bioconductor: ChIPpeakAnno | Projects

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

10.1371/journal.pgen.1004851

A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation
Cited by: 62
Author(s): Catherine Creppe, Anna M. Palau, Roberto Malinverni, Vanesa Valero, Marcus Buschbeck
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-018-37699-w

The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail
Cited by: 15
Author(s): Tyler Weaver, Jiachen Liu, Katelyn E. Connelly, Chris Coble, Katayoun Varzavand, Emily C. Dykhuizen, Catherine A. Musselman
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-45304-x

BioTarget: A Computational Framework Identifying Cancer Type Specific Transcriptional Targets of Immune Response Pathways
Cited by: 7
Author(s): Tham H. Hoang, Yue Zhao, Y. W. Lam, Stephanie Piekos, Yueh-Chiang Han, Cameron Reilly, Pujan Joshi, Seung-Hyun Hong, Chang Ohk Sung, Charles Giardina, Dong-Guk Shin
Software Mentions: 3
Published: over 5 years ago

10.1002/1878-0261.12168

Characterization of a FOXG1:TLE1 transcriptional network in glioblastoma‐initiating cells
Cited by: 21
Author(s): Rola Dali, Federica Verginelli, Albéna Pramatarova, Robert Sladek, Stefano Stifani
Software Mentions: 3
Published: over 6 years ago

10.1111/eva.12912

Population epigenetic divergence exceeds genetic divergence in the Eastern oyster <i>Crassostrea virginica</i> in the Northern Gulf of Mexico
Cited by: 35
Author(s): Kevin M. Johnson, Morgan W. Kelly
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13072-020-00333-z

Bromodomain and extra-terminal domain (BET) proteins regulate melanocyte differentiation
Cited by: 10
Author(s): Archit Trivedi, Aanchal Mehrotra, Caitlin E. Baum, Brandon Lewis, Tupa Basuroy, Thomas M. Blomquist, Robert Trumbly, Fabian V. Filipp, Vijayasaradhi Setaluri, Ivana L. de la Serna
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2021.642697

Tlx3 Exerts Direct Control in Specifying Excitatory Over Inhibitory Neurons in the Dorsal Spinal Cord
Cited by: 3
Author(s): Filipe Almeida Monteiro, Rafael Mendes Miranda, Marta C Samina, Ana Cristina Dias, Alexandre A.S.F. Raposo, Patrícia Oliveira, Carlos Reguenga, Diogo S. Castro, Deolinda Lima
Software Mentions: 3
Published: over 3 years ago

10.1186/s13148-016-0265-7

Neonatal monocytes exhibit a unique histone modification landscape
Cited by: 37
Author(s): Jennifer Bermick, Nathalie Lambrecht, Aaron D. denDekker, Steven L. Kunkel, Nicholas W. Lukacs, Cory M. Hogaboam, Matthew Schaller
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2020.00850

Genome-Wide Transcriptional Regulation of the Long Non-coding RNA Steroid Receptor RNA Activator in Human Erythroblasts
Cited by: 5
Author(s): Waritta Sawaengdee, Kairong Cui, Keji Zhao, Suradej Hongeng, Suthat Fucharoen, Patompon Wongtrakoongate
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0242211

Ikaros antagonizes DNA binding by STAT5 in pre-B cells
Cited by: 7
Author(s): Beate Heizmann, Stéphanie Le Gras, Célestine Simand, Patricia Marchal, Susan Chan, Philippe Kastner
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pbio.1001950

A Trihelix DNA Binding Protein Counterbalances Hypoxia-Responsive Transcriptional Activation in Arabidopsis
Cited by: 77
Author(s): Beatrice Giuntoli, Seung Cho Lee, Francesco Licausi, Monika Kosmacz, Teruko Oosumi, Joost T. van Dongen, Julia Bailey‐Serres, Pierdomenico Perata
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0026837

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma
Cited by: 95
Author(s): Volkhard Seitz, Peter Butzhammer, Burkhard Hirsch, Jochen Hecht, Ines Gütgemann, Anke Ehlers, Dido Lenze, Elisabeth Oker, Anke Sommerfeld, Edda von der Wall, Christoph König, Christian Zinser, Rainer Spang, Michael Hummel
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0097513

A Novel Method for Identification and Quantification of Consistently Differentially Methylated Regions
Cited by: 4
Author(s): Ching Lin Hsiao, Ai-Ru Hsieh, Ie Bin Lian, Ying Lin, Hui‐Min David Wang, Cathy S.J. Fann
Software Mentions: 2
Published: over 10 years ago

10.1186/bcr3664

VAV3 mediates resistance to breast cancer endocrine therapy
Cited by: 27
Author(s): Helena Aguilar, Ander Urruticoechea, Pasi Halonen, Kazuma Kiyotani, Taisei Mushiroda, Xavier Barril, Jordi Serra-Musach, Abul B.M.M.K. Islam, Livia Caizzi, Luciano Di Croce, Ekaterina Nevedomskaya, Wilbert Zwart, Josefine Bostner, Elin Karlsson, Gizeh Pérez Tenorio, Tommy Fornander, Dennis Sgroi, Rafael Garcı́a-Mata, Maurice P.H.M. Jansen, Nadia García, Núria Bonifaci, Fina Climent, María Teresa Soler, Alejo Rodríguez‐Vida, Miguel Ángel Cobos Gil, Joan Brunet, Griselda Martrat, Laia Gómez-Baldó, Ana I. Extremera, Agnés Figueras, J. Balart, Robert Clarke, Kerry L. Burnstein, Kathryn E. Carlson, John A. Katzenellenbogen, Miguel Vizoso, Manel Esteller, Alberto Villanueva, Ana B. Rodríguez-Peña, Xosé R. Bustelo, Yusuke Nakamura, Hitoshi Zembutsu, Olle Stål, Roderick L. Beijersbergen, Miguel Ángel Pujana
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.54309

Caenorhabditis elegans nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3
Cited by: 28
Author(s): Lianna Schwartz-Orbach, Chenzhen Zhang, Simone Sidoli, Richa Amin, Diljeet Kaur, Anna Zhebrun, Julie Zhouli Ni, Sam Guoping Gu
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-018-4548-6

DNA methylation profiles correlated to striped bass sperm fertility
Cited by: 17
Author(s): L. Curry Woods, Yaokun Li, Yi Ding, Jianan Liu, Benjamin J. Reading, S. Adam Fuller, Jiuzhou Song
Software Mentions: 2
Published: over 6 years ago

10.1186/s13104-021-05781-8

ssvQC: an integrated CUT&RUN quality control workflow for histone modifications and transcription factors
Cited by: 4
Author(s): Joseph R. Boyd, Princess D. Rodriguez, Hilde Schjerven, Seth Frietze
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-017-14336-6

Unravelling pathways downstream Sox6 induction in K562 erythroid cells by proteomic analysis
Cited by: 6
Author(s): Gloria Barbarani, Antonella Ronchi, Margherita Ruoppolo, Lucia Santorelli, Robert S. Steinfelder, Sudharshan Elangovan, Cristina Fugazza, Marianna Caterino
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.ppat.1003830

Lysine Acetyltransferase GCN5b Interacts with AP2 Factors and Is Required for Toxoplasma gondii Proliferation
Cited by: 61
Author(s): Jiachen Wang, Stacy E. Dixon, Li Min Ting, Ting-Kai Liu, Victoria Jeffers, Matthew McKnight Croken, Myrasol Calloway, Dominique Cannella, Mohamed‐Ali Hakimi, Kami Kim, William J. Sullivan
Software Mentions: 2
Published: almost 11 years ago

10.3390/cancers11111741

Cell-Free DNA Methylation Profiling Analysis—Technologies and Bioinformatics
Cited by: 35
Author(s): Jinyong Huang, Liang Wang
Software Mentions: 2
Published: about 5 years ago

10.1128/mBio.00136-20

Barrier-to-Autointegration Factor 1 Protects against a Basal cGAS-STING Response
Cited by: 31
Author(s): Hongming Ma, Wei Qian, Monika Bambousková, Patrick L. Collins, Sofia I. Porter, Andrea K. Byrum, Rong Zhang, Maxim N. Artyomov, Eugene M. Oltz, Nima Mosammaparast, Jonathan J. Miner, Michael S. Diamond
Software Mentions: 2
Published: over 4 years ago

10.1038/srep44825

Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells
Cited by: 14
Author(s): Wen Juan Tu, Kristine Hardy, Christopher R Sutton, Robert McCuaig, Jasmine Li, Jenny C. Dunn, Abel Tan, Vedran Brezar, Melanie S. Morris, Gareth Denyer, Sau Kuen Lee, Stephen J. Turner, Nabila Seddiki, Corey Smith, Rajiv Khanna, Sudha Rao
Software Mentions: 2
Published: over 7 years ago

10.1007/s00439-020-02222-7

Genome-wide landscape establishes novel association signals for metabolic traits in the Arab population
Cited by: 11
Author(s): Prashantha Hebbar, Jehad Abubaker, Mohamed Abu‐Farha, Osama Alsmadi, Naser Elkum, Fadi Alkayal, Sumi Elsa John, Arshad Channanath, Rasheeba Iqbal, Janne Pitkäniemi, Jaakko Tuomilehto, Robert Sladek, Fahd Al-Mulla, Thangavel Alphonse Thanaraj
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-018-24915-w

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

10.1186/gb-2013-14-1-r3

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion
Cited by: 53
Author(s): Henar Hernando, Claire Shannon-Lowe, Abul B.M.M.K. Islam, Fátima Al‐Shahrour, Javier Rodríguez-Ubreva, Virginia C. Rodríguez-Cortez, Biola M. Javierre, Cristina Mangas, Agustín F. Fernández, Maribel Parra, Henri Jacques Delecluse, Manel Esteller, Eduardo López‐Granados, Mario F. Fraga, Núria López‐Bigas, Esteban Ballestar
Software Mentions: 2
Published: almost 12 years ago

10.1186/s40246-020-00285-1

Aberration of the modulatory functions of intronic microRNA hsa-miR-933 on its host gene ATF2 results in type II diabetes mellitus and neurodegenerative disease development
Cited by: 5
Author(s): Abul B.M.M.K. Islam, Eusra Mohammad, A. A. Khan
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-018-30330-y

Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia
Cited by: 33
Author(s): Paola Orsini, Crescenzio Francesco Minervini, Cosimo Cumbo, Luisa Anelli, Antonella Zagaria, Angela Minervini, Nicoletta Coccaro, Giuseppina Tota, Paola Casieri, Luciana Impera, Elisa Parciante, Claudia Brunetti, Annamaria Giordano, Giorgina Specchia, Francesco Albano
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-1104

Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo
Cited by: 16
Author(s): Poshen B. Chen, Lihua Julie Zhu, Sarah J. Hainer, Kurtis N. McCannell, Thomas G. Fazzio
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0024023

Co-Regulation of Histone-Modifying Enzymes in Cancer
Cited by: 14
Author(s): Abul B.M.M.K. Islam, William F. Richter, Laura A. Jacobs, Núria López‐Bigas, Elizaveta V. Benevolenskaya
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1005615

Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes
Cited by: 37
Author(s): Patompon Wongtrakoongate, Gregory Riddick, Suthat Fucharoen, Gary Felsenfeld
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2164-13-S1-S1

Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information
Cited by: 5
Author(s): Hatice U. Osmanbeyoglu, Ryan J. Hartmaier, Steffi Oesterreich, Xinghua Lu
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13578-018-0201-y

Epigenetic alterations in TRAMP mice: epigenome DNA methylation profiling using MeDIP-seq
Cited by: 7
Author(s): Wenji Li, Ying Huang, Davit Sargsyan, Tin Oo Khor, Yue Guo, Limin Shu, Anne Yuqing Yang, Chengyue Zhang, Ximena Paredes-Gonzalez, Michael P. Verzi, Ronald P. Hart, Ah‐Ng Tony Kong
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12885-015-1819-3

The unique transcriptional response produced by concurrent estrogen and progesterone treatment in breast cancer cells results in upregulation of growth factor pathways and switching from a Luminal A to a Basal-like subtype
Cited by: 28
Author(s): Eleanor F. Need, Luke A. Selth, Andrew P. Trotta, Damien A. Leach, Lauren Giorgio, Melissa A. O’Loughlin, Eric Smith, P. Grantley Gill, Wendy V. Ingman, J. Dinny Graham, Grant Buchanan
Software Mentions: 1
Published: about 9 years ago

10.1186/s12885-020-06890-6

Independence of HIF1a and androgen signaling pathways in prostate cancer
Cited by: 25
Author(s): Maxine Tran, Becky A.S. Bibby, Lingjian Yang, Franklin Lo, Anne Y. Warren, Deepa Shukla, Michelle Osborne, James Hadfield, Thomas Carroll, Rory Stark, Helen E. Scott, Antonio Ramos-Montoya, Charlie E. Massie, Patrick H. Maxwell, Catharine West, Ian G. Mills, David E. Neal
Software Mentions: 1
Published: over 4 years ago

10.1186/s13578-015-0013-2

Association of aberrant DNA methylation in Apcmin/+ mice with the epithelial-mesenchymal transition and Wnt/β-catenin pathways: genome-wide analysis using MeDIP-seq
Cited by: 10
Author(s): Yue Guo, Jong-Hun Lee, Limin Shu, Ying Huang, Wenji Li, Chengyue Zhang, Anne Yuqing Yang, Sarandeep S.S. Boyanapalli, Ansu O. Perekatt, Ronald P. Hart, Michael P. Verzi, Ah‐Ng Tony Kong
Software Mentions: 1
Published: over 9 years ago

10.3390/v5112898

Development of Hematopoietic Stem Cell Based Gene Therapy for HIV-1 Infection: Considerations for Proof of Concept Studies and Translation to Standard Medical Practice
Cited by: 43
Author(s): David DiGiusto, Rodica Stan, Amrita Krishnan, Haitang Li, John J. Rossi, John A. Zaia
Software Mentions: 1
Published: about 11 years ago

10.1590/1678-4685-GMB-2020-0080

Molecular evolution and diversification of the GRF transcription factor family
Cited by: 12
Author(s): Leila Spagnolo Fonini, Fernanda Lazzarotto, Pedro M. Barros, Caroline Cabreira-Cagliari, Mario Martins, Nelson J. M. Saibo, Andreia Carina Turchetto‐Zolet, Márcia Margis‐Pinheiro
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0163155

Analysis of SOX2-Regulated Transcriptome in Glioma Stem Cells
Cited by: 11
Author(s): Arlet María Acanda de la Rocha, Hernando López-Bertoni, Elizabeth Guruceaga, Marisol González-Huarriz, Naiara Martínez-Vélez, Enric Xipell, Juan Fueyo, Candelaria Gomez-Manzano, Marta M. Alonso
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0070184

Pleiohomeotic Interacts with the Core Transcription Elongation Factor Spt5 to Regulate Gene Expression in Drosophila
Cited by: 4
Author(s): R Harvey, Eugene F. Schuster, Barbara Jennings
Software Mentions: 1
Published: over 11 years ago

10.1186/s13058-014-0464-0

Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer
Cited by: 36
Author(s): Helit Cohen, Rotem Ben‐Hamo, Moriah Gidoni, Ilana Yitzhaki, Renana Kozol, Alona Zilberberg, Sol Efroni
Software Mentions: 1
Published: about 10 years ago

10.1038/s41389-021-00332-z

PRMT6 activates cyclin D1 expression in conjunction with the transcription factor LEF1
Cited by: 12
Author(s): Lucas Schneider, Stefanie Herkt, Lei Wang, Ch. Feld, Josephine Wesely, Olga N. Kuvardina, Annekarin Meyer, Thomas Oellerich, Björn Häupl, Erhard Seifried, Halvard Bönig, Joern Lausen
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.ppat.1002621

Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein
Cited by: 112
Author(s): Benjamin Blasco, Jeffrey M. Chen, Ruben C. Hartkoorn, Claudia Sala, Swapna Uplekar, Jacques Rougemont, F. Pojer, Stewart T. Cole
Software Mentions: 1
Published: over 12 years ago

10.1038/srep11763

Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes
Cited by: 64
Author(s): Luming Liang, Luoyan Ai, Jin Qian, Jing‐Yuan Fang, Jin-Quan Xu
Software Mentions: 1
Published: over 9 years ago

Projects: bioconductor: ChIPpeakAnno

Papers Mentioning ChIPpeakAnno 145