bioconductor: GenomicRanges | Projects

10.3390/cancers13163929

Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AML
Cited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
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

10.1186/s13059-018-1582-2

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis
Cited by: 77
Author(s): Anna R. Poetsch, Simon J. Boulton, Nicholas M. Luscombe
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13059-018-1521-2

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
Cited by: 18
Author(s): Philipp Drewe-Boß, Hans-Hermann Wessels, Uwe Ohler
Software Mentions: 7
Published: about 6 years ago

10.1186/1756-8935-8-6

De novo identification of differentially methylated regions in the human genome
Cited by: 639
Author(s): Timothy J. Peters, Michael Buckley, Aaron L. Statham, Ruth Pidsley, Katherine Samaras, Reginald V. Lord, Susan J. Clark, Peter L. Molloy
Software Mentions: 7
Published: almost 10 years ago

10.1093/bioinformatics/btu638

HTSeq—a Python framework to work with high-throughput sequencing data
Cited by: 14,991
Author(s): Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Software Mentions: 7
Published: about 10 years ago

10.1186/s13072-021-00415-6

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
Cited by: 1
Author(s): Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana I. Shashkova, Marion Arnoux, Édouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul Lyons, Michel Georges, Jörn Walter
Software Mentions: 7
Published: about 3 years ago

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: almost 11 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

10.3390/v13081614

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression
Cited by: 7
Author(s): Muhammad Hafiz Ismail, Katharine A. Michie, Yu Fen Goh, Parisa Noorian, Staffan Kjelleberg, Iain G. Duggin, Diane McDougald, Scott A. Rice
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2164-15-702

Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves
Cited by: 58
Author(s): Adrienne N. Moran Lauter, Gregory A. Peiffer, Tao Yin, Steven A. Whitham, Dianne Cook, Randy C. Shoemaker, Michelle A. Graham
Software Mentions: 7
Published: over 10 years ago

10.3389/fimmu.2020.609891

Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype
Cited by: 26
Author(s): Christopher Kressler, Gilles Gasparoni, Karl Nordström, Dania Hamo, Abdulrahman Salhab, Christoforos Dimitropoulos, Sascha Tierling, Petra Reinke, Hans‐Dieter Volk, Jörn Walter, Alf Hamann, Julia K. Polansky
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41431-020-0675-z

Evaluation of CNV detection tools for NGS panel data in genetic diagnostics
Cited by: 63
Author(s): José Marcos Moreno-Cabrera, Jesús Del Valle, Elisabeth Castellanos, Lídia Feliubadaló, Marta Pineda, Joan Brunet, Eduard Serra, Gabriel Capellá, Conxi Lázaro, Bernat Gel
Software Mentions: 7
Published: over 4 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: over 3 years ago

10.1186/s12864-021-07721-z

Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation
Cited by: 10
Author(s): Dorothea Seiler Vellame, Isabel Castanho, Aisha Dahir, Jonathan Mill, Eilís Hannon
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0126545

Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability
Cited by: 15
Author(s): Karolis Uziela, Antti Honkela
Software Mentions: 7
Published: over 9 years ago

10.1186/s12864-016-3300-3

Assessing characteristics of RNA amplification methods for single cell RNA sequencing
Cited by: 32
Author(s): Hannah Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian–Bing Fan, Stephen Fisher, Jennifer Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin, Rui Li, William J. Mack, Sean McGroty, Joseph Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher Walker, Jinhui Wang, Kai Wang, Wei Wang, André Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim
Software Mentions: 7
Published: almost 8 years ago

10.1186/s12864-019-5924-6

A catalog of CasX genome editing sites in common model organisms
Cited by: 4
Author(s): Elisha D.O. Roberson
Software Mentions: 7
Published: over 5 years ago

10.1186/s13072-018-0205-1

Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
Cited by: 243
Author(s): Dafni Anastasiadi, Anna Esteve‐Codina, Francesc Piferrer
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2105-14-S5-S10

An optimized algorithm for detecting and annotating regional differential methylation
Cited by: 101
Author(s): Shengyong Li, Francine E. Garrett-Bakelman, Altuna Akalin, Paul Zumbo, Ross L. Levine, Bik To, Ian D. Lewis, Anna L. Brown, Richard J. D’Andrea, Ari Melnick, Christopher E. Mason
Software Mentions: 6
Published: over 11 years ago

10.1186/1471-2164-15-353

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Cited by: 49
Author(s): Richard Landstorfer, Svenja Simon, Steffen Schober, Daniel A. Keim, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 6
Published: over 10 years ago

10.1016/j.ccell.2017.03.007

TIAM1 Antagonizes TAZ/YAP Both in the Destruction Complex in the Cytoplasm and in the Nucleus to Inhibit Invasion of Intestinal Epithelial Cells
Cited by: 69
Author(s): Zoi Diamantopoulou, Gavin R M White, Muhammad Zaki Hidayatullah Fadlullah, Marcel Dreger, Karen Pickering, Joe Maltas, Garry Ashton, Ruth MacLeod, George S. Baillie, Valérie Kouskoff, Georges Lacaud, Graeme I. Murray, Owen J. Sansom, Adam Hurlstone, Angeliki Malliri
Software Mentions: 6
Published: over 7 years ago

10.1186/s12943-017-0691-y

Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies
Cited by: 212
Author(s): Kaja Christine Graue Berg, Peter W. Eide, Ina A. Eilertsen, Bjarne Johannessen, Jarle Bruun, Stine A. Danielsen, Merete Bjørnslett, Leonardo A. Meza‐Zepeda, Mette Eknæs, Guro Elisabeth Lind, Ola Myklebost, Rolf Inge Skotheim, Anita Sveen, Ragnhild Lothe
Software Mentions: 6
Published: over 7 years ago

10.15252/msb.20199156

Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver
Cited by: 19
Author(s): Vanessa Dubois, Céline Gheeraert, Wouter Vankrunkelsven, Julie Dubois-Chevalier, Hélène Dehondt, Marie Bobowski-Gérard, Manjula Vinod, Francesco Paolo Zummo, Fabian Güiza, Maheul Ploton, Emilie Dorchies, Laurent Pineau, Alexis Boulinguiez, Emmanuelle Vallez, Eloïse Woitrain, Eric Baugé, Fanny Lalloyer, Christian Duhem, Nabil Rabhi, Ronald E. van Kesteren, Cheng Ming Chiang, Steve Lancel, Hélène Duez, Jean-Sébastien Annicotte, Réjane Paumelle, Ilse Vanhorebeek, Greet Van den Berghe, Bart Staels, Philippe Lefèbvre, Jérôme Eeckhoute
Software Mentions: 6
Published: over 4 years ago

10.7717/peerj.8192

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model
Cited by: 21
Author(s): Gökhan Karakülah, Nazmiye Arslan, Cihangir Yandım, Aslı Süner
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pbio.3000559

Human sperm displays rapid responses to diet
Cited by: 102
Author(s): Daniel Nätt, Unn Kugelberg, Eduard Casas, Elizabeth Nedstrand, Stefan Zalavary, Pontus Henriksson, Carola Nijm, Julia Jäderquist, Johanna Sandborg, Eva Flinke, Rashmi Ramesh, Lovisa Örkenby, Filip Appelkvist, Thomas Lingg, Nicola Guzzi, Cristian Bellodi, Marie Löf, Tanya Vavouri, Anita Öst
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pgen.1009162

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation
Cited by: 18
Author(s): Laure Bridoux, Peyman Zarrineh, Joshua Mallen, Mike Phuycharoen, Víctor Latorre, Frank Ladam, Marta Losa, Syed Murtuza Baker, Charles G. Sagerström, Kimberly A. Mace, Magnus Rattray, Nicoletta Bobola
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pntd.0005246

The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni
Cited by: 39
Author(s): Kathrin K. Geyer, Umar Niazi, David Timothy Duval, Céline Cosseau, Chad Tomlinson, Iain W. Chalmers, Martin Swain, David Cutress, Utibe Bickham-Wright, Sabrina E. Munshi, Christoph Grunau, Timothy P. Yoshino, Karl F. Hoffmann
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0086536

Dual Targeting of MEK and PI3K Pathways Attenuates Established and Progressive Pulmonary Fibrosis
Cited by: 22
Author(s): Satish K. Madala, Ramakrishna Edukulla, Mukta Phatak, Stephanie Schmidt, Cynthia Davidson, Thomas H. Acciani, Thomas R. Korfhagen, Mario Medvedovic, Timothy D. Le Cras, Kimberly Wagner, William D. Hardie
Software Mentions: 6
Published: almost 11 years ago

10.1371/journal.pone.0152034

System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination
Cited by: 45
Author(s): Michael T. Zimmermann, Ann L. Oberg, Diane E. Grill, Inna G. Ovsyannikova, Iana H. Haralambieva, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 6
Published: over 8 years ago

10.1016/j.cell.2018.09.040

Nervous System Regionalization Entails Axial Allocation before Neural Differentiation
Cited by: 116
Author(s): Vicki Metzis, Sebastian Steinhauser, Edvinas Pakanavicius, Mina Gouti, Despina Stamataki, Kenzo Ivanovitch, Thomas Watson, Teresa Rayón, S. Neda Mousavy Gharavy, Robin Lovell-Badge, Nicholas M. Luscombe, James Briscoe
Software Mentions: 6
Published: about 6 years ago

10.1016/j.cell.2011.11.058

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Cited by: 504
Author(s): Dominic Schmidt, Petra Schwalie, Michael D. Wilson, Benoît Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Software Mentions: 6
Published: almost 13 years ago

10.1016/j.stem.2018.06.014

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells
Cited by: 137
Author(s): Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, Ian Chambers
Software Mentions: 6
Published: over 6 years ago

10.1186/s13148-015-0123-z

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Cited by: 32
Author(s): Daniel Nätt, I. Johansson, Tomas Faresjö, Johnny Ludvigsson, Annika Thorsell
Software Mentions: 6
Published: about 9 years ago

10.1242/dev.199604

The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotency
Cited by: 16
Author(s): Nicola Festuccia, Nick Owens, Almira Chervova, Agnès Dubois, Pablo Navarro
Software Mentions: 6
Published: about 3 years ago

10.1289/ehp.1307297

Disruption of Aryl Hydrocarbon Receptor Homeostatic Levels during Embryonic Stem Cell Differentiation Alters Expression of Homeobox Transcription Factors that Control Cardiomyogenesis
Cited by: 46
Author(s): Qin Wang, Jing Chen, Chih‐Wei Ko, Yunxia Fan, Vinicius Carreira, Yinglei Chen, Ying Xia, Mario Medvedovic, Alvaro Puga
Software Mentions: 6
Published: about 11 years ago

10.12688/f1000research.11355.2

Arkas: Rapid reproducible RNAseq analysis
Cited by: 9
Author(s): Anthony Colombo, Timothy J. Triche, Giridharan Ramsingh
Software Mentions: 6
Published: over 7 years ago

10.3389/fgene.2016.00031

A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe
Cited by: 17
Author(s): Stefano Berto, Alvaro Perdomo‐Sabogal, Daniel Gerighausen, Jing Qin, Katja Nowick
Software Mentions: 6
Published: over 8 years ago

10.3389/fimmu.2021.724015

Transcriptional, Epigenetic, and Functional Reprogramming of Monocytes From Non-Human Primates Following Chronic Alcohol Drinking
Cited by: 11
Author(s): Sloan A. Lewis, Suhas Sureshchandra, Brianna Doratt, Vanessa Jiménez, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-017-1165-7

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Cited by: 20
Author(s): Inês de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A.J. Ponder, Kerstin B. Meyer, Florian Markowetz
Software Mentions: 6
Published: over 7 years ago

10.1186/s13059-017-1335-7

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis
Cited by: 27
Author(s): Dei M. Elurbe, Sarita S. Paranjpe, Γεώργιος Γεωργίου, Ila van Kruijsbergen, Ozren Bogdanović, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen, Gert Jan C. Veenstra
Software Mentions: 6
Published: about 7 years ago

10.3390/jcm9051499

Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy
Cited by: 10
Author(s): Weng‐Tein Gi, Jan Haas, Farbod Sedaghat‐Hamedani, Elham Kayvanpour, Rewati Tappu, David Lehmann, Omid Shirvani Samani, Michael Wisdom, Andreas Keller, Hugo A. Katus, Benjamin Meder
Software Mentions: 6
Published: over 4 years ago

10.1073/pnas.1819788116

Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs
Cited by: 48
Author(s): Zhangming Yan, Norman Huang, Weixin Wu, Weizhong Chen, Yiqun Jiang, Jingyao Chen, Xuerui Huang, Xingzhao Wen, Jie Xu, Qiushi Jin, Kang Zhang, Zhe Chen, Shu Chien, Sheng Zhong
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12931-016-0459-8

Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations
Cited by: 47
Author(s): Robert S. Busch, Weiliang Qiu, Jessica Lasky‐Su, Jarrett Morrow, Gerard J. Criner, Dawn L. DeMeo
Software Mentions: 6
Published: about 8 years ago

10.1038/sdata.2016.73

Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands
Cited by: 7
Author(s): Panagiotis Moulos, Martina Samiotaki, George Panayotou, Skarlatos G. Dedos
Software Mentions: 6
Published: about 8 years ago

10.1038/s41598-019-44302-3

Dose-dependent effects of chronic alcohol drinking on peripheral immune responses
Cited by: 41
Author(s): Suhas Sureshchandra, Anthony M. Raus, Allen Jankeel, Brian Jin Kee Ligh, Nicole A.R. Walter, Natali Newman, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-019-57214-z

5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation
Cited by: 14
Author(s): Santiago Uribe-Lewis, Thomas Carroll, Suraj Menon, Anna M. Nicholson, Piotr J. Manasterski, Douglas J. Winton, Simon Buczacki, Adele Murrell
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-020-69905-z

A lncRNA landscape in breast cancer reveals a potential role for AC009283.1 in proliferation and apoptosis in HER2-enriched subtype
Cited by: 20
Author(s): Alberto Cedro‐Tanda, Magdalena Ríos-Romero, Sandra Romero-Córdoba, Mireya Cisneros-Villanueva, Rosa Rebollar-Vega, Luis Alfaro-Ruiz, Silvia Jiménez-Morales, Carlos Alberto Domínguez-Reyes, Felipe Villegas-Carlos, Alberto Tenorio-Torres, Verónica Bautista-Piña, Fredy Omar Beltrán-Anaya, Alfredo Hidalgo‐Miranda
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-020-75688-0

Analysis of open chromatin regions in bladder cancer links β-catenin mutations and Wnt signaling with neuronal subtype of bladder cancer
Cited by: 3
Author(s): Aleyna Eray, Perihan Yağmur Güneri, Gülden Özden Yılmaz, Gökhan Karakülah, Serap Erkek
Software Mentions: 6
Published: about 4 years ago

10.1093/hmg/ddv449

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation
Cited by: 42
Author(s): Isabel Mendizabal, Soojin V. Yi
Software Mentions: 6
Published: about 9 years ago

10.7554/eLife.52648

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
Cited by: 34
Author(s): Anneke Dixie Kakebeen, Alexander Daniel Chitsazan, Madison Corinne Williams, Lauren Saunders, Andrea E. Wills
Software Mentions: 6
Published: over 4 years ago

10.7554/eLife.63632

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
Cited by: 119
Author(s): Elliott Swanson, Cara Lord, Julian Reading, Alexander T Heubeck, Palak C. Genge, Zachary Thomson, Morgan Weiss, Xiaojun Li, Adam K. Savage, Richard Green, Troy R. Torgerson, Thomas F. Bumol, Lucas T. Graybuck, Peter J. Skene
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.45672

Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination
Cited by: 27
Author(s): Lee Langer, James M. Ward, Trevor Archer
Software Mentions: 6
Published: over 5 years ago

10.1007/s13238-020-00762-2

A human circulating immune cell landscape in aging and COVID-19
Cited by: 158
Author(s): Yingfeng Zheng, Xiuxing Liu, Wenqing Le, Lihui Xie, Li He, Wen Wen, Si Wang, Shuai Ma, Zhaofeng Huang, Jinguo Ye, Wen Shi, Yanxia Ye, Zunpeng Liu, Moshi Song, Weiqi Zhang, Jing‐Dong J. Han, Juan Carlos Izpisúa Belmonte, Chuan-Le Xiao, Jing Qu, Hongyang Wang, Guang‐Hui Liu, Wenru Su
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-017-4364-4

Pronounced strain-specific chemosensory receptor gene expression in the mouse vomeronasal organ
Cited by: 16
Author(s): Kyle Duyck, Vasha DuTell, Limei Ma, Ariel Paulson, Chong Yu
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-021-84667-y

Neuron-specific spinal cord translatomes reveal a neuropeptide code for mouse dorsal horn excitatory neurons
Cited by: 15
Author(s): Rebecca R Das Gupta, Louis Scheurer, Paweł Pelczar, Hendrik Wildner, Hanns Ulrich Zeilhofer
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2015.00169

Identifying differential transcription factor binding in ChIP-seq
Cited by: 21
Author(s): Dai-Ying Wu, Danielle Bittencourt, Michael R. Stallcup, Kimberly D. Siegmund
Software Mentions: 5
Published: over 9 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-78288-0

Common and personal target genes of the micronutrient vitamin D in primary immune cells from human peripheral blood
Cited by: 19
Author(s): Andrea Hanel, Antonio Neme, Marjo Malinen, Emmi Hämäläinen, Henna-Riikka Malmberg, Stéphane Etheve, Tomi‐Pekka Tuomainen, Jyrki K. Virtanen, Igor Bendik, Carsten Carlberg
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-021-07774-0

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
Cited by: 10
Author(s): Aileen R Ferraro, Abigail J Ameri, Zefu Lu, Masayuki Kamei, Robert J. Schmitz, Zachary A. Lewis
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pcbi.1008195

VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution
Cited by: 9
Author(s): Wei Wen, Adam J. Mead, Supat Thongjuea
Software Mentions: 5
Published: about 4 years ago

10.1038/sdata.2018.218

Small non-coding RNA expression in mouse nephrogenic mesenchymal progenitors
Cited by: 4
Author(s): Yu Leng Phua, Andrew Clugston, Kevin Hong Chen, Dennis Kostka, Jacqueline Ho
Software Mentions: 5
Published: about 6 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-019-40867-1

Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development
Cited by: 17
Author(s): Naomi D. Chrispijn, Dei M. Elurbe, Michaela Mickoleit, Marco Aben, Dennis E. M. de Bakker, Karolina M. Andralojc, Jan Huisken, Jeroen Bakkers, Leonie M. Kamminga
Software Mentions: 5
Published: over 5 years ago

10.1242/dev.131664

Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β‑catenin recruitment
Cited by: 99
Author(s): Yukio Nakamura, Eduardo Rodrigues Alves, Gert Jan C. Veenstra, Stefan Hoppler
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12864-021-07552-y

Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential
Cited by: 20
Author(s): Juanita Engelbrecht, Tuan A. Duong, S. Prabhu, Mohamed Seedat, Noëlani van den Berg
Software Mentions: 5
Published: over 3 years ago

10.18632/oncotarget.24907

Racial differences in endometrial cancer molecular portraits in The Cancer Genome Atlas
Cited by: 34
Author(s): David S. Guttery, Kevin Blighe, Konstantinos Polymeros, R. Paul Symonds, Salvador Macip, Esther L. Moss
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.37072

Changes in the genetic requirements for microbial interactions with increasing community complexity
Cited by: 60
Author(s): Manon Morin, Emily C Pierce, Rachel J Dutton
Software Mentions: 5
Published: about 6 years ago

10.1016/j.gdata.2015.07.002

RNAome sequencing delineates the complete RNA landscape
Cited by: 1
Author(s): Kasper Derks, Joris Pothof
Software Mentions: 5
Published: about 9 years ago

10.12688/f1000research.15433.1

Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets
Cited by: 5
Author(s): Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Héctor Corrada Bravo
Software Mentions: 5
Published: over 6 years ago

10.1002/ctm2.498

An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single‐base resolution methylome and hydroxymethylome
Cited by: 6
Author(s): Yingxin Han, Liyan Ji, Yanfang Guan, Mengya Ma, Pansong Li, Yinge Xue, Yinxin Zhang, Wanqiu Huang, Yuhua Gong, Li Jiang, Xipeng Wang, Hong Xie, Boping Zhou, Jiayin Wang, Junwen Wang, Jinghua Han, Yuliang Deng, Xin Yi, Fei Gao, Jian Huang
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-015-0605-5

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
Cited by: 61
Author(s): Santiago Uribe-Lewis, Rory Stark, Thomas Carroll, Mark J. Dunning, Martin Bachman, Yoko Itō, Lovorka Stojic, Silvia Halim, Sarah L. Vowler, Andy G. Lynch, Benjamin Delatte, Eric James de Bony, Laurence Colin, Matthieu Defrance, Felix Krueger, Ana Luísa Silva, Rogier ten Hoopen, Ashraf E.K. Ibrahim, François Fuks, Adele Murrell
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.34042

Differential 3’ processing of specific transcripts expands regulatory and protein diversity across neuronal cell types
Cited by: 21
Author(s): Saša Jereb, Hun‐Way Hwang, Eric Van Otterloo, Eve-Ellen Govek, John Fak, Yuan Yuan, Mary E. Hatten, Robert B. Darnell
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-015-0856-1

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation
Cited by: 85
Author(s): Stephan Busche, Xiaojian Shao, Maxime Caron, Tony Kwan, Fiona Allum, Warren A. Cheung, Bing Ge, Susan Westfall, Simon Maguire, Amy Barrett, Jordana T. Bell, Mark I. McCarthy, Panos Deloukas, Mathieu Blanchette, Guillaume Bourque, Timothy D. Spector, Mark Lathrop, Tomi Pastinen, Elin Grundberg
Software Mentions: 5
Published: almost 9 years ago

10.1007/s00253-016-7588-3

Ploidy influences the functional attributes of de novo lager yeast hybrids
Cited by: 65
Author(s): Kristoffer Krogerus, Mikko Arvas, Matteo De Chiara, Frederico Magalhães, Laura Mattinen, Merja Oja, Virve Vidgren, Jia-Xing Yue, Gianni Liti, Brian Gibson
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.27159

Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancer
Cited by: 29
Author(s): Laura Cato, Antje Neeb, Adam Sharp, Víctor Buzón, Scott B. Ficarro, Linxiao Yang, Claudia Muhle‐Goll, Nane C. Kuznik, Ruth Riisnaes, Daniel Nava Rodrigues, Olivier Armant, Victor Gourain, Guillaume Adelmant, Emmanuel Amankwah Ntim, Thomas Westerling, David Dolling, Pasquale Rescigno, Ines Figueiredo, Friedrich Fauser, Jiansheng Wu, Jaice T. Rottenberg, L. Shatkina, Claudia Ester, Burkhard Luy, Holger Puchta, Jakob Troppmair, Nicole Jung, Stefan Bräse, Uwe Strähle, Jarrod A. Marto, G. Ulrich Nienhaus, Bissan Al‐Lazikani, Xavier Salvatella, Johann S. de Bono, Andrew C. B. Cato, Myles Brown
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2105-15-141

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
Cited by: 17
Author(s): Martin A. Rijlaarsdam, Yvonne G. van der Zwan, Lambert C. J. Dorssers, Leendert H. J. Looijenga
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pgen.1006587

Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease
Cited by: 38
Author(s): Katrina Soderquest, Arnulf Hertweck, Claudia Giambartolomei, Stephen Henderson, Mohamed Rosmawati, Rimma Goldberg, Esperanza Perucha, Lude Franke, Javier Herrero, Vincent Plagnol, Richard G. Jenner, Graham M. Lord
Software Mentions: 5
Published: almost 8 years ago

10.1093/bioinformatics/btx099

DeepBlueR: large-scale epigenomic analysis in R
Cited by: 6
Author(s): Felipe Albrecht, Markus List, Christoph Bock, Thomas Lengauer
Software Mentions: 5
Published: almost 8 years ago

10.3389/fgene.2019.00184

Associations Between Behavioral Effects of Bisphenol A and DNA Methylation in Zebrafish Embryos
Cited by: 38
Author(s): Pål A. Olsvik, Paul Whatmore, Samuel Penglase, Kaja H. Skjærven, Marc Anglès d’Auriac, Ståle Ellingsen
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-4800-0

Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits
Cited by: 20
Author(s): Min Wang, Tim Hancock, Amanda J. Chamberlain, Christy J. Vander Jagt, J.E. Pryce, Benjamin G. Cocks, Michael E. Goddard, Ben J. Hayes
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-020-02013-3

FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
Cited by: 33
Author(s): Magali Hennion, Jean‐Michel Arbona, Laurent Lacroix, Corinne Cruaud, Bertrand Theulot, Benoît Le Tallec, Florence Proux, Xia Wu, Elizaveta Novikova, Stéfan Engelen, Arnaud Lemainque, Benjamin Audit, Olivier Hyrien
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-021-04208-2

TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes
Cited by: 12
Author(s): Maxim Ivanov, Albin Sandelin, Sebastian Marquardt
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-016-2738-7

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102
Cited by: 22
Author(s): Nathan Brown, Robert F. Mueller, Jonathan W. Shepardson, Zachary C. Landry, Jeff Morré, Christoph Maier, F. Joan Hardy, Theo W. Dreher
Software Mentions: 4
Published: over 8 years ago

10.1186/s12915-018-0556-x

Evolutionary stability of topologically associating domains is associated with conserved gene regulation
Cited by: 108
Author(s): Jan Krefting, Miguel A. Andrade‐Navarro, Jonas Ibn-Salem
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-27979-w

Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea
Cited by: 22
Author(s): Himanshi Bhatia, Niraj Khemka, Mukesh Jain, Rohini Garg
Software Mentions: 4
Published: over 6 years ago

10.1016/j.stem.2019.05.013

Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis
Cited by: 53
Author(s): Miller Huang, Jignesh Tailor, Qiqi Zhen, Aaron H. Gillmor, Matthew Miller, Holger Weishaupt, Justin Chen, Tina Zheng, Emily K. Nash, Lauren McHenry, Zhenyi An, Fubaiyang Ye, Yasuhiro Takashima, James Clarke, Harold Ayetey, Florence M.G. Cavalli, Betty Luu, Branden S. Moriarity, Shirin Ilkhanizadeh, Lukas Chávez, Chunying Yu, Kathreena M. Kurian, Thierry Magnaldo, Nicolas Sévenet, Philipp Koch, Steven M. Pollard, Peter B. Dirks, M Snyder, David A. Largaespada, Yoon Jae Cho, Joanna J. Phillips, Fredrik J. Swartling, A. Sorana Morrissy, Marcel Kool, Stefan M. Pfister, Michael D. Taylor, Austin Smith, William A. Weiss
Software Mentions: 4
Published: about 5 years ago

10.3390/cancers12061618

Rare Tumor-Normal Matched Whole Exome Sequencing Identifies Novel Genomic Pathogenic Germline and Somatic Aberrations
Cited by: 1
Author(s): Ryan Sprissler, Bryce Perkins, Laurel Johnstone, Hani M. Babiker, Pavani Chalasani, Branden Lau, Michael F. Hammer, Daruka Mahadevan
Software Mentions: 4
Published: over 4 years ago

10.1186/s13072-018-0190-4

“Same difference”: comprehensive evaluation of four DNA methylation measurement platforms
Cited by: 26
Author(s): Thadeous J. Kacmarczyk, Mame P. Fall, Xihui Zhang, Xin Yuan, Yushan Li, Alicia Alonso, Doron Betel
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.16048

HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Cited by: 26
Author(s): Barbara Schrörs, Silke Lübcke, Volker Lennerz, Martina Fatho, Anne Bicker, Catherine Wölfel, Patrick Derigs, Thomas Hankeln, Dirk Schadendorf, Annette Paschen, Thomas Wölfel
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.8867

intansv: an R package for integrative analysis of structural variations
Cited by: 4
Author(s): Jia Lee, Na Liu, Fangfang Huang, Zhengfu Zhou, Xin He, Haoran Li, Zhizhan Wang, Wen Yao
Software Mentions: 4
Published: over 4 years ago

10.1038/s42003-020-01413-2

A haplotype-led approach to increase the precision of wheat breeding
Cited by: 62
Author(s): Jemima Brinton, Ricardo H. Ramírez-González, James Simmonds, Luzie U. Wingen, Simon Orford, Simon Griffiths, Wheat Genome, Georg Haberer, Manuel Spannagl, Sean Walkowiak, Curtis Pozniak, Cristóbal Uauy
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.59111

Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution
Cited by: 5
Author(s): Shanaya Shital Shah, Stella R. Hartono, Frédéric Chédin, Wolf Dietrich Heyer
Software Mentions: 4
Published: about 4 years ago

10.3389/fnmol.2021.672614

Bisulfite Amplicon Sequencing Can Detect Glia and Neuron Cell-Free DNA in Blood Plasma
Cited by: 11
Author(s): Zac Chatterton, Natalia Mendelev, Sean Chen, Walter Carr, Gary H. Kamimori, Yongchao Ge, Andrew J. Dwork, Fatemeh Haghighi
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-016-1428-4

An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Cited by: 45
Author(s): Roberto A. Barrero, Kathryn R. Napier, J. H. Cunnington, L. W. Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás Szabó, Simon Bulman, Adam Hunter, L. I. Ward, Mark Whattam, M. Bellgard
Software Mentions: 4
Published: almost 8 years ago

10.1155/2013/340620

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity
Cited by: 79
Author(s): Matteo Carrara, Marco Beccuti, Fulvio Lazzarato, Federica Cavallo, Francesca Cordero, Susanna Donatelli, Raffaele Calogero
Software Mentions: 4
Published: almost 12 years ago

10.7554/eLife.41641

IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiation
Cited by: 104
Author(s): Esther Zumaquero, Sara L Stone, Christopher D. Scharer, Scott A. Jenks, Anoma Nellore, Betty Mousseau, Antonio Rosal-Vela, Davide Botta, John E. Bradley, Wojciech Wojciechowski, Travis Ptacek, Maria I. Danila, Jeffrey C. Edberg, S. Louis Bridges, Robert P. Kimberly, W. Winn Chatham, Trenton R. Schoeb, Alexander F. Rosenberg, Jeremy M. Boss, Igñacio Sanz, Frances E. Lund
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0070387

Link between Epigenomic Alterations and Genome-Wide Aberrant Transcriptional Response to Allergen in Dendritic Cells Conveying Maternal Asthma Risk
Cited by: 31
Author(s): Lyudmila Mikhaylova, Yiming Zhang, Lester Kobzik, Alexey V. Fedulov
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

10.1186/1471-2105-14-244

RCircos: an R package for Circos 2D track plots
Cited by: 425
Author(s): Hongen Zhang, Paul S. Meltzer, Sean Davis
Software Mentions: 4
Published: over 11 years ago

Projects: bioconductor: GenomicRanges

Papers Mentioning GenomicRanges 323