bioconductor: ChIPpeakAnno | Projects

10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data
Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: about 8 years ago

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: almost 5 years ago

10.3390/cancers12040948

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility
Cited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: over 4 years ago

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.26508/lsa.202000766

Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1high memory phenotype CD4 T cells
Cited by: 6
Author(s): Alistair L. J. Symonds, Wei Zheng, Tizong Miao, Ang Li, Tieshang Wang, Ruth Kiome, Xiaofeng Hou, Suling Li, Ping Wang
Software Mentions: 15
Published: over 4 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.1186/s12864-018-4559-3

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Cited by: 133
Author(s): Jianhong Ou, Haibo Li, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
Software Mentions: 14
Published: almost 7 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 9 years ago

10.26508/lsa.201900461

Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotion
Cited by: 5
Author(s): Antonio Vitobello, Juliane Perner, Johanna Beil, Jiang Zhu, Alberto Del Río-Espínola, Laurent Morawiec, Magdalena Westphal, Valérie Dubost, Marc Altorfer, Ulrike Naumann, Arne Mueller, Karen Kapur, Mark Borowsky, Colin J. Henderson, Charles Wolf, Michael Schwarz, Jonathan G. Moggs, Rémi Terranova
Software Mentions: 12
Published: about 5 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: over 7 years ago

10.7717/peerj.1981

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
Cited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: over 8 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: almost 14 years ago

10.1186/s12859-016-1125-3

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis
Cited by: 3
Author(s): Nathan James Allen Cormier, Tyler Kolisnik, Mark Bieda
Software Mentions: 10
Published: over 8 years ago

10.1371/journal.pgen.1003209

Centromere-Like Regions in the Budding Yeast Genome
Cited by: 36
Author(s): Philippe Lefrançois, Raymond K. Auerbach, Christopher M. Yellman, G. Shirleen Roeder, M Snyder
Software Mentions: 10
Published: almost 12 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: about 7 years ago

10.1038/s41388-018-0450-6

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
Cited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: over 6 years ago

10.15252/embj.2020104983

Interactions between lineage‐associated transcription factors govern haematopoietic progenitor states
Cited by: 17
Author(s): Iwo Kuciński, Nicola K. Wilson, Rebecca Hannah, Sarah Kinston, Pierre Cauchy, Aurelie Lenaerts, Rudolf Grosschedl, Berthold Göttgens
Software Mentions: 9
Published: about 4 years ago

10.7554/eLife.59073

Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism
Cited by: 15
Author(s): Krystal A. Orlando, Amber K Douglas, Aierken Abudu, Yemin Wang, Basile Tessier‐Cloutier, Weiping Su, Alec Peters, Larry S. Sherman, Regan P. Moore, Vinh Nguyen, Gian Luca Negri, Shane Colborne, Gregg B. Morin, Friedrich Kommoss, Jessica D. Lang, William P.D. Hendricks, Elizabeth A. Raupach, Patrick Pirrotte, David G. Huntsman, Jeffrey M. Trent, Joel S. Parker, Jesse R. Raab, Bernard E. Weissman
Software Mentions: 9
Published: almost 4 years ago

10.3389/fgene.2015.00339

Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome
Cited by: 23
Author(s): Emanuele Libertini, Alice Lebreton, Goran Lakisic, Marie‐Agnès Dillies, Stephan Beck, Jean‐Yves Coppée, Pascale Cossart, Hélène Bierne
Software Mentions: 9
Published: about 9 years ago

10.7554/eLife.42675

The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila
Cited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: over 5 years ago

10.1093/gigascience/giz147

Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa
Cited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: about 5 years ago

10.1038/tp.2015.169

Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain
Cited by: 56
Author(s): Aslihan Dincer, David P. Gavin, Ke Xu, B Zhang, Joel T. Dudley, Eric E. Schadt, Schahram Akbarian
Software Mentions: 8
Published: about 9 years ago

10.1371/journal.pone.0031630

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis
Cited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: almost 13 years ago

10.26508/lsa.202101113

Statistical guidelines for quality control of next-generation sequencing techniques
Cited by: 1
Author(s): Maximilian Sprang, Matteo Krüger, Miguel A. Andrade‐Navarro, Jean-Fred Fontaine
Software Mentions: 8
Published: over 3 years ago

10.1186/s13104-019-4473-z

RepViz: a replicate-driven R tool for visualizing genomic regions
Cited by: 0
Author(s): Thomas Faux, Kalle T. Rytkönen, Asta Laiho, Laura L. Elo
Software Mentions: 8
Published: over 5 years ago

10.1186/s12864-017-3746-y

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases
Cited by: 29
Author(s): Lihua Julie Zhu, Michael C. Lawrence, Ankit Gupta, Hervé Pagès, Alper Küçükural, Manuel Garber, Scot A. Wolfe
Software Mentions: 8
Published: over 7 years ago

10.1371/journal.pgen.1009763

Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
Cited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: over 3 years ago

10.3389/fgene.2018.00250

GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data
Cited by: 15
Author(s): Mayur Divate, Edwin Cheung
Software Mentions: 7
Published: over 6 years ago

10.12688/f1000research.7016.2

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data
Cited by: 16
Author(s): Aaron T. L. Lun
Software Mentions: 7
Published: almost 9 years ago

10.1038/s41388-021-01876-5

The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct and separable from its DNA-binding function in Ewing sarcoma
Cited by: 12
Author(s): Megann A. Boone, Cenny Taslim, Julie Crow, Julia Selich‐Anderson, Andrea K. Byrum, Iftekhar A. Showpnil, Benjamin D. Sunkel, Meng Wang, Benjamin Z. Stanton, Emily R. Theisen, Stephen L. Lessnick
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-019-50485-6

Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors
Cited by: 28
Author(s): Sumona P. Dhara, Andrea Rau, Michael J. Flister, Nicole M. Recka, Michael D. Laiosa, Paul L. Auer, Ava J. Udvadia
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pntd.0008262

Global changes in nitration levels and DNA binding profile of Trypanosoma cruzi histones induced by incubation with host extracellular matrix
Cited by: 5
Author(s): Rubens Daniel Miserani Magalhães, Eliciane Cevolani Mattos, Andrei Rozanski, Pedro A. F. Galante, Giuseppe Palmisano, Ângela K. Cruz, Walter Colli, Anamaria A. Camargo, Maria Júlia M. Alves
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-017-1197-z

H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity
Cited by: 66
Author(s): Yue Zhou, Francisco J. Romero–Campero, Ángeles Gómez-Zambrano, Franziska Turck, Myriam Calonje
Software Mentions: 7
Published: over 7 years ago

10.7554/eLife.59654

HNRNPM controls circRNA biogenesis and splicing fidelity to sustain cancer cell fitness
Cited by: 19
Author(s): Jessica Sy Ho, Federico Di Tullio, Megan Schwarz, Diana Low, Danny Incarnato, Tommaso Tabaglio, Jingxian Zhang, Heike Wollmann, Leilei Chen, Ömer An, Tim Chan, Alexander Hall Hickman, Simin Zheng, Vladimir Roudko, Sujun Chen, Alcida Karz, Musaddeque Ahmed, Housheng Hansen He, Benjamin Greenbaum, Salvatore Oliviero, Michela Serresi, Gaetano Gargiulo, Karen Mann, Eva Hernando, David J. Mulholland, Ivan Marazzi, Dave Keng Boon Wee, Ernesto Guccione
Software Mentions: 7
Published: over 3 years ago

10.1186/gb-2013-14-2-r18

The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila
Cited by: 29
Author(s): Tobias Kockmann, Moritz Gerstung, Tommy Beat Schlumpf, Zhu Xhinzhou, Daniel Heß, Niko Beerenwinkel, Christian Beisel, Renato Paro
Software Mentions: 7
Published: almost 12 years ago

10.3389/fnmol.2021.680280

Impaired SNF2L Chromatin Remodeling Prolongs Accessibility at Promoters Enriched for Fos/Jun Binding Sites and Delays Granule Neuron Differentiation
Cited by: 1
Author(s): Laura Rose Goodwin, Gerardo Zapata, Sara Timpano, Jacob Marenger, David J. Picketts
Software Mentions: 7
Published: over 3 years ago

10.3390/cancers13092126

Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential
Cited by: 7
Author(s): Syuzo Kaneko, Toutai Mitsuyama, Kouya Shiraishi, Noriko Ikawa, Kanto Shozu, Ai Dozen, Hidenori Machino, Ken Asada, Masaaki Komatsu, Asako Kukita, Kenbun Sone, Hiroshi Yoshida, Noriko Motoi, Shinya Hayami, Yutaka Yoneoka, Tomoyasu Kato, Takashi Kohno, Toru Natsume, Gottfried von Keudell, Vassiliki Saloura, Hiroki Yamaue, Ryuji Hamamoto
Software Mentions: 7
Published: over 3 years ago

10.1186/1745-6150-6-51

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data
Cited by: 12
Author(s): Iros Barozzi, Alberto Termanini, Saverio Minucci, Gioacchino Natoli
Software Mentions: 6
Published: almost 14 years ago

10.1186/1471-2105-13-102

Workflows for microarray data processing in the Kepler environment
Cited by: 14
Author(s): Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda
Software Mentions: 6
Published: over 12 years ago

10.7554/eLife.58123

TBX3 acts as tissue-specific component of the Wnt/β-catenin transcriptional complex
Cited by: 28
Author(s): Dario Zimmerli, Costanza Borrelli, Amaia Jauregi-Miguel, Simon Söderholm, Salome Brütsch, Nikolaos Doumpas, Jan Reichmuth, Fabienne Murphy-Seiler, Michel Aguet, Konrad Basler, Andreas E. Moor, Claudio Cantù
Software Mentions: 6
Published: over 4 years ago

10.1186/s13072-021-00391-x

Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster
Cited by: 15
Author(s): Marat Sabirov, Olga Kyrchanova, Galina V. Pokholkova, Artem Bonchuk, Natalia Klimenko, Elena Belova, И. Ф. Жимулев, Oksana Maksimenko, Pavel Georgiev
Software Mentions: 6
Published: almost 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: about 8 years ago

10.1002/1878-0261.12954

The evolutionarily conserved long non‐coding RNA LINC00261 drives neuroendocrine prostate cancer proliferation and metastasis via distinct nuclear and cytoplasmic mechanisms
Cited by: 21
Author(s): Rebecca Mather, Abhijit Parolia, Sandra E. Carson, Erik Venalainen, David Roig-Carles, Mustapha Jaber, Shih‐Chun Chu, Ilaria Alborelli, Rebecca Wu, Dong Lin, Noushin Nabavi, Elena Jachetti, Mario P. Colombo, Hui Xue, Perla Pucci, Xinpei Ci, Cheryl A. Hawkes, Yinglei Li, Hardev Pandha, Igor Ulitsky, Crystal N. Marconett, Luca Quagliata, Wei Jiang, Ignacio A. Romero, Yuzhuo Wang, Francesco Crea
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-018-31192-0

Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid
Cited by: 18
Author(s): Qing Liu, Kevin Van Bortle, Yue Zhang, Ming Zhao, Joe Z. Zhang, Benjamin Geller, Joshua J. Gruber, Chao Jiang, Joseph C. Wu, M Snyder
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pbio.3000378

Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells
Cited by: 33
Author(s): Yiqin Ma, Daniel J. McKay, Laura Buttitta
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-94805-1

AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators
Cited by: 4
Author(s): Arno Meiler, Fabio Marchianò, Margaux Haering, Manuela Weitkunat, Frank Schnorrer, Bianca Habermann
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007337

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets
Cited by: 15
Author(s): M. Vijayabaskar, Debbie K. Goode, Nadine Obier, Monika Lichtinger, Amber M.L. Emmett, Fatin N Zainul Abidin, Nisar Ahmed Shar, Rebecca Hannah, Salam A. Assi, Michael Lie-A-Ling, Berthold Göttgens, Georges Lacaud, Valérie Kouskoff, Constanze Bonifer, David R. Westhead
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.19127

Regulation of X-linked gene expression during early mouse development by Rlim
Cited by: 36
Author(s): Feng Wang, Jongdae Shin, Jeremy Shea, Jun Yu, Ana Bošković, Meg Byron, Xiaochun Zhu, Alex K. Shalek, Aviv Regev, Jeanne B. Lawrence, Eduardo M. Torres, Lihua Julie Zhu, Oliver J. Rando, Ingolf Bach
Software Mentions: 6
Published: over 8 years ago

10.1186/s13072-019-0285-6

H3K4me2 functions as a repressive epigenetic mark in plants
Cited by: 46
Author(s): Kun Wang, Kunpeng Liu, Liufan Yin, Yu Yu, Ji Qi, Wen‐Hui Shen, Jun Zhu, Yijing Zhang, Dong Ao
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2019.00277

Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs
Cited by: 19
Author(s): Kun Han, Ruimin Ren, Jianhua Cao, Shuhong Zhao, Mei Yu
Software Mentions: 5
Published: over 5 years ago

10.1186/s13619-021-00092-6

Coordination of EZH2 and SOX2 specifies human neural fate decision
Cited by: 3
Author(s): Yuan Zhao, Tianyu Wang, Yanqi Zhang, Liang Shi, Cong Zhang, Jingyuan Zhang, Jiao Yao, Qianyu Chen, Xiaofen Zhong, Yanxing Wei, Yongli Shan, Guangjin Pan
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-015-0597-1

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis
Cited by: 127
Author(s): Julieta L. Mateos, Pedro Madrigal, Kazuhiko Tsuda, Vimal Rawat, René Richter, Maida Romera-Branchat, Fabio Fornara, Korbinian Schneeberger, Paweł Krajewski, George Coupland
Software Mentions: 5
Published: almost 10 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: about 10 years ago

10.26508/lsa.201900318

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay
Cited by: 11
Author(s): Junaid Akhtar, Piyush More, Steffen Albrecht, Fédérico Marini, Walter Kaiser, Apurva Kulkarni, Leszek Wojnowski, Jean-Fred Fontaine, Miguel A. Andrade‐Navarro, Marion Silies, Christian Berger
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1002887

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Cited by: 46
Author(s): S. Huang, David Clarke, Sara J.C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
Software Mentions: 5
Published: almost 12 years ago

10.1186/1471-2105-15-280

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
Cited by: 49
Author(s): Huihuang Yan, Jared M. Evans, Mike Kalmbach, Raymond M. Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Liu, Zhifu Sun, Xianfeng Chen, Jean-Pierre A. Kocher
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2020.508809

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes
Cited by: 16
Author(s): Fábio Pértille, A. M. G. Ibelli, Maj El Sharif, Mirele Daiana Poleti, Anna Sophie Fröhlich, Shiva Rezaei, Mônica Corrêa Ledur, Per Jensen, Carlos Guerrero-Bosagna, Luiz Lehmann Coutinho
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.57683

EHMT2 epigenetically suppresses Wnt signaling and is a potential target in embryonal rhabdomyosarcoma
Cited by: 14
Author(s): Ananya Pal, Jia Yu Leung, Gareth Chin Khye Ang, Vinay Kumar Rao, Luca Pignata, Huey Jin Lim, Maxime Hebrard, Kenneth Tou En Chang, Victor Kwan Min Lee, Ernesto Guccione, Reshma Taneja
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-017-3673-y

Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Cited by: 95
Author(s): Jenna Kropp Schmidt, José A. Carrillo, Hadjer Namous, Daniels Alyssa, Sana M. Salih, Jiuzhou Song, Hasan Khatib
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2021.648701

Multiomics Analysis Reveals Molecular Abnormalities in Granulosa Cells of Women With Polycystic Ovary Syndrome
Cited by: 14
Author(s): Ru-Song Zhao, Yonghui Jiang, Shigang Zhao, Han Zhao
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.05255

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Cited by: 402
Author(s): Manu Dubin, Pei Zhang, Dong Meng, Marie Stanislas Remigereau, Edward J. Osborne, Francesco Paolo Casale, Philipp Drewe, André Kahles, Géraldine Jean, Bjarni J. Vilhjálmsson, Joanna Jagoda, Selen Irez, Viktor Voronin, Qiang Song, Quan Long, Gunnar Rätsch, Oliver Stegle, Richard M. Clark, Magnus Nordborg
Software Mentions: 5
Published: over 9 years ago

10.1093/gigascience/giaa049

Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy
Cited by: 11
Author(s): Katarzyna Murat, Björn Grüning, Paulina Wiktoria Poterlowicz, Gillian Westgate, Desmond J. Tobin, Krzysztof Poterlowicz
Software Mentions: 5
Published: over 4 years ago

10.1186/s13072-018-0230-0

CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands
Cited by: 19
Author(s): Louie N. van de Lagemaat, Maria Flenley, Magnus Lynch, David Garrick, Simon R. Tomlinson, Kamil R. Kranc, Douglas Vernimmen
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-021-02294-2

seqQscorer: automated quality control of next-generation sequencing data using machine learning
Cited by: 9
Author(s): Steffen Albrecht, Maximilian Sprang, Miguel A. Andrade‐Navarro, Jean-Fred Fontaine
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-017-3589-6

Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity
Cited by: 14
Author(s): Michael Chambers, Wiam Turki-Judeh, Min Woo Kim, Kenny Chen, Sean D. Gallaher, Albert J. Courey
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13059-017-1302-3

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Cited by: 127
Author(s): Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey, James Whelan
Software Mentions: 5
Published: over 7 years ago

10.3390/nu9040407

Prenatal Exposure to a Maternal High-Fat Diet Affects Histone Modification of Cardiometabolic Genes in Newborn Rats
Cited by: 24
Author(s): Bijaya Upadhyaya, Tricia D. Larsen, Shivon Barwari, Eli J. Louwagie, Michelle Baack, Moul Dey
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-14-331

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish
Cited by: 32
Author(s): Håvard Aanes, Oľga Østrup, Ingrid S. Andersen, Lars Fredrik Moen, Sinnakaruppan Mathavan, Philippe Collas, Peter Aleström
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-015-1706-y

Systematically dissecting the global mechanism of miRNA functions in mouse pluripotent stem cells
Cited by: 3
Author(s): Anyou Wang, Qianchuan He, Yan Zhong
Software Mentions: 4
Published: over 9 years ago

10.1038/s41380-020-0767-8

AP-1 controls the p11-dependent antidepressant response
Cited by: 25
Author(s): Revathy U. Chottekalapanda, Salina Kalik, Jodi Gresack, Alyssa Ayala, Melanie Gao, Wei Wang, Sarah J. Meller, Ammar Aly, Anne Schaefer, Paul Greengard
Software Mentions: 4
Published: over 4 years ago

10.1186/s12989-017-0239-8

Maternal engineered nanomaterial inhalation during gestation alters the fetal transcriptome
Cited by: 36
Author(s): Phoebe A. Stapleton, Quincy A. Hathaway, C.E. Nichols, Alaeddin B. Abukabda, Mark V. Pinti, Danielle L. Shepherd, Carroll R. McBride, Jinghai Yi, Vincent Castranova, John M. Hollander, Timothy R. Nurkiewicz
Software Mentions: 4
Published: almost 7 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: about 11 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 10 years ago

10.1371/journal.pgen.1004604

Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation
Cited by: 77
Author(s): Andrew D. Hoffmann, Xinan Yang, Ozanna Burnicka-Turek, Joshua D. Bosman, Xiaomeng Ren, Jeffrey D. Steimle, Steven A. Vokes, Andrew P. McMahon, Vladimir V. Kalinichenko, Ivan P. Moskowitz
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0214559

DNA methylation, microRNA expression profiles and their relationships with transcriptome in grass-fed and grain-fed Angus cattle rumen tissue
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, Zan Liu, Jiuzhou Song
Software Mentions: 4
Published: about 5 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: about 4 years ago

10.1371/journal.pone.0088950

Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells
Cited by: 68
Author(s): Jeannine Diesch, Elaine Sanij, Omer Gilan, Christopher G. Love, Hoanh Tran, Nicholas I. Fleming, Jason Ellul, Amalia Marcia, Izhak Haviv, Richard B. Pearson, Eugene Tulchinsky, John M. Mariadason, Oliver M. Sieber, Ross D. Hannan, Amardeep S. Dhillon
Software Mentions: 4
Published: almost 11 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: over 11 years ago

10.3389/fgene.2020.595550

An Enhancer-Based Analysis Revealed a New Function of Androgen Receptor in Tumor Cell Immune Evasion
Cited by: 3
Author(s): Yuan Wang, Jiajia Li, Jingjing Li, Peipei Li, Li Wang, Lijun Di
Software Mentions: 4
Published: about 4 years ago

10.3389/fnmol.2020.00057

Sequences of Reverse Transcribed Brain DNA Are Modified by Learning
Cited by: 2
Author(s): Antonio Giuditta, Joyce Casalino
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-014-0513-0

TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator
Cited by: 120
Author(s): Ya-Ping Tsai, Hsiao-Fan Chen, Sung-Yuan Chen, Wei‐Chung Cheng, Hsei‐Wei Wang, Zih-Jie Shen, Chun-Xiao Song, Shan-Yuan Teng, Chuan He, Kou-Juey Wu
Software Mentions: 4
Published: about 10 years ago

10.1242/jcs.181248

Nuclear PKC-θ facilitates rapid transcriptional responses in human memory CD4+ T cells via p65 and H2B phosphorylation
Cited by: 11
Author(s): Jasmine Li, Kristine Hardy, Chansavath Phetsouphanh, Wen Juan Tu, Elissa L Sutcliffe, Robert McCuaig, Christopher R Sutton, Anjum Zafar, C. Mee Ling Munier, John Zaunders, Xu Yin, Angelo Theodoratos, Abel Tan, Pek Siew Lim, Tobias Knaute, Antonia Masch, Johannes Zerweck, Vedran Brezar, Peter J. Milburn, Jenny C. Dunn, Marco G. Casarotto, Stephen J. Turner, Nabila Seddiki, Anthony D. Kelleher, Sudha Rao
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.ppat.1008154

Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model
Cited by: 10
Author(s): Lorenz M. Loyola, Vasudevan Achuthan, Kathryn Gilroy, Gillian Borland, Anna Kilbey, Nancy MacKay, Margaret Bell, Jodie Hay, Sriram Aiyer, Dylan Fingerman, Rodrigo A. Villanueva, Ewan R. Cameron, Christine A. Kozak, Alan Engelman, James C. Neil, Monica J. Roth
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-78682-8

Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y
Cited by: 1
Author(s): Tatsuhiko Yamanaka, Haruko Miyazaki, Asako Tosaki, Sankar N. Maity, Tomomi Shimogori, Nobutaka Hattori, Nobuyuki Nukina
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.63556

Deficient spermiogenesis in mice lacking Rlim
Cited by: 7
Author(s): Feng Wang, María Gracia Gervasi, Ana Bošković, Fengyun Sun, Vera D. Rinaldi, Jun Yu, Mary C. Wallingford, Darya A Tourzani, Jesse Mager, Lihua Julie Zhu, Oliver J. Rando, Pablo E. Visconti, Lara Strittmatter, Ingolf Bach
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.62873

TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation
Cited by: 24
Author(s): Xiaochen Fan, V. Pragathi Masamsetti, Jing Sun, Kasper Engholm-Keller, Pierre Osteil, Joshua B. Studdert, Mark E. Graham, Nicolas Fossat, Patrick Tam
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.34864

Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Cited by: 51
Author(s): Maria A. Sacta, Bowranigan Tharmalingam, Maddalena Coppo, David A. Rollins, Dinesh K Deochand, Bradley Benjamin, Li Yu, Bin Zhang, Xiaoyu Hu, Rong Li, Yurii Chinenov, Inez Rogatsky
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms22052679

Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model
Cited by: 15
Author(s): Fábio Pértille, Manuel Álvarez‐Rodríguez, Arthur Nery da Silva, Isabel Barranco, Jordi Roca, Carlos Guerrero-Bosagna, Heriberto Rodríguez-Martinez
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms22105066

The AraC-Type Transcriptional Regulator GliR (PA3027) Activates Genes of Glycerolipid Metabolism in Pseudomonas aeruginosa
Cited by: 10
Author(s): Karolina Kotecka, Adam Kawałek, Kamil Kobyłecki, Aneta Agnieszka Bartosik
Software Mentions: 4
Published: over 3 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: almost 4 years ago

10.3389/fnins.2019.00460

Identification of Cholecystokinin by Genome-Wide Profiling as Potential Mediator of Serotonin-Dependent Behavioral Effects of Maternal Separation in the Amygdala
Cited by: 10
Author(s): Magdalena Weidner, Roy Lardenoije, Lars Eijssen, Floriana Mogavero, Lilian P. M. T. De Groodt, Sandy Popp, Rupert Palme, Konrad U. Förstner, Tatyana Strekalova, Harry W.M. Steinbusch, Angelika G. Schmitt-Böhrer, Jeffrey Glennon, Jonas Waider, Daniël L.A. van den Hove, Klaus–Peter Lesch
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0029450

Global Analysis of DNA Methylation by Methyl-Capture Sequencing Reveals Epigenetic Control of Cisplatin Resistance in Ovarian Cancer Cell
Cited by: 67
Author(s): Wei Yu, Chengmeng Jin, Xiaoyan Lou, Xu Han, Lisha Li, Yinghua He, Hongyu Zhang, Kelong Ma, Jingde Zhu, Li-Hua Cheng, Biaoyang Lin
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0187891

ChIP-Seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts
Cited by: 11
Author(s): Atilla Biçer, Serena Orlando, Abul B.M.M.K. Islam, Edurne Gallastegui, Arnaud Besson, Rosa Aligué, Oriol Bachs, María Jesús Pujol
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0196965

Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic-5
Cited by: 8
Author(s): Brian H. Lee, Michael R. Stallcup
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0120020

Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers
Cited by: 34
Author(s): Ignacio Blanco, Karoline Kuchenbaecker, Daniel Cuadras, Xianshu Wang, Daniel Barrowdale, Gorka Ruíz de Garibay, Pablo Librado, Alejandro Sánchez-Gracia, Julio Rozas, Núria Bonifaci, Lesley McGuffog, V. Shane Pankratz, Abul B.M.M.K. Islam, Francesca Mateo, Antoni Berenguer, Audrey Petit, Isabel Catalá, Joan Brunet, Lídia Feliubadaló, Eva Tornero, Javier Benı́tez, Ana Osorio, Teresa Ramón, Cajal Teresa, Heli Nevanlinna, Kristiina Aittomäki, Banu K. Arun, Amanda E. Toland, Beth Y. Karlan, Christine Walsh, Jenny Lester, Mark H. Greene, L. Phuong, Robert L. Nussbaum, Irene L. Andrulis, Susan M. Domchek, Katherine L. Nathanson, Timothy R. Rebbeck, Rósa B. Barkardóttir, Anna Jakubowska, Jan Lubiński, Katarzyna Durda, Katarzyna Jaworska–Bieniek, Kathleen Claes, Tom Van Maerken, Orland Dı́ez, Thomas V.O. Hansen, Lars Jønson, Anne–Marie Gerdes, Bent Ejlertsen, Miguel de la Hoya, Trinidad Caldés, Alison M. Dunning, Clare Oliver, Elena Fineberg, Margaret Cook, Susan Peock, Emma McCann, Alex Murray, Chris Jacobs, Gabriella Pichert, Fiona Lalloo, Carol Chu, Huw Dorkins, Joan Paterson, Kai Ren Ong, Manuel R. Teixeira, Thais Bonfim Teixeira, Frans B.L. Hogervorst, Annemarie H. van der Hout, Caroline Seynaeve, Rob B. van der Luijt, Marjolijn J. L. Ligtenberg, Peter Devilee, Juul T. Wijnen, Matti A. Rookus, Hanne Meijers-Heijboer, Marinus J. Blok, Ans M.W. van den Ouweland, Cora M. Aalfs, Gustavo C. Rodriguez, Kelly‐Anne Phillips, Marion Piedmonte, Stacy Nerenstone, Victoria Bae‐Jump, David M. O’Malley, Elena Ratner, Rita K. Schmutzler, Barbara Wappenschmidt, Kerstin Rhiem, Christoph Engel, Alfons Meindl, Nina Ditsch, Norbert Arnold, Hansjoerg Plendl, Dieter Niederacher, Christian Sutter, Shan Wang-Gohrke, Doris Steinemann, Sabine Preisler-Adams, Karin Kast, Raymonda Varon-Mateeva, Andrea Gehrig, Anders Bojesen, Inge Søkilde Pedersen, Lone Sunde, Uffe Birk Jensen, Mads Thomassen, Torben A. Kruse, Lenka Foretová, Paolo Peterlongo, Loris Bernard, Bernard Peissel, Giulietta Scuvera, Siranoush Manoukian, Paolo Radice, Laura Ottini, Marco Montagna, Simona Agata, Christine M. Maugard, Jacques Simard, Penny Soucy, Andreas Berger, A. Fink-Retter, Christian F. Singer, Christine Rappaport, Daphne Geschwantler-Kaulich, Muy Kheng Tea, Georg Pfeiler, Esther M. John, Alexander Miron, Susan L. Neuhausen, Mary Beth Terry, Wendy K. Chung, Mary B. Daly, David E. Goldgar, Ramūnas Janavičius, Cecilia M. Dorfling, Elizabeth J. van Rensburg, Florentia Fostira, Irene Konstantopoulou, Judy E. Garber, Andrew K. Godwin, Edith Olàh, Steven A. Narod, Gad Rennert, Shani Shimon Paluch, Yael Laitman, Eitan Friedman, Annelie Liljegren, Johanna Rantala, Marie Stenmark-Askmalm, Niklas Loman, Evgeny N. Imyanitov, Ute Hamann, Amanda B. Spurdle, Sue Healey, Jeffrey N. Weitzel, Josef Herzog, David A. Margileth, Chiara Gorrini, Manel Esteller, Antonio Gómez, Sergi Sayols, Enrique Vidal, Holger Heyn, Dominique Stoppa‐Lyonnet, Mélanie Léone, Laure Barjhoux, Marion Fassy-Colcombet, Antoine de Pauw, Christine Lasset, Sandra Fert Ferrer, Laurent Castéra, Pascaline Berthet, François Cornélis, Yves Jean Bignon, Francesca Damiola, Sylvie Mazoyer, Olga M. Sinilnikova, Christopher A. Maxwell, Joseph Vijai, Mark E. Robson, Noah D. Kauff, Marina Corines, Danylko Villano, Julie M. Cunningham, Adam F. Lee, Noralane M. Lindor, Conxi Lázaro, Douglas F. Easton, Kenneth Offit, Georgia Chenevix-Trench, Fergus J. Couch, Antonis C. Antoniou, Miguel Ángel Pujana
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0100476

Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine
Cited by: 9
Author(s): José A. Carrillo, Yanghua He, Juan Luo, Kimberly R. Menendez, Nathaniel L. Tablante, Keji Zhao, Joseph N. Paulson, Bichun Li, Jiuzhou Song
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.21964

DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells
Cited by: 25
Author(s): Sarah J. Hainer, Kurtis N. McCannell, Jun Yu, Ly-Sha Ee, Lihua Julie Zhu, Oliver J. Rando, Thomas G. Fazzio
Software Mentions: 3
Published: about 8 years ago

10.1093/jxb/ery142

Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions
Cited by: 46
Author(s): Waleed S. Albihlal, Irabonosi Obomighie, Thomas Blein, Ramona Persad, Igor Chernukhin, Martín Crespi, Ulrike Bechtold, Phil Mullineaux
Software Mentions: 3
Published: over 6 years ago

10.1093/jxb/erab223

AINTEGUMENTA and AINTEGUMENTA-LIKE6 directly regulate floral homeotic, growth, and vascular development genes in young Arabidopsis flowers
Cited by: 17
Author(s): Beth A. Krizek, Alexis Bantle, Jorman M. Heflin, Han Han, Nowlan H. Freese, Ann E. Loraine
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-1495-3

Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila
Cited by: 11
Author(s): Sarah H. Carl, Steven Russell
Software Mentions: 3
Published: over 9 years ago

Projects: bioconductor: ChIPpeakAnno

Papers Mentioning ChIPpeakAnno 145