bioconductor: TFBSTools | Projects

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

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices
Cited by: 21
Author(s): Claudia Racioppi, Keira A Wiechecki, Lionel Christiaen
Software Mentions: 11
Published: over 4 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: about 7 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: about 5 years ago

10.1155/2021/1031906

Development of a Ferroptosis-Related lncRNA Signature to Predict the Prognosis and Immune Landscape of Bladder Cancer
Cited by: 14
Author(s): Ranran Zhou, Jingjing Liang, Haijun Tian, Qi Chen, Cheng Yang, Cundong Liu
Software Mentions: 10
Published: about 3 years ago

10.1093/gbe/evaa191

Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance
Cited by: 17
Author(s): Darci A. Giacomini, Eric Patterson, Anita Küpper, Roland Beffa, Todd A. Gaines, Patrick J. Tranel
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-019-6047-9

Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni
Cited by: 9
Author(s): Austin T. Hilliard, Dan Xie, Zhihai Ma, M Snyder, Russell D. Fernald
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13073-021-00908-9

scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks
Cited by: 16
Author(s): Ting Jin, Peter Rehani, Mufang Ying, Jiawei Huang, Shuang Liu, Panagiotis Roussos, Daifeng Wang
Software Mentions: 7
Published: about 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: over 7 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

10.1038/s41598-020-68879-2

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

10.1128/mBio.00971-19

Evolution of Superinfection Immunity in Cluster A Mycobacteriophages
Cited by: 48
Author(s): Travis N. Mavrich, Graham F. Hatfull
Software Mentions: 6
Published: about 5 years ago

10.3389/fonc.2021.637911

Phenotypic Plasticity Conferred by the Metastatic Microenvironment of the Brain Strengthens the Intracranial Tumorigenicity of Lung Tumor Cells
Cited by: 0
Author(s): Xin Wei, Kewei Bi, Bo Li
Software Mentions: 5
Published: about 3 years ago

10.3389/fcvm.2021.694238

AKR1C3 and Its Transcription Factor HOXB4 Are Promising Diagnostic Biomarkers for Acute Myocardial Infarction
Cited by: 7
Author(s): Jingjing Liang, Yue Cao, Minqiang He, Weiwen Li, Guan‐Jiang Huang, Tianyi Ma, Meijun Li, Yuli Huang, Xiaohui Huang, Yunzhao Hu
Software Mentions: 5
Published: almost 3 years ago

10.3389/fmolb.2020.00220

Hyperconserved Elements in Human 5′UTRs Shape Essential Post-transcriptional Regulatory Networks
Cited by: 4
Author(s): Paola Zuccotti, Daniele Peroni, Valentina Potrich, Alessandro Quattrone, Erik Dassi
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.65381

Evidence for additive and synergistic action of mammalian enhancers during cell fate determination
Cited by: 53
Author(s): Jinmi Choi, Kseniia Lysakovskaia, Grégoire Stik, Carina Demel, Johannes Söding, Tian V. Tian, Thomas Graf, Patrick Cramer
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms19010271

Integrated Analyses Reveal Overexpressed Notch1 Promoting Porcine Satellite Cells’ Proliferation through Regulating the Cell Cycle
Cited by: 21
Author(s): Yiren Jiao, Bo Huang, Yu Chen, Guang-liang Hong, Jian Xu, Chen Hu, Chong Wang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1008197

Novel protective and risk loci in hip dysplasia in German Shepherds
Cited by: 8
Author(s): Lea Mikkola, Saila Holopainen, Anu K. Lappalainen, Tiina Pessa‐Morikawa, Thomas Pulikotial Augustine, Meharji Arumilli, Marjo K. Hytönen, Osmo Hakosalo, Hannes Lohi, Antti Iivanainen
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2021.628192

KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs
Cited by: 7
Author(s): Tao Wang, Yuanyuan Guo, Shengwei Liu, Chaoxin Zhang, Tongyan Cui, Kun Ding, Peng Wang, Xibiao Wang, Zhipeng Wang
Software Mentions: 4
Published: over 3 years ago

10.1186/s12711-021-00643-0

Genetic variation in recombination rate in the pig
Cited by: 15
Author(s): Martin Johnsson, Andrew Whalen, Roger Ros‐Freixedes, Gregor Gorjanc, Ching-Yi Chen, William Herring, Dirk-Jan de Koning, John M. Hickey
Software Mentions: 4
Published: about 3 years ago

10.1093/gbe/evy041

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee
Cited by: 19
Author(s): Jason Pizzollo, William Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E. Crawford, Gregory A. Wray, Courtney C. Babbitt
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-17730-2

Constitutively elevated levels of SOCS1 suppress innate responses in DF-1 immortalised chicken fibroblast cells
Cited by: 28
Author(s): Efstathios S. Giotis, CS Ross, RC Robey, Axel Nohturfft, Stephen Goodbourn, Michael A. Skinner
Software Mentions: 3
Published: over 6 years ago

10.1093/database/bav007

PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples
Cited by: 3
Author(s): Yiyu Zheng, Xiaoman Li, Haiyan Hu
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1009090

A genetic variant controls interferon-β gene expression in human myeloid cells by preventing C/EBP-β binding on a conserved enhancer
Cited by: 2
Author(s): Anaïs Assouvie, Maxime Rotival, Juliette Hamroune, Didier Busso, Paul-Henri Roméo, Lluís Quintana‐Murci, Germain Rousselet
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008659

A putative silencer variant in a spontaneous canine model of retinitis pigmentosa
Cited by: 9
Author(s): Maria Kaukonen, Ileana B. Quintero, Abdul Kadir Mukarram, Marjo K. Hytönen, Saila Holopainen, Kaisa Wickström, Kaisa Kyöstilä, Meharji Arumilli, Sari Jalomäki, Carsten O. Daub, Juha Kere, Hannes Lohi
Software Mentions: 3
Published: over 4 years ago

10.1093/bioinformatics/btw024

TFBSTools: an R/bioconductor package for transcription factor binding site analysis
Cited by: 239
Author(s): Ge Tan, Boris Lenhard
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-021-87970-w

Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
Cited by: 1
Author(s): Wojciech Rosikiewicz, J. Sikora, Tomasz Skrzypczak, Magdalena Regina Kubiak, Izabela Makałowska
Software Mentions: 2
Published: over 3 years ago

10.3390/genes12091394

Evolutionary Analysis of OAT Gene Family in River and Swamp Buffalo: Potential Role of SLCO3A1 Gene in Milk Performance
Cited by: 4
Author(s): Xiaoya Ma, Shasha Liang, Aixin Liang, Hossam E. Rushdi, Tingxian Deng
Software Mentions: 2
Published: almost 3 years ago

10.3390/ijms19041049

Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris
Cited by: 11
Author(s): Martina Lardi, Yilei Liu, Gaetano Giudice, Christian H. Ahrens, Nicola Zamboni, Gabriella Pessi
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-016-2453-4

Molecular foundations of chilling-tolerance of modern maize
Cited by: 43
Author(s): Alicja Sobkowiak, Maciej Jończyk, J. Adamczyk, Jarosław Szczepanik, Danuta Solecka, Iwona Kuciara, Katarzyna Hetmańczyk, Joanna Trzcińska-Danielewicz, Marcin Grzybowski, Marek Skoneczny, Jan Fronk, Paweł Sowiński
Software Mentions: 1
Published: over 8 years ago

10.3390/biom11030472

Differential MicroRNA Expression Involved in Endometrial Receptivity of Goats
Cited by: 9
Author(s): Xupeng Zang, Chunmei Zhou, Wenjing Wang, Jianyu Gan, Yaokun Li, Dewu Liu, Guangbin Liu, Linjun Hong
Software Mentions: 1
Published: over 3 years ago

10.1038/srep42663

Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster
Cited by: 7
Author(s): Hung Le Manh, Lain Guio, Miriam Merenciano, Quirze Rovira, Maite G. Barrón, Josefa González
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-016-3420-9

Identification of coding and non-coding mutational hotspots in cancer genomes
Cited by: 24
Author(s): Scott W. Piraino, Simon J. Furney
Software Mentions: 1
Published: over 7 years ago

Ecosyste.ms: Papers

Projects: bioconductor: TFBSTools

Papers Mentioning TFBSTools 33