bioconductor: GeneOverlap | Projects

10.1038/s41598-020-67753-5

Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples
Cited by: 13
Author(s): Shradha Mukherjee
Software Mentions: 14
Published: over 4 years ago

10.15252/emmm.201911900

Epigenetic gene expression links heart failure to memory impairment
Cited by: 13
Author(s): Rezaul Islam, Dawid Lbik, M. Sadman Sakib, Raoul Maximilian Hofmann, Tea Berulava, Martí Jiménez Mausbach, Julia Cha, Maria Amélia Azevêdo Goldberg, Elerdashvili Vakhtang, Christian Schiffmann, Anke Zieseniß, Dörthe M. Katschinski, Farahnaz Sananbenesi, Karl Toischer, André Fischer
Software Mentions: 11
Published: almost 4 years ago

10.1371/journal.pgen.1009240

Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior
Cited by: 5
Author(s): Colleen M Palmateer, Shawn C. Moseley, Surjyendu Ray, Savannah G Brovero, Michelle N. Arbeitman
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-021-94324-z

Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer’s disease
Cited by: 17
Author(s): Ruth Jones, Robert Andrews, Peter Holmans, Matthew Hill, Philip R. Taylor
Software Mentions: 11
Published: over 3 years ago

10.26508/lsa.202101108

Microglia show differential transcriptomic response to Aβ peptide aggregates ex vivo and in vivo
Cited by: 11
Author(s): Karen N. McFarland, Carolina Wiesner Ceballos, Awilda M. Rosario, Thomas B. Ladd, Brenda D. Moore, Griffin Golde, Xue Wang, Mariet Allen, Nilufer Ertekin‐Taner, Cory C. Funk, Max Robinson, Priyanka Baloni, Noa Rappaport, Paramita Chakrabarty, Todd E. Golde
Software Mentions: 9
Published: over 3 years ago

10.3389/fcimb.2020.00194

Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV Infections
Cited by: 2
Author(s): Malika Aïd, Daniel R. Ram, Steven E. Bosinger, Dan H. Barouch, R. Keith Reeves
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.52690

Sphingosine 1-phosphate-regulated transcriptomes in heterogenous arterial and lymphatic endothelium of the aorta
Cited by: 28
Author(s): Eric Engelbrecht, Michel V. Levesque, Liqun He, Michael Vanlandewijck, Anja Nitzsche, Hira Niazi, Andrew Kuo, Sasha A Singh, Masamichi Aikawa, Kristina M. Holton, Richard L. Proia, Mari Kono, William T. Pu, Eric Camerer, Christer Betsholtz, Timothy Hla
Software Mentions: 8
Published: over 4 years ago

10.1186/s12864-018-4902-8

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues
Cited by: 30
Author(s): Ruidong Xiang, Ben J. Hayes, Christy J. Vander Jagt, Iona M. MacLeod, Majid Khansefid, P.J. Bowman, Zehu Yuan, Claire P. Prowse-Wilkins, Coralie M. Reich, Brett Mason, Josie B. Garner, L. C. Marett, Yizhou Chen, Sunduimijid Bolormaa, Hans D. Daetwyler, Amanda J. Chamberlain, Michael E. Goddard
Software Mentions: 6
Published: over 6 years ago

10.1002/pld3.242

Lipophilic signals lead to organ‐specific gene expression changes in <i>Arabidopsis</i> seedlings
Cited by: 4
Author(s): Ashley E. Cannon, Chengshi Yan, David J. Burks, Xiaolan Rao, Rajeev K. Azad, Kent D. Chapman
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1006279

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity
Cited by: 43
Author(s): Barbara Mair, Tomasz Konopka, Claudia Kerzendorfer, Katia Sleiman, Šejla Šalic, Violeta Serra, Markus K. Muellner, Vassiliki Théodorou, Sebastian M. Nijman
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pgen.1009801

Tramtrack acts during late pupal development to direct ant caste identity
Cited by: 6
Author(s): Karl M. Glastad, Linyang Ju, Shelley L. Berger
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0212866

Dynamic changes in lung responses after single and repeated exposures to cigarette smoke in mice
Cited by: 10
Author(s): Michelle Engle, Justine N. Monk, Corey M. Jania, Jessica R. Martin, John C. Gomez, Hong Dang, Joel S. Parker, Claire M. Doerschuk
Software Mentions: 6
Published: over 5 years ago

10.1101/2020.04.24.059527

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 1
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-59808-4

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation
Cited by: 29
Author(s): Ian M. Traniello, Syed Bukhari, Jessica L. Kevill, Amy Cash Ahmed, Adam R. Hamilton, Nicholas L. Naeger, Declan C. Schroeder, Gene E. Robinson
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13148-017-0408-5

Newborn genome-wide DNA methylation in association with pregnancy anxiety reveals a potential role for GABBR1
Cited by: 29
Author(s): Elise Vangeel, Ehsan Pishva, Titia Hompes, Daniël L.A. van den Hove, Diether Lambrechts, Karel Allegaert, Kathleen Freson, Benedetta Izzi, Stephan Claes
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.64283

Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs
Cited by: 19
Author(s): Swati Gaikwad, Fardin Ghobakhlou, David J. Young, Jyothsna Visweswaraiah, Hongen Zhang, Alan G. Hinnebusch
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-98534-3

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy
Cited by: 4
Author(s): Nicholas Henkel, Marissa A. Smail, Xiaojun Wu, Heather A. Enright, Nicholas O. Fischer, Hunter M. Eby, Robert E. McCullumsmith, Rammohan Shukla
Software Mentions: 4
Published: about 3 years ago

10.3389/fnagi.2019.00083

Identification of Temporal Characteristic Networks of Peripheral Blood Changes in Alzheimer’s Disease Based on Weighted Gene Co-expression Network Analysis
Cited by: 18
Author(s): Run-Hong Tang, Huayan Liu
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-020-0823-6

Effect direction meta-analysis of GWAS identifies extreme, prevalent and shared pleiotropy in a large mammal
Cited by: 21
Author(s): Ruidong Xiang, I. van den Berg, Iona M. MacLeod, Hans D. Daetwyler, Michael E. Goddard
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-019-2886-2

Genes with human-specific features are primarily involved with brain, immune and metabolic evolution
Cited by: 9
Author(s): Mainá Bitar, Stefanie Kuiper, Elizabeth O’Brien, Guy Barry
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0242773

Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation
Cited by: 13
Author(s): Jamie Reilly, Louise Gallagher, Geraldine Leader, Sanbing Shen
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0222080

Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars
Cited by: 8
Author(s): Nathan A. Palmer, R. V. Chowda-Reddy, Anthony A. Muhle, T. Satyanarayana, Gary Y. Yuen, Serge J. Edmé, Robert B. Mitchell, Gautam Sarath
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-020-01990-9

A multidimensional systems biology analysis of cellular senescence in aging and disease
Cited by: 144
Author(s): Roberto A. Avelar, Javier Gómez Ortega, Robi Tăcutu, Eleanor J. Tyler, Dominic Bennett, Paolo Binetti, Arie Budovsky, Kasit Chatsirisupachai, Emily Johnson, Alex Murray, Samuel Shields, Daniela Tejada‐Martinez, Daniel Thornton, Vadim E. Fraifeld, Cleo L. Bishop, João Pedro de Magalhães
Software Mentions: 3
Published: over 4 years ago

10.1038/s41597-020-00628-6

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 23
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 3
Published: about 4 years ago

10.1038/srep28998

The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex
Cited by: 33
Author(s): Tatiana Popovitchenko, Kevin J. Thompson, Barbara Viljetić, Xuan Jiao, D. L. Kontonyiannis, Megerditch Kiledjian, Ronald P. Hart, Mladen-Roko Rašin
Software Mentions: 3
Published: over 8 years ago

10.1038/s41398-019-0550-2

Genome-wide profiling of DNA methylome and transcriptome in peripheral blood monocytes for major depression: A Monozygotic Discordant Twin Study
Cited by: 47
Author(s): Yun Zhu, Eric Strachan, Emily Fowler, Tamara J. Bacus, Peter Roy‐Byrne, Jinying Zhao
Software Mentions: 3
Published: about 5 years ago

10.1038/s41398-021-01528-y

Conserved immunomodulatory transcriptional networks underlie antipsychotic-induced weight gain
Cited by: 5
Author(s): Rizaldy C. Zapata, Besma Chaudry, Mariela Lopez Valencia, Dinghong Zhang, Scott A. Ochsner, Neil J. McKenna, Olivia Osborn
Software Mentions: 2
Published: over 3 years ago

10.1186/s12920-021-01005-x

Genome-wide analysis of retinal transcriptome reveals common genetic network underlying perception of contrast and optical defocus detection
Cited by: 6
Author(s): Tatiana V. Tkatchenko
Software Mentions: 2
Published: over 3 years ago

10.1186/s12920-019-0560-1

Analysis of genetic networks regulating refractive eye development in collaborative cross progenitor strain mice reveals new genes and pathways underlying human myopia
Cited by: 28
Author(s): Tatiana V. Tkatchenko, Rupal L. Shah, Takayuki Nagasaki
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0218352

Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass
Cited by: 15
Author(s): Nathan A. Palmer, Saumik Basu, Tiffany Heng-Moss, Jeffrey D. Bradshaw, Gautam Sarath, Joe Louis
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-018-2020-x

SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data
Cited by: 2
Author(s): Roman Prytuliak, Friedhelm Pfeiffer, Bianca Habermann
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-017-1611-2

Comparison of different cell type correction methods for genome-scale epigenetics studies
Cited by: 67
Author(s): Akhilesh Kaushal, Hongmei Zhang, Wilfried Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith, Shu Li Wang
Software Mentions: 2
Published: over 7 years ago

10.3389/fnagi.2018.00153

Integrative Analysis of Hippocampus Gene Expression Profiles Identifies Network Alterations in Aging and Alzheimer’s Disease
Cited by: 53
Author(s): Vinay Lanke, S.T.R. Moolamalla, Dipanjan Roy, P. Vinod
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.120.401088

Global Transcriptome Changes That Accompany Alterations in Serotonin Levels in<i>Caenorhabditis elegans</i>
Cited by: 8
Author(s): Johnny Cruz-Corchado, Felicia K. Ooi, Srijit Das, Veena Prahlad
Software Mentions: 2
Published: over 4 years ago

10.1016/j.biopsych.2019.03.977

The Psychiatric Risk Gene NT5C2 Regulates Adenosine Monophosphate-Activated Protein Kinase Signaling and Protein Translation in Human Neural Progenitor Cells
Cited by: 25
Author(s): Rodrigo R.R. Duarte, Nathaniel D. Bachtel, Marie-Caroline Côtel, Sang Hyuck Lee, Sashika Selvackadunco, Iain A. Watson, Gary A. Hovsepian, Claire Troakes, Gerome Breen, Douglas F. Nixon, Robin M. Murray, Nicholas John Bray, Ioannis Eleftherianos, Anthony C. Vernon, Timothy R. Powell, Deepak P. Srivastava
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-09788-9

Genome-wide comparative analyses of correlated and uncorrelated phenotypes identify major pleiotropic variants in dairy cattle
Cited by: 28
Author(s): Ruidong Xiang, Iona M. MacLeod, Sunduimijid Bolormaa, Michael E. Goddard
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-10277-2

Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets
Cited by: 35
Author(s): Nina Riddell, Sheila G. Crewther
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0201986

The effect of Tmem135 overexpression on the mouse heart
Cited by: 13
Author(s): Sarah Lewis, Tetsuya Takimoto, Shima Mehrvar, Hitoshi Higuchi, Anna-Lisa Doebley, Giangela Stokes, Nader Sheibani, Shinya Ikeda, Mahsa Ranji, Akihiro Ikeda
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pbio.2006021

Gene expression in response to optical defocus of opposite signs reveals bidirectional mechanism of visually guided eye growth
Cited by: 49
Author(s): Tatiana V. Tkatchenko, David Troilo, Alexandra Benavente-Pérez, Andrei V. Tkatchenko
Software Mentions: 1
Published: about 6 years ago

10.1186/s10020-021-00356-6

Identifying FDA-approved drugs with multimodal properties against COVID-19 using a data-driven approach and a lung organoid model of SARS-CoV-2 entry
Cited by: 15
Author(s): Rodrigo R.R. Duarte, Dennis C. Copertino, Luis P. Íñiguez, Jez L. Marston, Yaron Bram, Yuling Han, Robert E. Schwartz, Shuibing Chen, Douglas F. Nixon, Timothy R. Powell
Software Mentions: 1
Published: about 3 years ago

Projects: bioconductor: GeneOverlap

Papers Mentioning GeneOverlap 40