bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fphys.2016.00100

Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant
Cited by: 15
Author(s): Caixia Chen, Ailian Li
Software Mentions: 2
Published: over 10 years ago

10.3389/fphys.2021.628777

Inhibiting Mitochondrial Cytochrome c Oxidase Downregulates Gene Transcription After Traumatic Brain Injury in Drosophila
Cited by: 8
Author(s): Ekta Shah, Maik Hüttemann, Thomas H. Sanderson, Katherine Gurdziel, Douglas M. Ruden
Software Mentions: 2
Published: over 5 years ago

10.3389/fphys.2014.00487

Transcriptome analysis of host-associated differentiation in Bemisia tabaci (Hemiptera: Aleyrodidae)
Cited by: 14
Author(s): Wen Xie, Qingjun Wu, Shaoli Wang, Xiaoguo Jiao, Long Guo, Xuguo Zhou, Youjun Zhang
Software Mentions: 2
Published: almost 12 years ago

10.3389/fphys.2018.01758

Xenopus Hybrids Provide Insight Into Cell and Organism Size Control
Cited by: 11
Author(s): Romain Gibeaux, Kelly E. Miller, Rachael Acker, Taejoon Kwon, Rebecca Heald
Software Mentions: 2
Published: almost 8 years ago

10.3389/fphys.2019.00080

KLF4-Induced Connexin40 Expression Contributes to Arterial Endothelial Quiescence
Cited by: 20
Author(s): Jean‐Émile Denis, Mannekomba Roxane Diagbouga, Filippo Molica, Aurélie Hautefort, Tanja Linnerz, Masakatsu Watanabe, Sylvain Lemeille, Julien Bertrand, Brenda R. Kwak
Software Mentions: 2
Published: over 7 years ago

10.3389/fphys.2018.01089

Inflammatory Determinants of Pregravid Obesity in Placenta and Peripheral Blood
Cited by: 63
Author(s): Suhas Sureshchandra, Nicole Marshall, Randall M. Wilson, Tasha Barr, Maham Rais, Jonathan Q. Purnell, Kent L. Thornburg, Ilhem Messaoudi
Software Mentions: 2
Published: about 8 years ago

10.3389/fphys.2021.682441

FOSL2 Is Involved in the Regulation of Glycogen Content in Chicken Breast Muscle Tissue
Cited by: 2
Author(s): Xiaojing Liu, Lu Liu, Jie Wang, Huanxian Cui, Guiping Zhao, Jie Wen
Software Mentions: 2
Published: over 5 years ago

10.3389/fphys.2018.01051

Mulberry Leaf Regulates Differentially Expressed Genes in Diabetic Mice Liver Based on RNA-Seq Analysis
Cited by: 16
Author(s): Qi Ge, Shu Zhang, Liang Chen, Min Tang, Lanlan Liu, Mengna Kang, Lu Gao, Shangshang Ma, Yanhua Yang, Peng Lv, Ming Kong, Qin Yao, Fan Feng, Keping Chen
Software Mentions: 2
Published: about 8 years ago

10.3389/fphys.2018.00812

Transcriptional and Translational Relationship in Environmental Stress: RNAseq and ITRAQ Proteomic Analysis Between Sexually Reproducing and Parthenogenetic Females in Moina micrura
Cited by: 14
Author(s): Jingyi Jia, Xiangjiang Liu, Lü Li, Lei Chen, Ying Dong, Guoqiang Wu, Guangfu Hu
Software Mentions: 2
Published: over 8 years ago

10.3389/fphys.2018.00532

Effects of Acute Aerobic Exercise on Rats Serum Extracellular Vesicles Diameter, Concentration and Small RNAs Content
Cited by: 62
Author(s): Getúlio Pereira de Oliveira Júnior, William F. Porto, Cintia Palu, Lydyane Menezes Pereira, Bernardo A. Petriz, Jeeser Alves de Almeida, Juliane Cançado Viana, Nezio N. A. Filho, Octávio Luiz Franco, Rinaldo Wellerson Pereira
Software Mentions: 2
Published: over 8 years ago

10.3389/fphys.2018.00676

Stat5b Regulates Sexually Dimorphic Gene Expression in Zebrafish Liver
Cited by: 11
Author(s): Peipei Huang, Shuting Xiong, Jingliang Kang, Jie Mei, Jian‐Fang Gui
Software Mentions: 2
Published: over 8 years ago

10.3389/fpls.2021.666075

The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns
Cited by: 5
Author(s): Concetta Burgarella, Angélique Berger, Sylvain Glémin, Jacques David, Nancy Terrier, Monique Deu, David Pot
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2021.694289

Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation
Cited by: 2
Author(s): Thelma F. Madzima, Stefania Vendramin, Jason S. Lynn, Phebe Lemert, Katherine C. Lu, Karen M. McGinnis
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2020.01200

Dissection of Root Transcriptional Responses to Low pH, Aluminum Toxicity and Iron Excess Under Pi-Limiting Conditions in Arabidopsis Wild-Type and stop1 Seedlings
Cited by: 10
Author(s): Jonathan Odilón Ojeda-Rivera, Araceli Oropeza-Aburto, Luis Herrera‐Estrella
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2017.02021

Transcript Profiling Identifies Gene Cohorts Controlled by Each Signal Regulating Trans-Differentiation of Epidermal Cells of Vicia faba Cotyledons to a Transfer Cell Phenotype
Cited by: 5
Author(s): Huiming Zhang, Simon Wheeler, Xue Xia, Kim Colyvas, Christina E. Offler, John W. Patrick
Software Mentions: 2
Published: almost 9 years ago

10.3389/fpls.2021.700479

Biochar-Enhanced Resistance to Botrytis cinerea in Strawberry Fruits (But Not Leaves) Is Associated With Changes in the Rhizosphere Microbiome
Cited by: 8
Author(s): Caroline De Tender, Bart Vandecasteele, Bruno Verstraeten, Sarah Ommeslag, Tina Kyndt, Jane Debode
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2021.738261

Multi-Omics Analyses Reveal the Regulatory Network and the Function of ZmUGTs in Maize Defense Response
Cited by: 5
Author(s): Chunxia Ge, Yi-Ge Wang, Shouping Lu, Xiang Zhao, Bing-Kai Hou, Peter Balint‐Kurti, Guan‐Feng Wang
Software Mentions: 2
Published: about 5 years ago

10.3389/fpls.2021.666660

Comparative Transcriptome Analysis of Salt Stress-Induced Leaf Senescence in Medicago truncatula
Cited by: 15
Author(s): Shihao Dong, Lijun Sang, Hong Xie, Maofeng Chai, Zeng‐Yu Wang
Software Mentions: 2
Published: over 5 years ago

10.3390/genes11111301

PURα Promotes the Transcriptional Activation of PCK2 in Oesophageal Squamous Cell Carcinoma Cells
Cited by: 6
Author(s): Yan Sun, Jiajia Gao, Zongpan Jing, Yan Zhao, Yulin Sun, Xiaohang Zhao
Software Mentions: 2
Published: about 6 years ago

10.3390/genes12010100

Systematic Identification and Analysis of Circular RNAs of Japanese Flounder (Paralichthys olivaceus) in Response to Vibrio anguillarum Infection
Cited by: 5
Author(s): Xianhui Ning, Li Sun
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes12020180

Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats
Cited by: 19
Author(s): Jianfang Wang, Jie Sui, Chao Mao, Xiaorui Li, Xingyi Chen, Chengcheng Liang, Xiaohui Wang, Si-Hu Wang, Caixia Jia
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes12020189

Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions
Cited by: 23
Author(s): Kinga Kęska, Michał Wojciech Szcześniak, Izabela Makałowska, Małgorzata Czernicka
Software Mentions: 2
Published: almost 6 years ago

10.3390/genes12050614

Novel lincRNA Discovery and Tissue-Specific Gene Expression across 30 Normal Human Tissues
Cited by: 3
Author(s): Xianfeng Chen, Zhifu Sun
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12050630

Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis
Cited by: 0
Author(s): Yongqing Lan, Meng Li, Shuangli Mi
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12050760

Differential mRNA and miRNA Profiles Reveal the Potential Roles of Genes and miRNAs Involved in LPS Infection in Chicken Macrophages
Cited by: 1
Author(s): Qi Zhang, Jie Wang, Jin Zhang, Jie Wen, Guiping Zhao, Qinghe Li
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12060893

Differential Transcript Profiles in Cumulus-Oocyte Complexes Originating from Pre-Ovulatory Follicles of Varied Physiological Maturity in Beef Cows
Cited by: 9
Author(s): Sarah E. Moorey, Jenna Marie Monnig, Michael F. Smith, M. Sofía Ortega, Jonathan A. Green, Ky G Pohler, G.A. Bridges, Susanta K. Behura, T. W. Geary
Software Mentions: 2
Published: over 5 years ago

10.1186/s12711-017-0319-0

Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection
Cited by: 51
Author(s): Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen
Software Mentions: 2
Published: over 9 years ago

10.1186/s12711-018-0384-z

Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans
Cited by: 33
Author(s): Johan Bélteky, Beatrix Agnvall, Lejla Bektic, Andrey Höglund, Per Jensen, Carlos Guerrero-Bosagna
Software Mentions: 2
Published: over 8 years ago

10.1186/s12711-020-00532-y

An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens
Cited by: 12
Author(s): Dirk-Jan de Koning, Nazaret Domínguez-Gasca, Robert Fleming, Andrew C. Gill, Dominic Kurian, Andrew Law, Heather McCormack, David Morrice, Estefanía Sánchez-Rodríguez, Alejandro B. Rodrı́guez-Navarro, Rudolf Preisinger, M. Schmutz, Veronika Šmídová, Frances Turner, Peter W.F. Wilson, Rongyan Zhou, Ian C. Dunn
Software Mentions: 2
Published: over 6 years ago

10.1186/gb-2011-12-1-r7

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi
Cited by: 182
Author(s): Anke Burmester, Ekaterina Shelest, Gernot Glöckner, Christoph Heddergott, Susann Schindler, Peter Staib, Andrew J. Heidel, Marius Felder, A. Petzold, Karol Szafranski, Marc Feuermann, Ivo Pedruzzi, Stefan Priebe, Marco Groth, Robert Winkler, Wenjun Li, Olaf Kniemeyer, Volker Schroeckh, Christian Hertweck, Bernhard Hube, Theodore C. White, Matthias Platzer, Reinhard Guthke, Joseph Heitman, Johannes Wöstemeyer, Peter F. Zipfel, Michel Monod, Axel A. Brakhage
Software Mentions: 2
Published: almost 16 years ago

10.1186/gb-2013-14-1-r6

Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells
Cited by: 112
Author(s): Deborah A. Sanders, Caryn S. Ross-Innes, Dario Beraldi, Jason S. Carroll, Shankar Balasubramanian
Software Mentions: 2
Published: almost 14 years ago

10.1186/gb-2013-14-9-r98

The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells
Cited by: 44
Author(s): Gonçalo Castelo‐Branco, Paulo Amaral, Pär G. Engström, Samuel Robson, Sueli Marques, Paul Bertone, Tony Kouzarides
Software Mentions: 2
Published: almost 14 years ago

10.1186/gb-2013-14-3-r26

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome
Cited by: 92
Author(s): Katie Ayers, N. Davidson, Diana Demiyah, Kelly N. Roeszler, Frank Grützner, Andrew H. Sinclair, Alicia Oshlack, Craig A. Smith
Software Mentions: 2
Published: almost 14 years ago

10.1186/gb-2014-15-1-r15

Differential protein occupancy profiling of the mRNA transcriptome
Cited by: 69
Author(s): Markus Schueler, Mathias Munschauer, Lea H. Gregersen, Ana Finzel, Alexander Loewer, Weiwei Chen, Markus Landthaler, Christoph Dieterich
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13059-015-0706-1

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos
Cited by: 316
Author(s): Xiaoying Fan, Xiannian Zhang, Xinglong Wu, Hongshan Guo, Yuqiong Hu, Fuchou Tang, Yanyi Huang
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-015-0717-y

Global SUMOylation on active chromatin is an acute heat stress response restricting transcription
Cited by: 81
Author(s): Einari A. Niskanen, Marjo Malinen, Päivi Sutinen, Sari Toropainen, Ville Paakinaho, Anniina Vihervaara, Jenny Joutsen, Minna U. Kaikkonen, Lea Sistonen, Jorma J. Palvimo
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-015-0771-5

The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages
Cited by: 52
Author(s): Shruthi S. Vembar, Cameron Ross MacPherson, Odile Sismeiro, Jean‐Yves Coppée, Artur Scherf
Software Mentions: 2
Published: about 11 years ago

10.1186/s13059-015-0853-4

Meta-analysis of RNA-seq expression data across species, tissues and studies
Cited by: 115
Author(s): Peter H. Sudmant, Maria S. Alexis, Christopher B. Burge
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13059-016-1136-4

Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation
Cited by: 12
Author(s): Irene Cantone, Gopuraja Dharmalingam, Yi‐Wah Chan, Anne-Céline Kohler, Boris Lenhard, Matthias Merkenschlager, Amanda G. Fisher
Software Mentions: 2
Published: almost 10 years ago

10.1186/s13059-017-1338-4

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses
Cited by: 34
Author(s): Joseph L. Costello, Christopher J. Kershaw, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Simon J. Hubbard, Graham D. Pavitt
Software Mentions: 2
Published: about 9 years ago

10.1186/s13059-018-1538-6

CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens
Cited by: 34
Author(s): Timothy Daley, Zhixiang Lin, Xueqiu Lin, Yanxia Liu, Wing Hung Wong, Lei Qi
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-019-1682-7

DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis
Cited by: 21
Author(s): Bin Xiong, Yiben Yang, Frank R. Fineis, Ji Ping Wang
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-019-1722-3

Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana
Cited by: 25
Author(s): Stefan Grob, Ueli Grossniklaus
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-019-1786-0

Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes
Cited by: 81
Author(s): Nilusha Malmuthuge, Guanxiang Liang, Le Luo Guan
Software Mentions: 2
Published: about 7 years ago

10.1186/s13059-019-1865-2

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
Cited by: 130
Author(s): Yuanhua Huang, Davis J. McCarthy, Oliver Stegle
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13059-019-1915-9

RADAR: differential analysis of MeRIP-seq data with a random effect model
Cited by: 37
Author(s): Zijie Zhang, Qi Zhan, Mark A. Eckert, Allen Zhu, Agnieszka Chryplewicz, Dario F. De Jesus, Decheng Ren, Rohit Kulkarni, Ernst Lengyel, Chuan He, Mengjie Chen
Software Mentions: 2
Published: almost 7 years ago

10.1111/jeb.12895

Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy
Cited by: 21
Author(s): Luke T. Dunning, Helen Hipperson, William J. Baker, Roger K. Butlin, Céline Devaux, I. Hutton, Javier Igea, Alexander S. T. Papadopulos, Xiangqian Quan, Carole Smadja, Colin Turnbull, Vincent Savolainen
Software Mentions: 2
Published: over 10 years ago

10.1242/jeb.226233

High temperature induces transcriptomic changes in <i>Crassostrea gigas</i> that hinders progress of Ostreid herpesvirus (OsHV-1) and promotes survival
Cited by: 18
Author(s): Lizenn Delisle, Marianna Pauletto, Jérémie Vidal-Dupiol, Bruno Petton, Luca Bargelloni, Caroline Montagnani, Fabrice Pernet, Charlotte Corporeau, Elodie Fleury
Software Mentions: 2
Published: almost 7 years ago

10.1093/jxb/erw346

Analysis of high iron rice lines reveals new miRNAs that target iron transporters in roots
Cited by: 25
Author(s): Soumitra Paul, Dipak Gayen, Swapan K. Datta, Karabi Datta
Software Mentions: 2
Published: about 10 years ago

10.1093/jxb/erw347

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development
Cited by: 56
Author(s): Jelle Van Leene, Jonas Blomme, Shubhada Rajabhau Kulkarni, Bernard Cannoot, Nancy De Winne, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Leen Vercruysse, Robin Vanden Bossche, Ken S. Heyndrickx, Steffen Vanneste, Alain Goossens, Kris Gevaert, Klaas Vandepoele, Nathalie González, Dirk Inzé, Geert De Jaeger
Software Mentions: 2
Published: about 10 years ago

10.1093/jxb/erw361

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways
Cited by: 94
Author(s): Qili Fei, Yang Li, Wanqi Liang, Dabing Zhang, Blake C. Meyers
Software Mentions: 2
Published: about 10 years ago

10.1093/jxb/erx164

Increased temperature and CO2 alleviate photoinhibition in Desmarestia anceps: from transcriptomics to carbon utilization
Cited by: 28
Author(s): Concepción Iñíguez, S. Heinrich, Lars Harms, Francisco J. L. Gordillo
Software Mentions: 2
Published: over 9 years ago

10.1093/jxb/erx336

A disulfide bond A-like oxidoreductase is a strong candidate gene for self-incompatibility in apricot (Prunus armeniaca) pollen
Cited by: 20
Author(s): Juan Vicente Muñoz-Sanz, Elena Zuriaga, M. L. Badenes, Carlos Romero
Software Mentions: 2
Published: about 9 years ago

10.1093/jxb/erx254

Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
Cited by: 43
Author(s): Pavel Cherenkov, Daria D. Novikova, N. A. Omelyanchuk, Victor G. Levitsky, Ivo Große, Dolf Weijers, В. В. Миронова
Software Mentions: 2
Published: over 9 years ago

10.1093/jxb/ery020

The GARP/MYB-related grape transcription factor AQUILO improves cold tolerance and promotes the accumulation of raffinose family oligosaccharides
Cited by: 57
Author(s): Xiaoming Sun, José Tomás Matus, Darren Chern Jan Wong, Zemin Wang, Fengmei Chai, Langlang Zhang, Ting Fang, Li Zhao, Yi Wang, Yuepeng Han, Qingfeng Wang, Shaohua Li, Zhenchang Liang, H. P. Xin
Software Mentions: 2
Published: almost 9 years ago

10.1093/jxb/ery132

miR156-SPL modules regulate induction of somatic embryogenesis in citrus callus
Cited by: 72
Author(s): Long Jiang, Chaoyang Liu, Meng-Qi Feng, Yun Liu, Xiaomeng Wu, Wen‐Wu Guo
Software Mentions: 2
Published: over 8 years ago

10.1093/jxb/erz523

The DEAD-box RNA helicase SHI2 functions in repression of salt-inducible genes and regulation of cold-inducible gene splicing
Cited by: 15
Author(s): Bangshing Wang, Haoxi Chai, Yaohua Zhong, Yun Shen, Wei Yang, Junping Chen, Zhanguo Xin, Huazhong Shi
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.ppat.1003896

RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation
Cited by: 60
Author(s): Meleri Jones, Inga Dry, Dan Frampton, Manuraj Singh, Ravinder K. Kanda, Michael B. Yee, Paul Kellam, Michael Hollinshead, Paul R. Kinchington, Edel A. O’Toole, Judith Breuer
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.ppat.1003962

Reversible Silencing of Cytomegalovirus Genomes by Type I Interferon Governs Virus Latency
Cited by: 55
Author(s): Franziska Dağ, Lars Dölken, Julia Holzki, Anja Drabig, Adrien Weingärtner, Johannes Schwerk, Stefan Lienenklaus, Ianina Conte, Robert Geffers, Colin Davenport, Ulfert Rand, Mario Köster, Siegfried Weiß, Barbara Adler, Dagmar Wirth, Martin Messerle, Hansjörg Hauser, Luka Čičin‐Šain
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1004250

Infection with MERS-CoV Causes Lethal Pneumonia in the Common Marmoset
Cited by: 185
Author(s): Darryl Falzarano, Emmie de Wit, Friederike Feldmann, Angela L. Rasmussen, Atsushi Okumura, Xinxia Peng, Matthew Thomas, Neeltje van Doremalen, Elaine Haddock, Lee Nagy, Rachel LaCasse, Tingting Liu, Jiang Zhu, Jason S. McLellan, Dana Scott, Michael G. Katze, Heinz Feldmann, Vincent J. Munster
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.ppat.1004765

Exome and Transcriptome Sequencing of Aedes aegypti Identifies a Locus That Confers Resistance to Brugia malayi and Alters the Immune Response
Cited by: 35
Author(s): Punita Juneja, Cristina V. Ariani, Yung Shwen Ho, Jewelna Akorli, William J. Palmer, Arnab Pain, Francis M. Jiggins
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1005218

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
Cited by: 48
Author(s): Michael Tscherner, Florian Zwolanek, Sabrina Jenull, Fritz J. Sedlazeck, Andriy Petryshyn, Ingrid E. Frohner, John Mavrianos, Neeraj Chauhan, Arndt von Haeseler, Karl Kuchler
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.ppat.1005536

Wolbachia Blocks Viral Genome Replication Early in Infection without a Transcriptional Response by the Endosymbiont or Host Small RNA Pathways
Cited by: 75
Author(s): Stephanie M. Rainey, Julien Martinez, Melanie McFarlane, Punita Juneja, Peter Sarkies, Aleksei Lulla, Esther Schnettler, Margus Varjak, Andres Merits, Eric A. Miska, Francis M. Jiggins, Alain Kohl
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.ppat.1006046

Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection
Cited by: 25
Author(s): Mary F. Fontana, Gabrielly Lunkes de Melo, Chioma Anidi, Rebecca Hamburger, Charles C. Kim, So Youn Lee, Jennifer Pham
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.ppat.1006143

RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature
Cited by: 27
Author(s): Coralie Viollet, David A. Davis, Shewit S. Tekeste, Martin Reczko, Joseph M. Ziegelbauer, Francesco Pezzella, Jiannis Ragoussis, Robert Yarchoan
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.ppat.1006397

Ebola virus glycoprotein directly triggers T lymphocyte death despite of the lack of infection
Cited by: 52
Author(s): Mathieu Iampietro, Patrick Younan, Andrew Nishida, Mukta Dutta, Ndongala Michel Lubaki, Rodrigo I. Santos, Richard A. Koup, Michael G. Katze, Alexander Bukreyev
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.ppat.1006788

Lower temperatures reduce type I interferon activity and promote alphaviral arthritis
Cited by: 34
Author(s): Natalie A. Prow, Bing Tang, Joy Gardner, Thuy T. Le, Adam Taylor, Yee Suan Poo, Eri Nakayama, Thiago Dominguez Crespo Hirata, Helder I. Nakaya, Andrii Slonchak, Pamela Mukhopadhyay, Suresh Mahalingam, Wayne A. Schroder, William B. Klimstra, Andreas Suhrbier
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.ppat.1006882

AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica
Cited by: 25
Author(s): Kumiko Nakada‐Tsukui, Tsuyoshi Sekizuka, Emi Sato-Ebine, Aleyla Escueta-de Cadiz, Dar-Der Ji, Kentaro Tomii, Makoto Kuroda, Tomoyoshi Nozaki
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1007528

Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans
Cited by: 62
Author(s): Kirthi C. Reddy, Tal Dror, Ryan Underwood, Guled A. Osman, Corrina R. Elder, Christopher A. Desjardins, Christina A. Cuomo, Michalis Barkoulas, Emily R. Troemel
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1007729

Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution
Cited by: 16
Author(s): Audrey M. V. Ah‐Fong, Meenakshi S. Kagda, Melania Abrahamian, Howard S. Judelson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007841

DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes
Cited by: 37
Author(s): Taylor M. Nye, Kristin M. Jacob, Elena K. Holley, Juan M Nevarez, Suzanne Dawid, Lyle A. Simmons, Michael Watson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007960

Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism
Cited by: 31
Author(s): Guangxu Ma, Tao Wang, Pasi K. Korhonen, Neil D. Young, Shuai Nie, Ching‐Seng Ang, Nicholas A. Williamson, Gavin E. Reid, Robin B. Gasser
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1008468

Human papillomavirus E7 binds Oct4 and regulates its activity in HPV-associated cervical cancers
Cited by: 13
Author(s): Theofano Panayiotou, Stella Michael, Apostolos Zaravinos, Ece Demirag, Charis Achilleos, Katerina Strati
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008590

EBNA2-deleted Epstein-Barr virus (EBV) isolate, P3HR1, causes Hodgkin-like lymphomas and diffuse large B cell lymphomas with type II and Wp-restricted latency types in humanized mice
Cited by: 16
Author(s): Chunrong Li, James C. Romero-Masters, Shane M. Huebner, Makoto Ohashi, Mitchell Hayes, Jillian A. Bristol, Scott E. Nelson, Mark R. Eichelberg, Nicholas Van Sciver, Erik A. Ranheim, Rona S. Scott, Eric Johannsen, Shannon C. Kenney
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008760

Cell type- and replication stage-specific influenza virus responses in vivo
Cited by: 17
Author(s): Elizabeth J. Fay, Stephanie L. Aron, Marissa Macchietto, Matthew W. Markman, Katharina Esser-Nobis, Michael Gale, Steven S. Shen, Ryan A. Langlois
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1008740

A-to-I RNA editing in bacteria increases pathogenicity and tolerance to oxidative stress
Cited by: 19
Author(s): Wenhan Nie, Sai Wang, Rui He, Qin Xu, Peihong Wang, Yan Wu, Fang Tian, Junhua Yuan, Bao‐Ku Zhu, Gongyou Chen
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1008919

Sclerotinia sclerotiorum utilizes host-derived copper for ROS detoxification and infection
Cited by: 18
Author(s): Yijuan Ding, Jiaqin Mei, Yaru Chai, Wenjing Yang, Yi Mao, Baoqin Yan, Yang Yu, Joseph Onwusemu Disi, Kusum Rana, Jiana Li, Wei Qian
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1008953

YebC regulates variable surface antigen VlsE expression and is required for host immune evasion in Borrelia burgdorferi
Cited by: 6
Author(s): Yan Zhang, Tong Chen, Sajith Raghunandanan, Xuwu Xiang, Jing Yang, Qiang Liu, Diane G. Edmondson, Steven J. Norris, Xiuli Yang, Yongliang Lou
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1009118

Auxin response factors (ARFs) differentially regulate rice antiviral immune response against rice dwarf virus
Cited by: 40
Author(s): Qingqing Qin, Guangyao Li, Lian Jin, Yu Huang, Yu Wang, Chunhong Wei, Zhi-Hong Xu, Zhirui Yang, Haiyang Wang, Yang Li
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1009198

Metabolic reprogramming of the myeloid lineage by Schistosoma mansoni infection persists independently of antigen exposure
Cited by: 11
Author(s): Diana Cortés-Selva, Lisa Gibbs, J. Alan Maschek, Márcia Nascimento, Tyler Van Ry, James E. Cox, Eyal Amiel, Keke C. Fairfax
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1009446

The herpesvirus accessory protein γ134.5 facilitates viral replication by disabling mitochondrial translocation of RIG-I
Cited by: 15
Author(s): Liu Xing, Yijie Ma, Kathleen Voss, Michiel van Gent, Ying Chan, Michaela U. Gack, Michael Gale, Bin He
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009696

Novel aspects of iron homeostasis in pathogenic bloodstream form Trypanosoma brucei
Cited by: 5
Author(s): Carla Gilabert Carbajo, Lucy J. Cornell, Youssef Madbouly, Zhihao Lai, Phillip A. Yates, Michele Tinti, Calvin Tiengwe
Software Mentions: 2
Published: over 5 years ago

10.1186/s40813-021-00226-x

Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs
Cited by: 3
Author(s): Xueqin Ran, Hu Fengbin, Ning Mao, Yi-Qi Ruan, Fanli Yi, Xi Niu, Shihui Huang, Sheng Li, Longjiang You, Fuping Zhang, Liang-Ting Tang, Jiafu Wang, Jianfeng Liu
Software Mentions: 2
Published: about 5 years ago

10.1016/j.pneurobio.2020.101790

MeCP2 mediates transgenerational transmission of chronic pain
Cited by: 10
Author(s): Wenjuan Tao, Changmao Chen, Yuping Wang, Wenjie Zhou, Yan Jin, Yu Mao, Haitao Wang, Likui Wang, Wen Xie, Xulai Zhang, Jie Li, Juan Li, Xiang-Yao Li, Zhen Quan Tang, Chenghua Zhou, Zhizhong Z. Pan, Zhi Zhang
Software Mentions: 2
Published: over 6 years ago

10.1007/s13238-018-0533-8

Chemical genomics reveals inhibition of breast cancer lung metastasis by Ponatinib via c-Jun
Cited by: 23
Author(s): Wei Shao, Shasha Li, Liwei Lu, Kequan Lin, Xinhong Liu, Haiyan Wang, Huili Wang, Dong Wang
Software Mentions: 2
Published: over 8 years ago

10.1007/s13238-019-0630-3

Mutations in foregut SOX2+ cells induce efficient proliferation via CXCR2 pathway
Cited by: 3
Author(s): Tomoaki Hishida, Eric Vazquez-Ferrer, Yuriko Hishida-Nozaki, Ignacio Sancho‐Martinez, Yuta Takahashi, Fumiyuki Hatanaka, Jun Wu, Alejandro Ocampo, Pradeep Reddy, Min-Zu Wu, Laurie Gerken, Reuben J. Shaw, Concepción Rodrı́guez Esteban, Chris Benner, Hiroshi Nakagawa, Pedro Guillén García, Estrella Núñez-Delicado, Antoni Castells, Josep M. Campistol, Guanghui Liu, Juan Carlos Izpisúa Belmonte
Software Mentions: 2
Published: over 7 years ago

10.3390/proteomes8030025

Serum Glycoproteomic Alterations in Patients with Diabetic Retinopathy
Cited by: 3
Author(s): Ashok Sharma, James Shell Cox, Joshua Glass, Tae Jin Lee, Sai Karthik Kodeboyina, Wenbo Zhi, Lane Ulrich, Zachary L. Lukowski, Shruti Sharma
Software Mentions: 2
Published: about 6 years ago

10.1098/rsos.191640

Swimming exercise enhances brain plasticity in fish
Cited by: 20
Author(s): Daan Mes, Arjan P. Palstra, Christiaan V. Henkel, Ian Mayer, Marco A. Vindas
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12958-021-00771-8

The effect of lysophosphatidic acid-supplemented culture medium on human immature oocytes matured in vitro
Cited by: 7
Author(s): Qingji Xie, Yaxin Xing, Jianhong Zhou, Ling Wang, Jie Wu, Ri‐Cheng Chian
Software Mentions: 2
Published: over 5 years ago

10.1186/s12931-017-0576-z

Genome-wide DNA methylation analysis in lung fibroblasts co-cultured with silica-exposed alveolar macrophages
Cited by: 17
Author(s): Juan Li, Wu Yao, Lin Zhang, Lei Bao, Huiting Chen, Di Wang, Zhongzheng Yue, Yiping Li, Miao Zhang, Changfu Hao
Software Mentions: 2
Published: over 9 years ago

10.1186/s12284-016-0121-6

High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice
Cited by: 47
Author(s): Likai Chen, Weiwei Gao, Siping Chen, Liping Wang, Ji-Yong Zou, Yongzhu Liu, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 2
Published: about 10 years ago

10.1186/s12284-019-0270-5

Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection
Cited by: 8
Author(s): Zhenhui Zhong, Lian‐Yu Lin, Meilian Chen, Lili Lin, Xiaofeng Chen, Yunzhi Lin, Xi Chen, Zonghua Wang, Justice Norvienyeku, Huakun Zheng
Software Mentions: 2
Published: over 7 years ago

10.1186/s12284-020-00421-4

Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains
Cited by: 11
Author(s): Tai‐Hsi Wu, Marlen Müller, Wilhelm Gruissem, Navreet K. Bhullar
Software Mentions: 2
Published: about 6 years ago

10.1186/s12284-021-00502-y

Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress
Cited by: 21
Author(s): Qiqun Cheng, Peng Wang, Guangliang Wu, Yanning Wang, Jingai Tan, Caijing Li, Xiangyu Zhang, Shilei Liu, Shiying Huang, Tao Huang, Mengmeng Yang, Haohua He, Jianmin Bian
Software Mentions: 2
Published: over 5 years ago

10.1186/s12284-021-00524-6

Metabolomic and Transcriptomic Changes Induced by Potassium Deficiency During Sarocladium oryzae Infection Reveal Insights into Rice Sheath Rot Disease Resistance
Cited by: 9
Author(s): Jianglin Zhang, Zhifeng Lu, Tao Ren, Rihuan Cong, Xiaokun Li
Software Mentions: 2
Published: about 5 years ago

10.1038/sdata.2015.30

Comparative, transcriptome analysis of self-organizing optic tissues
Cited by: 10
Author(s): Munazah Andrabi, Shigehiro Kuraku, Nozomu Takata, Yoshiki Sasai, Nick R. Love
Software Mentions: 2
Published: over 11 years ago

10.1038/sdata.2015.15

De novo transcriptome assembly databases for the central nervous system of the medicinal leech
Cited by: 22
Author(s): Dror Hibsh, Hadas Schori, Sol Efroni, Orit Shefi
Software Mentions: 2
Published: over 11 years ago

10.1038/sdata.2015.63

A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues
Cited by: 23
Author(s): Jocelyn Yeen Hui Choy, Priscilla Li Shan Boon, Nicolas Bertin, Melissa J. Fullwood
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-018-25605-3

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle
Cited by: 45
Author(s): Robert Mukiibi, Michael Vinsky, Kate Keogh, Carolyn Fitzsimmons, Paul Stothard, Sinéad M. Waters, Changxi Li
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-25845-3

De novo characterization of Phenacoccus solenopsis transcriptome and analysis of gene expression profiling during development and hormone biosynthesis
Cited by: 13
Author(s): Shashi Arya, Yogeshwar Vikram Dhar, Santosh Kumar Upadhyay, Mehar Hasan Asif, Praveen Chandra Verma
Software Mentions: 2
Published: over 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568