bioconductor: GenomicFeatures | Projects

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

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: over 7 years ago

10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Software Mentions: 19
Published: over 4 years ago

10.1186/s13059-021-02335-w

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: about 3 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: about 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: almost 4 years ago

10.1371/journal.pcbi.1003118

Software for Computing and Annotating Genomic Ranges
Cited by: 2,902
Author(s): Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vincent J. Carey
Software Mentions: 14
Published: almost 11 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: almost 9 years ago

10.1186/s13059-020-02071-7

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Cited by: 56
Author(s): Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W. K. Ho, Richard P. Harvey, Kitty Lo
Software Mentions: 13
Published: almost 4 years ago

10.3389/fgene.2021.665888

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Cited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: almost 3 years ago

10.1186/s12864-019-5700-7

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Cited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: about 5 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: about 7 years ago

10.1038/s41598-018-19655-w

msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data
Cited by: 10
Author(s): Benjamin Mayne, Shalem Leemaqz, Sam Buckberry, Carlos M. Rodríguez López, Claire T. Roberts, Tina Bianco‐Miotto, James Breen
Software Mentions: 12
Published: over 6 years ago

10.1186/s13059-020-02070-8

The regulatory landscape of early maize inflorescence development
Cited by: 28
Author(s): Rajiv Krishna Parvathaneni, Edoardo Bertolini, Md. Shamimuzzaman, Daniel Vera, Pei Yau Lung, Brian R. Rice, Jinfeng Zhang, Patrick J. Brown, Alexander E. Lipka, Hank W. Bass, Andrea L. Eveland
Software Mentions: 12
Published: almost 4 years ago

10.3389/fgene.2018.00278

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
Cited by: 11
Author(s): Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kévin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh
Software Mentions: 12
Published: almost 6 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: over 3 years ago

10.1371/journal.pcbi.1008585

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data
Cited by: 43
Author(s): Charlotte Soneson, Avi Srivastava, Rob Patro, Michael Stadler
Software Mentions: 11
Published: over 3 years ago

10.3389/fgene.2020.00548

Rcirc: An R Package for circRNA Analyses and Visualization
Cited by: 8
Author(s): Peisen Sun, Haoming Wang, Guanglin Li
Software Mentions: 11
Published: almost 4 years ago

10.1038/s41598-019-41601-7

Characteristics and homogeneity of N6-methylation in human genomes
Cited by: 13
Author(s): Clare Pacini, Charles R. Bradshaw, Nigel Garrett, Magdalena J. Koziol
Software Mentions: 11
Published: about 5 years ago

10.3390/ijms22083975

Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive Compounds
Cited by: 11
Author(s): Debosmita Sardar, Brittney Lozzi, Junsung Woo, Teng-Wei Huang, Caroline Cvetkovic, Chad J. Creighton, Robert Krencik, Benjamin Deneen
Software Mentions: 10
Published: about 3 years ago

10.1186/s12859-021-04254-w

ORFik: a comprehensive R toolkit for the analysis of translation
Cited by: 13
Author(s): Håkon Tjeldnes, Kornel Labun, Yamila Torres Cleuren, Katarzyna Chyżyńska, Michał Świrski, Eivind Valen
Software Mentions: 10
Published: almost 3 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: over 6 years ago

10.3389/fncel.2021.648570

Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-Drivers
Cited by: 5
Author(s): Rachel A. Keuls, Ronald J. Parchem
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pone.0220518

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
Cited by: 4
Author(s): Albert Fradera-Sola, Ann Thomas, Dagmara Gasior, John A. Harper, Matthew J. Hegarty, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0066902

Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data
Cited by: 16
Author(s): Darragh G. McArt, Philip D. Dunne, Jaine K. Blayney, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Peter Hamilton, Shudong Zhang
Software Mentions: 9
Published: almost 11 years ago

10.3390/jof6030182

ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicans
Cited by: 14
Author(s): Sabrina Jenull, Michael Tscherner, Theresia Mair, Karl Kuchler
Software Mentions: 9
Published: over 3 years ago

10.1093/bioinformatics/bts477

easyRNASeq: a bioconductor package for processing RNA-Seq data
Cited by: 96
Author(s): Nicolas Delhomme, Ismaël Padioleau, Eileen E. M. Furlong, Lars M. Steinmetz
Software Mentions: 9
Published: almost 12 years ago

10.3389/fnins.2020.00061

Regionally Distinct Astrocytes Display Unique Transcription Factor Profiles in the Adult Brain
Cited by: 35
Author(s): Brittney Lozzi, Teng-Wei Huang, Debosmita Sardar, Anna Yu-Szu Huang, Benjamin Deneen
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.55862

Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
Cited by: 16
Author(s): Carlos Martínez-Ruiz, Rodrigo Pracana, Eckart Stolle, Carolina Ivon Paris, Richard A. Nichols, Yannick Wurm
Software Mentions: 9
Published: almost 4 years ago

10.1073/pnas.2100542118

Self-mediated positive selection of T cells sets an obstacle to the recognition of nonself
Cited by: 9
Author(s): Balázs Koncz, Gergő Mihály Balogh, Benjamin Tamás Papp, Leó Asztalos, Lajos Kemény, Máté Manczinger
Software Mentions: 9
Published: over 2 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: over 8 years ago

10.1128/mBio.01369-21

HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 + T Cells Early Postinfection
Cited by: 6
Author(s): Hélène Bauby, Christopher Ward, Rupert Hugh-White, Chad M. Swanson, Reiner Schulz, Caroline Goujon, Michael H. Malim
Software Mentions: 8
Published: almost 3 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: over 8 years ago

10.1038/s41597-019-0183-6

CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder
Cited by: 127
Author(s): Gabriel E. Hoffman, Jaroslav Bendl, Georgios Voloudakis, Kelsey S. Montgomery, Laura Sloofman, Ying-Chih Wang, Hardik Shah, Mads E. Hauberg, Jessica Johnson, Kiran Girdhar, Lingyun Song, John F. Fullard, Robin Kramer, Chang-Gyu Hahn, Raquel E. Gur, Stefano Marenco, Barbara K. Lipska, David A. Lewis, Vahram Haroutunian, Scott E. Hemby, Patrick F. Sullivan, Schahram Akbarian, Andrew Chess, Joseph D. Buxbaum, Greg Crawford, Enrico Domenici, Bernie Devlin, Solveig K. Sieberts, Mette A. Peters, Panos Roussos
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.41673

Genetic effects on promoter usage are highly context-specific and contribute to complex traits
Cited by: 48
Author(s): Kaur Alasoo, Julia Rodrigues, John Danesh, Daniel F. Freitag, Dirk S. Paul, Daniel J Gaffney
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: about 7 years ago

10.1371/journal.pone.0224879

Long non-coding RNAs and latent HIV – A search for novel targets for latency reversal
Cited by: 17
Author(s): Wim Trypsteen, Cory H. White, Amey Mukim, Celsa A. Spina, Ward De Spiegelaere, Steve Lefever, Vicente Planelles, Alberto Bosque, Christopher H. Woelk, Linos Vandekerckhove, Nadejda Beliakova-Bethell
Software Mentions: 8
Published: over 4 years ago

10.1128/mSystems.00917-20

FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses
Cited by: 7
Author(s): Matthew Chung, Ricky S. Adkins, John Mattick, Katie R. Bradwell, Amol Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pcbi.1006169

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data
Cited by: 115
Author(s): Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J N Groen, Thomas H. Gillingwater, Gabriella Viero
Software Mentions: 7
Published: almost 6 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: almost 5 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: over 10 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: over 5 years ago

10.26508/lsa.202101080

Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes
Cited by: 9
Author(s): Melissa Bothe, René Buschow, Sebastiaan H. Meijsing
Software Mentions: 7
Published: almost 3 years ago

10.3390/microorganisms8020270

In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays
Cited by: 15
Author(s): Rossella Gratton, Paola Maura Tricarico, Almerinda Agrelli, Heverton Valentim Colaço da Silva, Lucas Coêlho Bernardo, Sérgio Crovella, Antônio Victor Campos Coelho, Ronald Moura, Lucas André Cavalcanti Brandão
Software Mentions: 7
Published: over 4 years ago

10.3390/microorganisms9050996

Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions
Cited by: 1
Author(s): Karen Cristine Gonçalves dos Santos, G. Pelletier, Armand Séguin, François Guillemette, Jeffrey A. Hawkes, Isabel Desgagné‐Penix, Hugo Germain
Software Mentions: 7
Published: about 3 years ago

10.3390/genes11091107

Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina
Cited by: 5
Author(s): Long Song, Jing Qin Wu, Chongmei Dong, Robert Park
Software Mentions: 7
Published: over 3 years ago

10.1186/s13007-021-00791-w

Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture
Cited by: 3
Author(s): Amir Mahboubi, Nicolas Delhomme, Sara Lea Häggström, Johannes Hanson
Software Mentions: 7
Published: almost 3 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: over 8 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: about 9 years ago

10.1371/journal.ppat.1005438

Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
Cited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: over 8 years ago

10.1186/s12864-020-06987-z

Global transcriptomic responses orchestrate difenoconazole resistance in Penicillium spp. causing blue mold of stored apple fruit
Cited by: 6
Author(s): Franz J. Lichtner, Verneta L. Gaskins, Kerik D. Cox, Wayne M. Jurick
Software Mentions: 6
Published: almost 4 years ago

10.3390/plants9040545

Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.)
Cited by: 3
Author(s): Cristina Gómez-Martín, Carmen Capel, Ana M. González, Ricardo Lebrón, Fernando J. Yuste‐Lisbona, Michael Hackenberg, José Luis Tejera Oliver, Marta Santalla, Rafael Lozano
Software Mentions: 6
Published: about 4 years ago

10.1534/g3.119.400180

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
Cited by: 12
Author(s): Lorrayne Serra, Marissa Macchietto, Aide Macias-Muñoz, Cassandra McGill, Isaryhia Rodriguez, Bryan Rodriguez, Rabi Murad, A Mortazavi
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.ajhg.2019.05.010

Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver
Cited by: 33
Author(s): Minal Çalışkan, Elisabetta Manduchi, Harish Rao, Julian A. Segert, Márcia Holsbach Beltrame, Marco Trizzino, YoSon Park, Samuel White Baker, Alessandra Chesi, Matthew E. Johnson, Kenyaita M. Hodge, Michelle E. Leonard, Bao‐Li Loza, Xin Dong, Andrea M. Berrido, Nicholas J. Hand, Robert C. Bauer, Andrew D. Wells, Kim M. Olthoff, Abraham Shaked, Daniel J. Rader, Struan F.A. Grant, Christopher D. Brown
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.ppat.1008589

High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis
Cited by: 12
Author(s): Julián Naipauer, Daria Salyakina, Guy Journo, Santas Rosario, Siôn L. Williams, Martı́n C. Abba, Meir Shamay, Enrique A. Mesri
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0239495

Sources of variation in cell-type RNA-Seq profiles
Cited by: 16
Author(s): Johan Gustafsson, Felix Held, Jonathan L. Robinson, Elias Björnson, Rebecka Jörnsten, Jens Nielsen
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: over 6 years ago

10.3390/ijms21197407

LINC00885 a Novel Oncogenic Long Non-Coding RNA Associated with Early Stage Breast Cancer Progression
Cited by: 14
Author(s): Martı́n C. Abba, Romina Canzoneri, Agustina Gurruchaga, Jae-Ho Lee, Pradeep Tatineni, Hyunsuk Kil, Ezequiel Lacunza, C. Marcelo Aldaz
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-017-1808-4

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Cited by: 36
Author(s): Lian Liu, Shao Wu Zhang, Yufei Huang, Jia Meng
Software Mentions: 6
Published: almost 7 years ago

10.1186/s13287-020-01983-2

IRF-1 expressed in the inner cell mass of the porcine early blastocyst enhances the pluripotency of induced pluripotent stem cells
Cited by: 8
Author(s): Bingbo Shi, Dengfeng Gao, Zhong Liu, Minglei Zhi, Xiaogang Weng, Junjun Xu, Junhong Li, Xuguang Du, Yanli Xin, Jie Gao, Qianqian Zhu, Suying Cao, Liu Z
Software Mentions: 6
Published: over 3 years ago

10.1093/icb/icaa138

Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird
Cited by: 11
Author(s): Kees van Oers, Bernice Sepers, William Sies, Fleur Gawehns, Koen Verhoeven, Veronika N. Laine
Software Mentions: 6
Published: over 3 years ago

10.1186/s13073-017-0454-9

Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines
Cited by: 45
Author(s): Javier A. Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C. Boutros, Thomas Kislinger
Software Mentions: 6
Published: almost 7 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: over 10 years ago

10.1016/j.cell.2013.11.043

The Architecture of Parent-of-Origin Effects in Mice
Cited by: 79
Author(s): Richard Mott, Yuan Wei, Pamela J. Kaisaki, Xiangchao Gan, James Cleak, Andrew Edwards, Amelie Baud, Jonathan Flint
Software Mentions: 6
Published: over 10 years ago

10.7554/eLife.66398

Tetrahydroxanthohumol, a xanthohumol derivative, attenuates high-fat diet-induced hepatic steatosis by antagonizing PPARγ
Cited by: 7
Author(s): Yang Zhang, Gerd Bobe, Cristobal L. Miranda, Malcolm B. Lowry, Victor L. Hsu, Christiane V. Löhr, Carmen P. Wong, Donald Β. Jump, Matthew M. Robinson, Thomas J. Sharpton, Claudia S. Maier, Jan F. Stevens, Adrian F. Gombart
Software Mentions: 6
Published: almost 3 years ago

10.1186/gm509

Comparison of methods to identify aberrant expression patterns in individual patients: augmenting our toolkit for precision medicine
Cited by: 5
Author(s): Daniel Bottomly, Peter Ryabinin, Jeffrey W. Tyner, Bill H. Chang, Marc Loriaux, Brian J. Druker, Shannon K. McWeeney, Beth Wilmot
Software Mentions: 6
Published: over 11 years ago

10.7150/thno.47627

Multi-omics study of silicosis reveals the potential therapeutic targets PGD2 and TXA2
Cited by: 25
Author(s): Junling Pang, Xianmei Qi, Yunbo Luo, Xiaona Li, Ting Shu, Baicun Li, Meiyue Song, Ying Liu, Wei Dong, Jingyu Chen, Jing Wang, Chen Wang
Software Mentions: 6
Published: over 3 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: about 8 years ago

10.3389/fgene.2019.00209

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data
Cited by: 23
Author(s): Shenhe Liu, Tingzhu Ye, Zipeng Li, Jun Li, Muhammad Jamil Ahmad, Yang Zhou, Guohua Hua, Aixin Liang, Tingxian Deng, Liguo Yang
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-019-5613-5

Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes
Cited by: 25
Author(s): Isabelle Rosinski‐Chupin, Elisabeth Sauvage, Agnès Fouet, Claire Poyart, Philippe Glaser
Software Mentions: 5
Published: about 5 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: about 8 years ago

10.1186/s12864-021-07451-2

Multi-species transcriptome meta-analysis of the response to retinoic acid in vertebrates and comparative analysis of the effects of retinol and retinoic acid on gene expression in LMH cells
Cited by: 5
Author(s): Clemens Falker‐Gieske, Andrea Mott, Sören Franzenburg, Jens Tetens
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-019-6426-2

Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis
Cited by: 17
Author(s): Karen Cristine Gonçalves dos Santos, Isabel Desgagné‐Penix, Hugo Germain
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-019-5801-3

Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum
Cited by: 15
Author(s): Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, C. Liang, Caixia Jia
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-020-07225-2

Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice
Cited by: 25
Author(s): Pabodha Hettige, Uzma Tahir, Kiisa C. Nishikawa, Matthew J. Gage
Software Mentions: 5
Published: over 3 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: over 10 years ago

10.1186/s40170-020-00216-7

Fine-tuning the metabolic rewiring and adaptation of translational machinery during an epithelial-mesenchymal transition in breast cancer cells
Cited by: 3
Author(s): Tamara Fernández-Calero, Marcos Davyt, Karen Perelmuter, Cora Chalar, Giovana Bavia Bampi, Helena Persson, Juan Pablo Tosar, Völundur Hafstað, Hugo Naya, Carlos Rovira, Mariela Bollati-Fogolín, Ricardo Ehrlich, Gilles Flouriot, Zoya Ignatova, Mónica Marı́n
Software Mentions: 5
Published: almost 4 years ago

10.1186/1744-8069-10-7

A Comparison of RNA-Seq and Exon Arrays for Whole Genome Transcription Profiling of the L5 Spinal Nerve Transection Model of Neuropathic Pain in the Rat
Cited by: 72
Author(s): James R. Perkins, Ana Antunes-Martins, Margarita Calvo, John Grist, Werner Rust, RM Schmid, Tobias Hildebrandt, Matthias Kohl, Christine A. Orengo, Stephen B. McMahon, David L.H. Bennett
Software Mentions: 5
Published: over 10 years ago

10.1111/mpp.13003

Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode Hirschmanniella oryzae , increase host susceptibility by manipulating secondary metabolite content of rice
Cited by: 8
Author(s): Lander Bauters, Tina Kyndt, Tim De Meyer, Kris Morreel, Wout Boerjan, Hannes Lefevere, Godelieve Gheysen
Software Mentions: 5
Published: over 3 years ago

10.1111/tpj.14193

Kernel size‐related genes revealed by an integrated<scp>eQTL</scp>analysis during early maize kernel development
Cited by: 30
Author(s): Junling Pang, Junjie Fu, Na Zong, Jing Wang, Dandan Song, Xia Zhang, Cheng He, Ting Fang, Hongwei Zhang, Yanting Fan, Guoying Wang, Jun Zhao
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008917

Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites
Cited by: 23
Author(s): Élodie Gazanion, Laurent Lacroix, Patrizia Alberti, Pratima Gurung, Sharon Wein, Ming Cheng, Jean‐Louis Mergny, Ana Gomes, José-Juan Lopez-Rubio
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.dib.2019.103909

RNA-sequencing data highlighting the time-of-day-dependent transcriptome of the central circadian pacemaker in Sox2-deficient mice
Cited by: 4
Author(s): Arthur H. Cheng, Pascale Bouchard-Cannon, Rob W. Ness, Hai-Ying Mary Cheng
Software Mentions: 5
Published: about 5 years ago

10.1242/dmm.034124

Epigenetic regulators Rbbp4 and Hdac1 are overexpressed in a zebrafish model of RB1 embryonal brain tumor, and are required for neural progenitor survival and proliferation
Cited by: 37
Author(s): Linda Schultz, Jeffrey A. Haltom, Maira P. Almeida, Wesley A. Wierson, Staci L. Solin, Trevor Weiss, Jordan A Helmer, Elizabeth J. Sandquist, Heather R. Shive, Maura McGrail
Software Mentions: 5
Published: about 6 years ago

10.15252/emmm.201809456

Alternative oxidase‐mediated respiration prevents lethal mitochondrial cardiomyopathy
Cited by: 47
Author(s): Jayasimman Rajendran, Janne Purhonen, Saara Tegelberg, Olli‐Pekka Smolander, Matthias Mörgelin, Jan Rozman, Valérie Gailus‐Durner, Helmut Fuchs, Martin Hrabě de Angelis, Petri Auvinen, Eero Mervaala, Howard T. Jacobs, Marten Szibor, Vineta Fellman, Jukka Kallijärvi
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2020.00557

Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer
Cited by: 10
Author(s): Nan Xiao, Yang Hu, Liran Juan
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-021-02386-z

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
Cited by: 4
Author(s): Johan Gustafsson, Jonathan L. Robinson, Jens Nielsen, Lior Pachter
Software Mentions: 5
Published: almost 3 years ago

10.1371/journal.ppat.1008221

PDGFRA defines the mesenchymal stem cell Kaposi’s sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment
Cited by: 23
Author(s): Julián Naipauer, Santas Rosario, Sachin Gupta, Courtney Premer, Omayra Méndez-Solís, Mariana Schlesinger, Virginia Ponzinibbio, Vaibhav Jain, Rolf Renne, Ho Lam Chan, Lluís Morey, Daria Salyakina, Martı́n C. Abba, Siôn L. Williams, Joshua M. Hare, Pascal J. Goldschmidt‐Clermont, Enrique A. Mesri
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.55792

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
Cited by: 56
Author(s): Nathan D. Lawson, Rui Li, Masahiro Shin, Ann S. Grosse, Onur Yukselen, Oliver A. Stone, Alper Küçükural, Lihua Julie Zhu
Software Mentions: 5
Published: almost 4 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: over 5 years ago

10.3390/ijms21051894

The Polymorphic PolyQ Tail Protein of the Mediator Complex, Med15, Regulates the Variable Response to Diverse Stresses
Cited by: 7
Author(s): Gallagher Jeg, Ser Sl, Michael C. Ayers, C Nassif, Amaury Pupo
Software Mentions: 5
Published: about 4 years ago

10.3390/genes11111381

Differential Gene Expression in Longissimus Dorsi Muscle of Hanwoo Steers—New Insight in Genes Involved in Marbling Development at Younger Ages
Cited by: 10
Author(s): Sara de las Heras‐Saldana, Ki Yong Chung, Hyounju Kim, Dajeong Lim, Cedric Gondro, J. H. J. van der Werf
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2019.01178

Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins
Cited by: 7
Author(s): Ronaldo da Silva Francisco, Cristina dos Santos Ferreira, Juan Carlo Santos e Silva, Douglas Terra Machado, Yasmmin Martins, Víctor Ramos, Gustavo Simões Carnivali, Anice Garcia, Enrique Medina‐Acosta
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0094164

From Human Monocytes to Genome-Wide Binding Sites - A Protocol for Small Amounts of Blood: Monocyte Isolation/ChIP-Protocol/Library Amplification/Genome Wide Computational Data Analysis
Cited by: 4
Author(s): Sebastian Weiterer, Florian Uhle, Sabin Bhuju, Michael Jarek, Markus A. Weigand, Marek Bartkuhn
Software Mentions: 4
Published: about 10 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: almost 11 years ago

10.1172/jci.insight.145346

Systemic and adipocyte transcriptional and metabolic dysregulation in idiopathic intracranial hypertension
Cited by: 39
Author(s): Connar Westgate, Hannah Botfield, Zerin Alimajstorovic, Andreas Yiangou, Mark D. Walsh, Gabrielle Smith, Rishi Singhal, James Mitchell, Olivia Grech, Keira Markey, Daniel Hebenstreit, Daniel A. Tennant, Jeremy W. Tomlinson, Susan P Mollan, Christian Ludwig, İldem Akerman, Gareth G. Lavery, Alexandra J Sinclair
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj.9371

pulseTD: RNA life cycle dynamics analysis based on pulse model of 4sU-seq time course sequencing data
Cited by: 0
Author(s): Xin Wang, Siyu He, Jian Li, Jun Wang, Chengyi Wang, Mingwei Wang, Danni He, Xingfeng Lv, Qiuyan Zhong, Hongjiu Wang, Zhenzhen Wang
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-78589-4

GRAS-Di system facilitates high-density genetic map construction and QTL identification in recombinant inbred lines of the wheat progenitor Aegilops tauschii
Cited by: 16
Author(s): Yuka Miki, Kentaro Yoshida, Hiroyuki Enoki, Saburô Kômura, Kazuko Suzuki, Minoru Inamori, Ryo Nishijima, Shigeo Takumi
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-015-2164-2

The direction of cross affects obesity after puberty in male but not female offspring
Cited by: 5
Author(s): Stefan Kärst, Danny Arends, Sebastian Heise, Jan Trost, Marie–Laure Yaspo, Vyacheslav Amstislavskiy, Thomas S. Risch, Hans Lehrach, Gudrun A. Brockmann
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-019-5530-7

Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus
Cited by: 17
Author(s): Sara de las Heras‐Saldana, Ki Yong Chung, Seung Hwan Lee, Cedric Gondro
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00341-21

Multi-omics Study of Planobispora rosea, Producer of the Thiopeptide Antibiotic GE2270A
Cited by: 1
Author(s): Francesco Del Carratore, Marianna Iorio, Mercedes Pérez-Bonilla, Kamila Schmidt, Rosario Pérez‐Redondo, Margherita Sosio, Sandy MacDonald, Ivan Gyulev, Areti Tsigkinopoulou, Gavin H. Thomas, Olga Genilloud, Antonio Rodríguez‐García, Stefano Donadio, Rainer Breitling, Eriko Takano
Software Mentions: 4
Published: almost 3 years ago

Projects: bioconductor: GenomicFeatures

Papers Mentioning GenomicFeatures 141