jia
Software Mentions: 8
Published: almost 3 years ago

10.1007/s12559-020-09773-x

Deep Learning in Mining Biological Data
Cited by: 197
Author(s): Mufti Mahmud, M. Shamim Kaiser, TM McGinnity, Amir Hussain
Software Mentions: 7
Published: over 3 years ago

10.3389/fnins.2021.682247

Decreased MEF2A Expression Regulated by Its Enhancer Methylation Inhibits Autophagy and May Play an Important Role in the Progression of Alzheimer’s Disease
Cited by: 8
Author(s): Hui Li, Rui Wang, Xuqi Guo, Yugang Jiang
Software Mentions: 7
Published: almost 3 years ago

10.7554/eLife.59610

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Cited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.59067

Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development
Cited by: 11
Author(s): Ryan J Geusz, Allen Wang, Joshua Chiou, Joseph J. Lancman, Nichole Wetton, Samy Kefalopoulou, Jinzhao Wang, Yunjiang Qiu, Jian Yan, Anthony Aylward, Bing Ren, Peng Dong, Kyle J. Gaulton, Maike Sander
Software Mentions: 7
Published: over 3 years ago

10.1002/jev2.12127

Inflammasome‐induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses
Cited by: 26
Author(s): Christina F. Budden, Linden J. Gearing, Romina Kaiser, Lena Standke, Paul J. Hertzog, Eicke Latz
Software Mentions: 7
Published: almost 3 years ago

10.1186/s12859-021-04126-3

Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources
Cited by: 6
Author(s): Neel Patel, William S. Bush
Software Mentions: 7
Published: about 3 years ago

10.3389/fcell.2021.688798

QSOX2 Is an E2F1 Target Gene and a Novel Serum Biomarker for Monitoring Tumor Growth and Predicting Survival in Advanced NSCLC
Cited by: 3
Author(s): Yaqi Li, Mei Liu, Zhuoxian Zhang, Libin Deng, Zhenyu Zhai, Hua Liu, Yiting Wang, Cheng Zhang, Jianping Xiong, Chao Shi
Software Mentions: 7
Published: almost 3 years ago

10.15252/msb.20167507

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation
Cited by: 43
Author(s): Margaux Michel, Carina Demel, Benedikt Zacher, Björn Schwalb, Stefan Krebs, Helmut Blum, Julien Gagneur, Patrick Cramer
Software Mentions: 7
Published: about 7 years ago

10.1186/1745-6150-9-4

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data
Cited by: 48
Author(s): Ngoc Tam L. Tran, Chun-Hsi Huang
Software Mentions: 7
Published: over 10 years ago

10.1038/s41598-019-55453-8

MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment
Cited by: 2
Author(s): Andigoni Malousi, Sofia Kouidou, Maria Tsagiopoulou, Nikos Papakonstantinou, Emmanouil Bouras, Elisavet Georgiou, Georgios Tzimagiorgis, Kostas Stamatopoulos
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-020-02049-5

Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping
Cited by: 13
Author(s): Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B. Fraser, Thomas Quertermous
Software Mentions: 7
Published: almost 4 years ago

10.26508/lsa.202101080

Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes
Cited by: 9
Author(s): Melissa Bothe, René Buschow, Sebastiaan H. Meijsing
Software Mentions: 7
Published: over 2 years ago

10.1186/s12862-015-0499-6

Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals
Cited by: 7
Author(s): Nathaniel J. Davies, Peter Krusche, Eran Tauber, Sascha Ott
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pgen.1008546

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation
Cited by: 53
Author(s): Máté Pálfy, G Schulze, Eivind Valen, Nadine L. Vastenhouw
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-020-03739-4

MEIRLOP: improving score-based motif enrichment by incorporating sequence bias covariates
Cited by: 5
Author(s): Nathaniel Delos Santos, Lorane Texari, Christopher Benner
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-82429-4

Molecular characterization of atherosclerosis in HIV positive persons
Cited by: 5
Author(s): Adam Cornwell, Rohith Palli, Meera V. Singh, Lauren Benoodt, Alicia Tyrell, Jun Abe, Giovanni Schifitto, Sanjay B. Maggirwar, Juilee Thakar
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2020.108545

CDK8 Fine-Tunes IL-6 Transcriptional Activities by Limiting STAT3 Resident Time at the Gene Loci
Cited by: 23
Author(s): Jonathan Martínez-Fábregas, Luopin Wang, Elizabeth Pöhler, Adeline Cozzani, Stephan Wilmes, Majid Kazemian, Suman Mitra, Ignacio Moraga
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2015.11.024

Differential DNA Methylation Analysis without a Reference Genome
Cited by: 35
Author(s): Johanna Klughammer, Paul Datlinger, Dieter Printz, Nathan C. Sheffield, Matthias Farlik, Johanna Hadler, Gerhard Fritsch, Christoph Bock
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pcbi.1003731

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
Cited by: 654
Author(s): Rekin’s Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval-Sánchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean‐Christophe Marine, Stein Aerts
Software Mentions: 6
Published: almost 10 years ago

10.15252/msb.20167435

Transcriptional regulatory networks underlying gene expression changes in Huntington's disease
Cited by: 51
Author(s): Seth A. Ament, Jocelynn Pearl, Jeffrey P. Cantle, Robert M. Bragg, Peter J. Skene, Sydney R. Coffey, Dani E Bergey, Vanessa C. Wheeler, Marcy E. MacDonald, Nitin S. Baliga, Jim Rosinski, Leroy Hood, Jeffrey B. Carroll, Nathan D. Price
Software Mentions: 6
Published: about 6 years ago

10.1186/s13073-016-0382-0

Non-coding single nucleotide variants affecting estrogen receptor binding and activity
Cited by: 5
Author(s): Amir Bahreini, Kevin M. Levine, Lucas Santana-Santos, Panayiotis V. Benos, Peilu Wang, Courtney Andersen, Steffi Oesterreich, Adrian V. Lee
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0004571

Transcription Factor Binding Sites Are Genetic Determinants of Retroviral Integration in the Human Genome
Cited by: 98
Author(s): Barbara Felice, Claudia Cattoglio, Davide Cittaro, Anna Testa, Annarita Miccio, G. Ferrari, Lucilla Luzi, Alessandra Recchia, Fulvio Mavilio
Software Mentions: 6
Published: about 15 years ago

10.1186/s12864-019-6061-y

Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks
Cited by: 12
Author(s): Jim A. Mossman, Leann M. Biancani, David M. Rand
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-016-1298-9

Evaluating tools for transcription factor binding site prediction
Cited by: 75
Author(s): Narayan Jayaram, Daniel Usvyat, Andrew C.R. Martin
Software Mentions: 6
Published: over 7 years ago

10.1186/s12864-015-1303-0

Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line
Cited by: 34
Author(s): Lauren A. Solomon, Stephen K. H. Li, Jan Piskorz, Li Xu, Rodney P. DeKoter
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0155802

Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis
Cited by: 6
Author(s): Bernard Fongang, Andrzej Kudlicki
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12859-020-3403-3

Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes
Cited by: 1
Author(s): Vasudha Sharma, Sharmistha Majumdar
Software Mentions: 6
Published: about 4 years ago

10.3390/v12111303

Human Endogenous Retrovirus K Rec Forms a Regulatory Loop with MITF that Opposes the Progression of Melanoma to an Invasive Stage
Cited by: 16
Author(s): Manvendra Singh, Huiqiang Cai, Mario Bunse, Cédric Feschotte, Zsuzsanna Izsvák
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-019-40697-1

Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control
Cited by: 3
Author(s): Petar Petrov, Alexey V Sarapulov, Lél Eöry, Cristina Scielzo, Lydia Scarfò, Jacqueline Smith, David W. Burt, Pieta K. Mattila
Software Mentions: 6
Published: about 5 years ago

10.1186/s13059-018-1589-8

Enhancers in the Peril lincRNA locus regulate distant but not local genes
Cited by: 20
Author(s): Abigail F. Groff, A. Rasim Barutcu, Jordan P. Lewandowski, John L. Rinn
Software Mentions: 6
Published: over 5 years ago

10.1093/bioinformatics/btz855

Improved linking of motifs to their TFs using domain information
Cited by: 1
Author(s): Nina Baumgarten, Florian Schmidt, Marcel H. Schulz
Software Mentions: 6
Published: over 4 years ago

10.1186/gb-2011-12-8-r83

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

10.3389/fpls.2019.00698

PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation
Cited by: 5
Author(s): Hongryul Ahn, Kyuri Jo, Dabin Jeong, Minwoo Pak, Jihye Hur, Wi Hoon Jung, Sun Kim
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12870-014-0315-2

The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes
Cited by: 8
Author(s): Gopal Misra, Piyush Priya, Nitesh Bandhiwal, Neha Bareja, Mukesh Jain, Sabhyata Bhatia, Debasis Chattopadhyay, Akhilesh K. Tyagi, Gitanjali Yadav
Software Mentions: 6
Published: over 9 years ago

10.3389/fgene.2016.00183

Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans
Cited by: 78
Author(s): Benjamin Mayne, Tina Bianco‐Miotto, Sam Buckberry, James Breen, Vicki L. Clifton, Cheryl Shoubridge, Claire T. Roberts
Software Mentions: 6
Published: over 7 years ago

10.3389/fcell.2021.583555

DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon
Cited by: 8
Author(s): Jolien Diddens, Louis Coussement, Carolina Frankl-Vilches, Gaurav Majumdar, Sandra Steyaert, Sita M. ter Haar, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Wim Van Criekinge, Charlotte Cornil, Jacques Balthazart, Annemie Van der Linden, Tim De Meyer, Wim Vanden Berghe
Software Mentions: 6
Published: about 3 years ago

10.3389/fimmu.2018.02120

Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development
Cited by: 18
Author(s): Adam E. Handel, Noriko Shikama-Dorn, Saule Zhanybekova, Stefano Maio, Annina N. Graedel, Saulius Žuklys, Chris P. Ponting, Georg A. Holländer
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.34077

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver
Cited by: 51
Author(s): Bryan J. Matthews, David J. Waxman
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pgen.1006231

Linking Core Promoter Classes to Circadian Transcription
Cited by: 7
Author(s): Pål O. Westermark
Software Mentions: 5
Published: almost 8 years ago

10.1152/ajpendo.00473.2013

Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice
Cited by: 289
Author(s): Meritxell Rosell, Myrsini Kaforou, Andrea Frontini, Anthony Okolo, Yi‐Wah Chan, Evanthia Nikolopoulou, Steven Millership, Matthew Fenech, David A. MacIntyre, J. Turner, Jonathan D. Moore, E. K. Blackburn, William J. Gullick, Saverio Cinti, Giovanni Montana, Malcolm G. Parker, Mark Christian
Software Mentions: 5
Published: about 10 years ago

10.7554/eLife.51325

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18
Cited by: 21
Author(s): Huan Liu, Kaylia Duncan, Annika Helverson, Priyanka Kumari, Camille Mumm, Yuchen Xiao, Jenna C. Carlson, Fabrice Darbellay, Axel Visel, Elizabeth J. Leslie, Patrick Breheny, Albert Erives, Robert A. Cornell
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-016-3288-8

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

10.1371/journal.pcbi.1009308

DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions
Cited by: 14
Author(s): Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphaël Mourad
Software Mentions: 5
Published: over 2 years ago

10.1371/journal.pcbi.1002638

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

10.3390/cells8101196

Genome-Wide Distribution of Nascent Transcripts in Sperm DNA, Products of a Late Wave of General Transcription
Cited by: 6
Author(s): Leila Kianmehr, Homayoun Khazali, Hassan Rajabi‐Maham, Ali Sharifi‐Zarchi, François Cuzin, Minoo Rassoulzadegan
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00323-18

Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation
Cited by: 62
Author(s): Allison L. Richards, Amanda L. Muehlbauer, Adnan Alazizi, Michael B. Burns, Anthony Findley, Francesco Messina, Trevor Gould, Camilla Cascardo, Roger Piqué-Regi, Ran Blekhman, Francesca Luca
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pbio.2006347

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

10.1371/journal.pcbi.1006982

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Cited by: 83
Author(s): Ivan Jurić, Miao Yu, Armen Abnousi, Ramya Raviram, Rongxin Fang, Yuan Zhao, Yanxiao Zhang, Yunjiang Qiu, Yuchen Yang, Yun Li, Bing Ren, Maowen Hu
Software Mentions: 5
Published: about 5 years ago

10.1016/j.celrep.2021.109101

Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation
Cited by: 18
Author(s): Nicholas T. Crump, Andreas V. Hadjinicolaou, Meng Xia, John Walsby-Tickle, Uzi Gileadi, Ji‐Li Chen, Mashiko Setshedi, Lars Rønn Olsen, I-Jun Lau, Laura Godfrey, Lynn Quek, Zhanru Yu, Erica Ballabio, Mike Bogetofte Barnkob, Giorgio Napolitani, Mariolina Salio, Hashem Koohy, Benedikt M. Kessler, Stephen Taylor, Paresh Vyas, James McCullagh, Thomas A. Milne, Vincenzo Cerundolo
Software Mentions: 5
Published: about 3 years ago

10.1038/s41598-020-69494-x

Immune network dysregulation precedes clinical diagnosis of asthma
Cited by: 3
Author(s): Yi-Shin Chang, Benjamin A. Turturice, Cody Schott, Patricia W. Finn, David L. Perkins
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12885-021-08362-x

Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours
Cited by: 2
Author(s): Bhavya Dhaka, Radhakrishnan Sabarinathan
Software Mentions: 5
Published: almost 3 years ago

10.1002/1878-0261.12726

Characterization of super‐enhancer‐associated functional lncRNAs acting as ceRNAs in ESCC
Cited by: 22
Author(s): Qiuyu Wang, Peng Liu, Chen Yang, Lian‐Di Liao, Jiaxin Chen, Meng Li, Yanyu Li, Fengcui Qian, Yuexin Zhang, Fan Wang, Chunquan Li, De–Chen Lin, Li‐Yan Xu, En‐Min Li
Software Mentions: 5
Published: almost 4 years ago

10.3390/cancers12082261

MiR-302b as a Combinatorial Therapeutic Approach to Improve Cisplatin Chemotherapy Efficacy in Human Triple-Negative Breast Cancer
Cited by: 12
Author(s): Alessandra Cataldo, Sandra Romero-Córdoba, Ilaria Plantamura, Giulia Cosentino, Alfredo Hidalgo‐Miranda, Elda Tagliabue, Marilena V. Iorio
Software Mentions: 5
Published: over 3 years ago

10.1186/s13073-021-00863-5

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

10.1038/s41598-018-25748-3

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9
Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-020-02129-6

sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression
Cited by: 16
Author(s): Yuan He, Surya B. Chhetri, Marios Arvanitis, Kaushik Srinivasan, François Aguet, Kristin Ardlie, Alvaro N. Barbeira, Rodrigo Bonazzola, Hae Kyung Im, Christopher D. Brown, Alexis Battle
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-020-02139-4

COCOA: coordinate covariation analysis of epigenetic heterogeneity
Cited by: 10
Author(s): John T. Lawson, Jason P. Smith, Stefan Bekiranov, Francine E. Garrett-Bakelman, Nathan C. Sheffield
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-021-02378-z

GRiNCH: simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization
Cited by: 14
Author(s): Da-Inn Lee, Sushmita Roy
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13059-019-1721-4

Chromatin accessibility plays a key role in selective targeting of Hox proteins
Cited by: 35
Author(s): Damiano Porcelli, Bettina Fischer, Steven Russell, Robert A. White
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-014-0560-6

Gateways to the FANTOM5 promoter level mammalian expression atlas
Cited by: 634
Author(s): Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J. Mungall, Peter Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D. Diehl, Emmanuel Dimont, Tom C. Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F. Meehan, Koro Nishikata, Ono Hiromasa, Michael Rehli, Albin Sandelin, Erik Schultes, Peter A.C. ’t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W. Wright, Carsten O. Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2164-15-472

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment
Cited by: 43
Author(s): Rebecca Worsley Hunt, Anthony Mathelier, Luis del Peso, Wyeth W. Wasserman
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13059-016-1057-2

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis
Cited by: 52
Author(s): Nina Koenecke, Jeff Johnston, Bjoern Gaertner, Malini Natarajan, Julia Zeitlinger
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-014-0494-z

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

10.3389/fcell.2020.593653

PECAM1 Combines With CXCR4 to Trigger Inflammatory Cell Infiltration and Pulpitis Progression Through Activating the NF-κB Signaling Pathway
Cited by: 10
Author(s): Liu Yong-hong, Zhiyong Zhang, Wenjing Li, Shaomin Tian
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1007289

Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity
Cited by: 14
Author(s): Arya Zandvakili, Ian K. Campbell, Lisa M. Gutzwiller, Matthew T. Weirauch, Brian Gebelein
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0179613

A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells
Cited by: 7
Author(s): Benjamin Ulfenborg, Alexander Karlsson, Maria Riveiro, Caroline Améen, Karolina Åkesson, Christian X. Andersson, Peter Sartipy, Jane Synnergren
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12859-020-03927-2

WACS: improving ChIP-seq peak calling by optimally weighting controls
Cited by: 2
Author(s): Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins
Software Mentions: 5
Published: about 3 years ago

10.3390/cancers11010101

SP1 and STAT3 Functionally Synergize to Induce the RhoU Small GTPase and a Subclass of Non-canonical WNT Responsive Genes Correlating with Poor Prognosis in Breast Cancer
Cited by: 16
Author(s): Emanuele Monteleone, Valeria Orecchia, Paola Corrieri, Davide Schiavone, Lidia Avalle, Enrico Moiso, Aurora Savino, Ivan Molineris, Paolo Provero, Valeria Poli
Software Mentions: 5
Published: over 5 years ago

Projects: cran: JASPAR

Papers Mentioning JASPAR 1,283