bioconductor: Gviz | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

10.3389/fonc.2020.00423

Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago

10.12688/f1000research.13577.2

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
Cited by: 2
Author(s): Enrico Ferrero
Software Mentions: 21
Published: over 6 years ago

10.12688/f1000research.18456.1

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

10.1186/s12864-015-2140-x

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Cited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Software Mentions: 15
Published: about 9 years ago

10.3389/fcell.2021.642724

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

10.1186/s12859-019-3029-5

CAGEfightR: analysis of 5′-end data using R/Bioconductor
Cited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: about 5 years ago

10.3390/ijms22062790

Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy
Cited by: 4
Author(s): Steffan Noe Christiansen, Stine Jacobsen, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Linea C Trudsø, Karsten Olsen, Jacob Tfelt-Hansen, Jytte Banner, Niels Morling
Software Mentions: 13
Published: over 3 years ago

10.1186/s13059-021-02293-3

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells
Cited by: 47
Author(s): Drew Neavin, Quan Nguyen, Maciej Daniszewski, Helena Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W. Lukowski, Duncan E. Crombie, Grace E. Lidgerwood, Damián Hernández, James C. Vickers, Anthony Cook, Nathan J. Palpant, Alice Pébay, Alex W. Hewitt, Joseph E. Powell
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.8839.3

A cross-package Bioconductor workflow for analysing methylation array data
Cited by: 80
Author(s): Jovana Maksimovic, Belinda Phipson, Alicia Oshlack
Software Mentions: 12
Published: over 7 years ago

10.12688/f1000research.17082.2

Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk)
Cited by: 4
Author(s): Christophe D. Chabbert, Tanja Eberhart, Ilaria Guccini, Wilhelm Krek, Werner J. Kovacs
Software Mentions: 12
Published: over 5 years ago

10.3389/fgene.2020.580580

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)
Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: about 4 years ago

10.1186/s12859-019-2706-8

svist4get: a simple visualization tool for genomic tracks from sequencing experiments
Cited by: 32
Author(s): Artyom A. Egorov, Ekaterina Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev, Ivan V. Kulakovskiy
Software Mentions: 11
Published: over 5 years ago

10.1186/gb-2012-13-8-r77

ggbio: an R package for extending the grammar of graphics for genomic data
Cited by: 265
Author(s): Tao Yin, Dianne Cook, Michael C. Lawrence
Software Mentions: 11
Published: almost 13 years ago

10.1371/journal.pgen.1007102

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
Cited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: almost 7 years ago

10.1371/journal.pgen.1009376

Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae
Cited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: almost 4 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: over 5 years ago

10.7554/eLife.50004

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
Cited by: 15
Author(s): A.B. Hickman, Shweta Kailasan, Pavol Genzor, Astrid D. Haase, Fred Dyda
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13148-020-0824-9

Maternal diabetes and obesity influence the fetal epigenome in a largely Hispanic population
Cited by: 18
Author(s): Heather E. Rizzo, Elia N. Escaname, Nicholas B. Alana, Elizabeth Lavender, Jonathan Gelfond, Roman Fernandez, Matthew A. Hibbs, Julie King, Nicholas Carr, Cynthia L. Blanco
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13040-021-00267-6

eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals
Cited by: 11
Author(s): Theodore G. Drivas, Anastasia Lucas, Marylyn D. Ritchie
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0209656

A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn’s disease patients
Cited by: 14
Author(s): Andrew Y. Li Yim, Jessica R. de Bruyn, Nicolette W. Duijvis, Catriona Sharp, Enrico Ferrero, Wouter J. de Jonge, Manon E. Wildenberg, Marcel M.A.M. Mannens, Christianne J. Buskens, Geert R. D’Haens, Peter Henneman, Anje A. te Velde
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: about 6 years ago

10.1371/journal.ppat.1009374

SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event
Cited by: 31
Author(s): Madlen Stange, Alfredo Mari, Tim Roloff, Helena M. B. Seth-Smith, Michael Schweitzer, Myrta Brunner, Karoline Leuzinger, Kirstine Kobberøe Søgaard, Alexander Gensch, Sarah Tschudin‐Sutter, Simon Fuchs, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Rita Schneider-Sliwa, Manuel Battegay, Hans H. Hirsch, Adrian Egli
Software Mentions: 9
Published: over 3 years ago

10.1186/s13029-016-0059-5

A bedr way of genomic interval processing
Cited by: 19
Author(s): Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei‐Fei Liu, Paul C. Boutros
Software Mentions: 9
Published: almost 8 years ago

10.1016/j.molcel.2018.08.004

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development
Cited by: 226
Author(s): Mateusz Mendel, Kuan-Ming Chen, David Homolka, Pascal Gos, Radha Raman Pandey, A.A. McCarthy, Ramesh S. Pillai
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-019-44597-2

NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule
Cited by: 3
Author(s): Francisco Requena, Helena G Asenjo, Guillermo Barturen, Jordi Martorell-Marugán, Pedro Carmona-Sáez, David Landeira
Software Mentions: 8
Published: over 5 years ago

10.3389/fonc.2018.00100

Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues
Cited by: 35
Author(s): Erfan Aref‐Eshghi, Laila C. Schenkel, Peter Ainsworth, Hanxin Lin, David I. Rodenhiser, Jean‐Claude Cutz, Bekim Sadiković
Software Mentions: 8
Published: over 6 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/s12859-016-1051-4

gtrellis: an R/Bioconductor package for making genome-level Trellis graphics
Cited by: 17
Author(s): Zuguang Gu, Roland Eils, Matthias Schlesner
Software Mentions: 8
Published: over 8 years ago

10.1371/journal.pcbi.1007814

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility
Cited by: 4
Author(s): Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado‐Sainz, Felipe Cortés‐Ledesma
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pgen.1009094

Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
Cited by: 2
Author(s): Aziz Aiderus, Justin Y. Newberg, Liliana Guzmán-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song Choon Lee, Kenneth Ban, Keith Rogers, Susan Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen Mann, Michael B. Mann
Software Mentions: 8
Published: over 3 years ago

10.1186/s13148-016-0230-5

Peripheral blood methylation profiling of female Crohn’s disease patients
Cited by: 40
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Jing Hua Zhao, Wouter J. de Jonge, Geert R. D’Haens, Marcel M.A.M. Mannens, Adri N. Mul, Anje A. te Velde, Peter Henneman
Software Mentions: 8
Published: over 8 years ago

10.1186/s13072-016-0064-6

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing
Cited by: 59
Author(s): Andrew Keniry, Linden J. Gearing, Natasha Jansz, Joy Liu, Aliaksei Z. Holik, Peter Hickey, Sarah Kinkel, Darcy Moore, Kelsey Breslin, Kelan Chen, Ruijie Liu, Chris Phillips, Miha Pakusch, Christine Biben, Julie Sheridan, Benjamin T. Kile, Catherine Carmichael, Matthew E. Ritchie, Douglas J. Hilton, Marnie E. Blewitt
Software Mentions: 8
Published: over 8 years ago

10.3390/ijms22073296

Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases
Cited by: 5
Author(s): Markus Kwik, Stefan Hainzl, Jan Oppelt, Boris Tichý, Ulrich Koller, Emanuele Bernardinelli, Markus J. Steiner, Greta Zara, Charity Nofziger, Serge Weis, Markus Paulmichl, Silvia Dossena, Wolfgang Patsch, Selma M. Soyal
Software Mentions: 8
Published: over 3 years ago

10.1186/s13148-018-0453-8

Peripheral blood epi-signature of Claes-Jensen syndrome enables sensitive and specific identification of patients and healthy carriers with pathogenic mutations in KDM5C
Cited by: 55
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Cindy Skinner, Peter Ainsworth, Hanxin Lin, Guillaume Paré, David I. Rodenhiser, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12859-015-0568-2

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns
Cited by: 95
Author(s): Tiphaine Martin, İdil Yet, Pei-Chien Tsai, Jordana T. Bell
Software Mentions: 7
Published: over 9 years ago

10.1038/s41598-019-44491-x

The LL-100 panel: 100 cell lines for blood cancer studies
Cited by: 67
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Wilhelm G. Dirks, Sonja Eberth, Max Koeppel, Roderick A.F. MacLeod, Stefan Nagel, Klaus G. Steube, Cord C. Uphoff, Hans G. Drexler
Software Mentions: 7
Published: over 5 years ago

10.1136/jitc-2020-001335

Druggable epigenetic suppression of interferon-induced chemokine expression linked to MYCN amplification in neuroblastoma
Cited by: 15
Author(s): Johanna A Seier, Julia Reinhardt, Kritika Saraf, Susanna S. Ng, Julian Philipp Layer, Dillon Corvino, Kristina Althoff, Frank A. Giordano, Alexander Schramm, Matthias Fischer, Michael Hölzel
Software Mentions: 7
Published: over 3 years ago

10.1093/bioinformatics/btx346

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
Cited by: 451
Author(s): Bernat Gel, Eduard Serra
Software Mentions: 7
Published: over 7 years ago

10.1038/srep41531

Transcriptomic analysis of common carp anterior kidney during Cyprinid herpesvirus 3 infection: Immunoglobulin repertoire and homologue functional divergence
Cited by: 23
Author(s): Matthew J. Neave, Agus Sunarto, Kenneth A. McColl
Software Mentions: 7
Published: almost 8 years ago

10.1093/bioinformatics/btz031

ensembldb: an R package to create and use Ensembl-based annotation resources
Cited by: 76
Author(s): Johannes Michael Rainer, Laurent Gatto, Christian X. Weichenberger
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.ppat.1009130

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles
Cited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: almost 4 years ago

10.7554/eLife.66668

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo
Cited by: 66
Author(s): Marissa M Gaskill, Tyler J. Gibson, Elizabeth D Larson, Melissa M. Harrison
Software Mentions: 7
Published: over 3 years ago

10.1038/mt.2014.86

Characterizing Human Stem Cell–derived Sensory Neurons at the Single-cell Level Reveals Their Ion Channel Expression and Utility in Pain Research
Cited by: 105
Author(s): Gareth T. Young, Alex Gutteridge, Heather De Fox, Anna Wilbrey, Lishuang Cao, Lily T Cho, Adam R. Brown, Caroline Benn, Laura R Kammonen, Julia Friedman, Magda Bictash, Paul Whiting, James Bilsland, Edward B. Stevens
Software Mentions: 6
Published: over 10 years ago

10.1111/pce.13188

Global spatial analysis of Arabidopsis natural variants implicates 5′UTR splicing ofLATE ELONGATED HYPOCOTYLin responses to temperature
Cited by: 11
Author(s): Allan B. James, Stuart Sullivan, Hugh G. Nimmo
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2021.723519

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken
Cited by: 8
Author(s): Siyuan Xing, Ranran Liu, Guiping Zhao, M.A.M. Groenen, Ole Madsen, Lu Liu, Maiqing Zheng, Qiao Wang, Zhou Wu, R.P.M.A. Crooijmans, Jie Wen
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pcbi.1006940

CNEr: A toolkit for exploring extreme noncoding conservation
Cited by: 15
Author(s): Ge Tan, Dimitris Polychronopoulos, Boris Lenhard
Software Mentions: 6
Published: about 5 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

10.1093/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

10.1371/journal.pone.0075136

Synergistic Re-Activation of Epigenetically Silenced Genes by Combinatorial Inhibition of DNMTs and LSD1 in Cancer Cells
Cited by: 31
Author(s): Han Han, Xiaojing Yang, Kurinji Pandiyan, Gangning Liang
Software Mentions: 6
Published: about 11 years ago

10.1186/s12859-020-3434-9

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Cited by: 7
Author(s): Martin Lewinski, Yannik Bramkamp, Tino Köster, Dorothee Staiger
Software Mentions: 6
Published: over 4 years ago

10.18632/oncotarget.24656

TP53 and OSBPL10 alterations in diffuse large B-cell lymphoma: prognostic markers identified via exome analysis of cases with extreme prognosis
Cited by: 10
Author(s): Akito Dobashi, Yosuke Togashi, Norio Tanaka, Masahiro Yokoyama, Naoko Tsuyama, Satoko Baba, Seiichi Mori, Kiyohiko Hatake, Toshiharu Yamaguchi, Tetsuo Noda, Kengo Takeuchi
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.ppat.1009567

ATRX limits the accessibility of histone H3-occupied HSV genomes during lytic infection
Cited by: 7
Author(s): Joseph M Cabral, Camille H. Cushman, Catherine Sodroski, David M. Knipe
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-017-4386-y

Global accumulation of circRNAs during aging in Caenorhabditis elegans
Cited by: 127
Author(s): Mariela Cortés-López, Matthew Gruner, Daphne A. Cooper, Hannah N. Gruner, Alexandru-Ioan Voda, Alexander M. van der Linden, Pedro Miura
Software Mentions: 6
Published: almost 7 years ago

10.1186/s13059-014-0483-2

Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia
Cited by: 140
Author(s): Ruth Pidsley, Joana Viana, Eilís Hannon, Helen Spiers, Claire Troakes, Safa Al-Saraj, Naguib Mechawar, Gustavo Turecki, Leonard C. Schalkwyk, Nicholas John Bray, Jonathan Mill
Software Mentions: 6
Published: about 10 years ago

10.1186/s13059-017-1284-1

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
Cited by: 75
Author(s): N. Davidson, Anthony D. K. Hawkins, Alicia Oshlack
Software Mentions: 6
Published: over 7 years ago

10.3389/fpls.2021.642828

Natural Genetic Diversity in Tomato Flavor Genes
Cited by: 12
Author(s): Lara Pereira, Manoj Sapkota, Michael Alonge, Yi Zheng, Youjun Zhang, Hamid Razifard, Nathan K Taitano, Michael C. Schatz, Alisdair R. Fernie, Ying Wang, Zhangjun Fei, Ana L. Caicedo, Denise M. Tieman, Esther van der Knaap
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.ppat.1007634

The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response
Cited by: 49
Author(s): Leon Louis Seifert, Clara Si, Debjani Saha, Mohammad Sadic, Maren de Vries, Sarah Ballentine, Aaron Briley, Guojun Wang, Ana M. Valero-Jimenez, Adil Mohamed, Uwe Schaefer, Hong M. Moulton, Adolfo Garcı́a-Sastre, Shashank Tripathi, Brad R. Rosenberg, Meike Dittmann
Software Mentions: 6
Published: about 5 years ago

10.3390/v10090512

Robust Innate Immunity of Young Rabbits Mediates Resistance to Rabbit Hemorrhagic Disease Caused by Lagovirus Europaeus GI.1 But Not GI.2
Cited by: 28
Author(s): Matthew J. Neave, Robyn N. Hall, Nina Huang, Kenneth A. McColl, Peter J. Kerr, Marion Hoehn, Jennifer Taylor, Tanja Strive
Software Mentions: 6
Published: about 6 years ago

10.1128/mSphere.00535-21

A Comprehensive Map of Mycobacterium tuberculosis Complex Regions of Difference
Cited by: 11
Author(s): Dmitry Bespiatykh, Julia Bespyatykh, Igor Mokrousov, Egor Shitikov
Software Mentions: 6
Published: about 3 years ago

10.1128/mBio.01714-20

Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium
Cited by: 20
Author(s): Michael Seidl, Holger Kramer, David E. Cook, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Luigi Faino, B.P.H.J. Thomma
Software Mentions: 6
Published: about 4 years ago

10.1186/s12920-021-01003-z

Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia
Cited by: 5
Author(s): Megumi Onishi-Seebacher, Galina Erikson, Zoe Sawitzki, Devon P. Ryan, Gabriele Greve, Michael Lübbert, Thomas Jenuwein
Software Mentions: 6
Published: over 3 years ago

10.1038/srep34220

Widespread DNA hypomethylation and differential gene expression in Turner syndrome
Cited by: 99
Author(s): Christian Trolle, Morten Muhlig Nielsen, Anne Skakkebæk, Philippe Lamy, Søren Vang, Jakob Hedegaard, Iver Nordentoft, Torben F. Ørntoft, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 6
Published: about 8 years ago

10.1186/s13148-020-00998-z

Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer
Cited by: 8
Author(s): Louis El Khoury, Shuang Fu, Ryan A. Hlady, Ryan T. Wagner, Liguo Wang, Jeanette E. Eckel‐Passow, Erik P. Castle, Melissa L. Stanton, R. Houston Thompson, Alexander S. Parker, Thai H. Ho, Keith D. Robertson
Software Mentions: 6
Published: almost 4 years ago

10.3390/cancers12040792

Analysis of HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas and Paired Normal Mucosae Reveals Cyclin D1 Deregulation and Compensatory Effect of Cyclin D2
Cited by: 7
Author(s): Jiří Novotný, Veronika Bandúrová, Hynek Strnad, Martin Chovanec, Miluše Hradilová, Jana Šáchová, Martin Šteffl, Josipa Grušanović, Roman Kodet, Václav Pačes, Lukáš Lacina, Karel Smetana, Jan Plzák, Michal Kolář, Tomáš Vomastek
Software Mentions: 5
Published: over 4 years ago

10.3390/pathogens10091196

Nanopore Assay Reveals Cell-Type-Dependent Gene Expression of Vesicular Stomatitis Indiana Virus and Differential Host Cell Response
Cited by: 2
Author(s): Balázs Kakuk, A. Kiss, Gábor Torma, Zsolt Csabai, István Prazsák, Máté Mizik, Klára Megyeri, Dóra Tombácz, Zsolt Boldogkői
Software Mentions: 5
Published: about 3 years ago

10.3390/cells9030665

Dysregulated Antibody, Natural Killer Cell and Immune Mediator Profiles in Autoimmune Thyroid Diseases
Cited by: 17
Author(s): Tiphaine Martin, Kristina M. Ilieva, Alessia Visconti, Michelle Beaumont, Steven Kiddle, Richard Dobson, Massimo Mangino, Ee Mun Lim, Marija Pezer, Claire J. Steves, Jordana T. Bell, Scott G. Wilson, Gordan Lauc, Mario Roederer, John P. Walsh, Tim D. Spector, Sophia N. Karagiannis
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms22020678

JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions
Cited by: 15
Author(s): Tara Procida, Tobias Friedrich, Antonia Jack, Martina Peritore, Clemens Bönisch, H. Christian Eberl, Nadine Daus, Konstantin Kletenkov, Andrea Nist, Thorsten Stiewe, Tilman Borggrefe, Matthias Mann, Marek Bartkuhn, Sandra B. Hake
Software Mentions: 5
Published: almost 4 years ago

10.1186/1471-2164-14-853

Reprogramming of lysosomal gene expression by interleukin-4 and Stat6
Cited by: 18
Author(s): Louise M Brignull, Zsolt Czimmerer, Hafida Saidi, Bence Dániel, Izabel Vianna Villela, Nathan W. Bartlett, Sebastian L. Johnston, Lisiane B. Meira, László Nagy, Axel Nohturfft
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0123609

Mapsnp: An R Package to Plot a Genomic Map for Single Nucleotide Polymorphisms
Cited by: 5
Author(s): Fuquan Zhang, Yong Xu, Hongbao Cao, Chunhui Jin, Cheng Zhang, Guoqiang Wang, Yin Yao Shugart
Software Mentions: 5
Published: over 9 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

10.1073/pnas.2110758118

TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia
Cited by: 22
Author(s): Maike Bensberg, Olof Rundquist, Aida Selimović, Cathrine Lagerwall, Mikael Benson, Mika Gustafsson, Hartmut Vogt, Antonio Lentini, Colm E. Nestor
Software Mentions: 5
Published: over 3 years ago

10.1038/s41375-020-0856-3

Contribution of CTCF binding to transcriptional activity at the HOXA locus in NPM1-mutant AML cells
Cited by: 19
Author(s): Reza Ghasemi, Heidi Struthers, Elisabeth R. Wilson, David H. Spencer
Software Mentions: 5
Published: over 4 years ago

10.15252/emmm.201911115

Disease modeling of a mutation in α‐actinin 2 guides clinical therapy in hypertrophic cardiomyopathy
Cited by: 77
Author(s): Maksymilian Prondzynski, Marc D. Lemoine, Antonia T.L. Zech, András Horváth, Vittoria Di Mauro, Jussi T. Koivumäki, Nico Kresin, Josefine Busch, T. Krause, Elisabeth Krämer, Saskia Schlossarek, Michael Spohn, Felix W. Friedrich, Julia Münch, Sandra D. Laufer, Charles Redwood, Alexander E Volk, Arne Hansen, Giulia Mearini, Daniele Catalucci, Christian Meyer, Torsten Christ, Monica Patten, Thomas Eschenhagen, Lucie Carrier
Software Mentions: 5
Published: about 5 years ago

10.1128/mSystems.00195-17

Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome
Cited by: 8
Author(s): Kathy N. Lam, Eric C. Martens, Trevor C. Charles
Software Mentions: 5
Published: over 6 years ago

10.1016/j.celrep.2019.12.049

Trypanosoma brucei ATR Links DNA Damage Signaling during Antigenic Variation with Regulation of RNA Polymerase I-Transcribed Surface Antigens
Cited by: 21
Author(s): Jennifer Ann Black, Kathryn Crouch, Leandro Lemgruber, Craig Lapsley, Nicholas J. Dickens, Luíz Ricardo Orsini Tosi, Jeremy C. Mottram, Richard McCulloch
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-015-0620-2

AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing
Cited by: 13
Author(s): Jesper R. Gådin, Ferdinand M. van’t Hooft, Per Eriksson, Lasse Folkersen
Software Mentions: 4
Published: over 9 years ago

10.1186/s12915-020-00783-7

Tropomyosin 1 genetically constrains in vitro hematopoiesis
Cited by: 8
Author(s): Christopher S. Thom, Chintan Jobaliya, Kimberly Lorenz, Jean Ann Maguire, Alyssa Gagne, Paul Gadue, Deborah L. French, Benjamin F. Voight
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

10.7717/peerj.10234

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
Cited by: 48
Author(s): Alejandro Berrío, Valerie Gartner, Gregory A. Wray
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pbio.3000382

LATS1/2 suppress NFκB and aberrant EMT initiation to permit pancreatic progenitor differentiation
Cited by: 19
Author(s): Caitlin M. Braitsch, D. Berfin Azizoglu, Yadanar Htike, Haley R. Barlow, Ulrike Schnell, Christopher Chaney, Thomas J. Carroll, Ben Z. Stanger, Ondine Cleaver
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0130379

A FOXM1 Dependent Mesenchymal-Epithelial Transition in Retinal Pigment Epithelium Cells
Cited by: 13
Author(s): Parul Choudhary, Benjamin T Dodsworth, Ben S. Sidders, Alex Gutteridge, Christos Michaelides, Joshua K. Duckworth, Paul J. Whiting, Caroline Benn
Software Mentions: 4
Published: over 9 years ago

10.15252/embr.201847592

CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes
Cited by: 57
Author(s): Anil Paul Chirackal Manavalan, Květa Pilařová, Michael Kluge, Koen Bartholomeeusen, Michal Rájecký, Jan Oppelt, Prashant Khirsariya, Kamil Paruch, Lumír Krejčí, Caroline C. Friedel, Dalibor Blažek
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.686691

Dynamics of the Magnitude, Breadth and Depth of the Antibody Response at Epitope Level Following Dengue Infection
Cited by: 5
Author(s): Francesca Falconi-Agapito, Karen Kerkhof, Xiomara Merino, Johan Míchiels, Marjan Van Esbroeck, Koen Bartholomeeusen, Michael Talledo, Kevin K. Ariën
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2019.02451

Pan-Cancer Analysis Reveals Disrupted Circadian Clock Associates With T Cell Exhaustion
Cited by: 51
Author(s): Yingcheng Wu, Baorui Tao, Tianyang Zhang, Yihui Fan, Renfang Mao
Software Mentions: 4
Published: about 5 years ago

10.1186/s13059-016-1053-6

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms
Cited by: 114
Author(s): Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs Moed, Hailiang Mei, M.A. van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla Kallen, Albert Hofman, Diana van Heemst, Eco J. C. de Geus, Jenny van Dongen, Joris Deelen, Leonard H van den Berg, Joyce B. J. van Meurs, Ritsert C. Jansen, Peter A.C. ’t Hoen, Lude Franke, Cisca Wijmenga, Jan H. Veldink, Morris A. Swertz, Marleen M.J. van Greevenbroek, Cornelia M. van Duijn, Dorret I. Boomsma, P. Eline Slagboom, Bastiaan T. Heijmans
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-021-02272-8

A comprehensive enhancer screen identifies TRAM2 as a key and novel mediator of YAP oncogenesis
Cited by: 16
Author(s): Li Li, Alejandro P. Ugalde, Colinda L.G.J. Scheele, Sebastian M. Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gözde Korkmaz, Ran Elkon, Miao‐Ping Chien, You Li, Pin-Rui Su, Onno B. Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber, Ruiqi Han, Pieter C. van Breugel, Rui Lopes, Peter ten Dijke, Jacco van Rheenen, Reuven Agami
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms19082285

Effect of ACTH and hCG on the Expression of Gonadotropin-Inducible Ovarian Transcription Factor 1 (Giot1) Gene in the Rat Adrenal Gland
Cited by: 6
Author(s): Karol Jopek, Marianna Tyczewska, Manjunath Ramanjaneya, Marta Szyszka, Piotr Celichowski, Paulina Milecka, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 4
Published: over 6 years ago

10.1128/JVI.01399-20

Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level
Cited by: 22
Author(s): Caroline C. Friedel, Adam W. Whisnant, Lara Djaković, Andrzej Rutkowski, Marie-Sophie Friedl, Michael Kluge, James C Williamson, Somesh Sai, Ramón Vidal, Sascha Sauer, Thomas Hennig, Arnhild Grothey, Andrea Milić, Bhupesh K. Prusty, Paul J. Lehner, Nicholas J Matheson, Florian Erhard, Lars Dölken
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2018.00193

A Novel Loss-of-Function Variant in Transmembrane Protein 263 (TMEM263) of Autosomal Dwarfism in Chicken
Cited by: 13
Author(s): Zhou Wu, Martijn F.L. Derks, Bert Dibbits, Hendrik Jan Megens, M.A.M. Groenen, R.P.M.A. Crooijmans
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-36561-3

Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication
Cited by: 30
Author(s): Sebastian Theobald, Tammi Camilla Vesth, Jakob Kræmmer Haar Rendsvig, Kristian Fog Nielsen, Robert Riley, Lucas M. Abreu, Asaf Salamov, Jens Christian Frisvad, Thomas Ostenfeld Larsen, Mikael Rørdam Andersen, Jakob Blæsbjerg Hoof
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0122146

Genome Wide DNA Methylation Profiles Provide Clues to the Origin and Pathogenesis of Germ Cell Tumors
Cited by: 59
Author(s): Martin A. Rijlaarsdam, David M. J. Tax, Ad J. M. Gillis, Lambert C. J. Dorssers, Devin C. Koestler, Jeroen de Ridder, Leendert H. J. Looijenga
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.1008828

Conditional knockout of RAD51-related genes in Leishmania major reveals a critical role for homologous recombination during genome replication
Cited by: 16
Author(s): Jeziel D. Damasceno, João Luís Reis-Cunha, Kathryn Crouch, Dario Beraldi, Craig Lapsley, Luíz Ricardo Orsini Tosi, Daniella Castanheira Bartholomeu, Richard McCulloch
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-93593-y

Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome
Cited by: 7
Author(s): Balázs Kakuk, Dóra Tombácz, Zsolt Balázs, Norbert Moldován, Zsolt Csabai, Gábor Torma, Klára Megyeri, M Snyder, Zsolt Boldogkői
Software Mentions: 3
Published: over 3 years ago

10.1098/rspb.2020.0489

Extreme genomic volatility characterizes the evolution of the immunoglobulin heavy chain locus in cyprinodontiform fishes
Cited by: 10
Author(s): William J. Bradshaw, Dario Riccardo Valenzano
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.653399

Respiratory Co-Infections: Modulators of SARS-CoV-2 Patients’ Clinical Sub-Phenotype
Cited by: 21
Author(s): Priyanka Mehta, Shweta Sahni, Samreen Siddiqui, Neha Mishra, Pooja Sharma, Sachin Sharma, Akansha Tyagi, Partha Chattopadhyay, A Vivekanand, Priti Devi, Azka Khan, Swati Waghdhare, Sandeep Budhiraja, Bharathram Uppili, Ranjeet Maurya, Vivek Nangia, Uzma Shamim, Pranjal Pratim Hazarika, Saruchi Wadhwa, Nishu Tyagi, Arun Dewan, Bansidhar Tarai, Poonam Das, Mohammed Faruq, Anurag Agrawal, Sujeet Jha, Rajesh Pandey
Software Mentions: 3
Published: over 3 years ago

10.1038/tp.2015.177

Brain-specific epigenetic markers of schizophrenia
Cited by: 41
Author(s): Leesa Wockner, Charles P. Morris, Ernest P. Noble, Bruce R. Lawford, Vicki Whitehall, Ross McD. Young, Joanne Voisey
Software Mentions: 3
Published: about 9 years ago

10.3390/v12111320

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1
Cited by: 9
Author(s): Maria Kornienko, Gleb Y. Fisunov, Dmitry Bespiatykh, Nikita Kuptsov, Roman Gorodnichev, Ksenia M. Klimina, Eugene E. Kulikov, Elena N. Ilina, Andrey V. Letarov, Egor Shitikov
Software Mentions: 3
Published: about 4 years ago

10.1128/mBio.01568-20

Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
Cited by: 26
Author(s): Shirley E. Braspenning, Tomohiko Sadaoka, Judith Breuer, Georges M. G. M. Verjans, Werner J. D. Ouwendijk, Daniel P. Depledge
Software Mentions: 3
Published: about 4 years ago

10.1038/srep25474

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Cited by: 41
Author(s): Pamela Milani, Renan Escalante-Chong, Brandon Shelley, Natasha L. Patel-Murray, Xin X, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
Software Mentions: 3
Published: over 8 years ago

Projects: bioconductor: Gviz

Papers Mentioning Gviz 134