bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.12688/f1000research.3928.2

edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
Cited by: 68
Author(s): Zhiyin Dai, Julie Sheridan, Linden J. Gearing, Darcy Moore, Shian Su, Sam Wormald, Stephen Wilcox, Liam O’Connor, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-020-6528-x

Compacta: a fast contig clustering tool for de novo assembled transcriptomes
Cited by: 2
Author(s): Fernando G. Razo-Mendivil, Octavio Martínez, Corina Hayano-Kanashiro
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-16611-y

OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells
Cited by: 10
Author(s): Runsheng He, Besa Xhabija, Batool Al‐Qanber, Benjamin L. Kidder
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-021-07520-6

Assessment of the mechanism of drug resistance in Trichophyton mentagrophytes in response to various substances
Cited by: 3
Author(s): Chi Xiao, Jiaoyu Wang, Zhenfeng Liao, Yee Huang, Quanan Ji, Yan Liu, Fei Su, Lijun Xu, Qiang Wang, Yao Pan, Ké Li, Guolian Bao
Software Mentions: 1
Published: over 5 years ago

10.12688/f1000research.9094.2

Selective inhibition of ASIC1a confers functional and morphological neuroprotection following traumatic spinal cord injury
Cited by: 6
Author(s): Liam M. Koehn, Natassya M. Noor, Qing Dong, Sing-Yan Er, Lachlan D. Rash, Glenn F. King, Katarzyna M. Dzięgielewska, NR Saunders, Mark D. Habgood
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-11-282

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
Cited by: 136
Author(s): James R. Bradford, Yvonne Hey, Timothy Yates, Yaoyong Li, Stuart D Pepper, Crispin Miller
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-15-822

Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins
Cited by: 46
Author(s): Charley Christian Staats, Ângela Junges, Rafael Lucas Muniz Guedes, Claudia Elizabeth Thompson, Guilherme Loss de Morais, Juliano Tomazzoni Boldo, Luiz Gonzaga Paula de Almeida, Fábio Carrer Andreis, Alexandra Lehmkuhl Gerber, Nicolau Sbaraini, Rana Louise de Andrade da Paixão, Leonardo Broetto, Melissa Fontes Landell, Lucélia Santi, Walter O. Beys‐da‐Silva, Carolina Pereira Silveira, Thaiane Rispoli, Éder Silva de Oliveira, Lívia Kmetzsch, Marilene Henning Vainstein, Ana Tereza Ribeiro de Vasconcelos, Augusto Schrank
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-018-5081-3

Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species
Cited by: 4
Author(s): Bing Huang, Yingtong Lin, Chih-Wei Huang, Hsin Pei Lu, Min Xin Luo, Pei Chun Liao
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-017-3747-x

Transcriptome profiling of litchi leaves in response to low temperature reveals candidate regulatory genes and key metabolic events during floral induction
Cited by: 13
Author(s): Hongna Zhang, Jiyuan Shen, Yongzan Wei, Houbin Chen
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-4437-z

Transcriptomic analysis reveals unique molecular factors for lipid hydrolysis, secondary cell-walls and oxidative protection associated with thermotolerance in perennial grass
Cited by: 13
Author(s): Yi Xu, Bingru Huang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-019-6351-4

Comparative transcriptomic analysis of surf clams (Paphia undulate) infected with two strains of Vibrio spp. reveals the identity of key immune genes involved in host defense
Cited by: 6
Author(s): Mingjia Yu, Lin Zheng, Xiaobo Wang, Min-Fu Wu, Ming Qi, Wei Fu, Yang Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-2898-5

Lipopolysaccharide treatment induces genome-wide pre-mRNA splicing pattern changes in mouse bone marrow stromal stem cells
Cited by: 7
Author(s): Ao Zhou, Meng Li, Bo He, Weixing Feng, Fei Huang, Bing Xu, A. Keith Dunker, Curt Balch, Bai‐Yan Li, Yunlong Liu, Yue Wang
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-017-3831-2

Gene expression and adaptive noncoding changes during human evolution
Cited by: 14
Author(s): Courtney C. Babbitt, Ralph Haygood, William Nielsen, Gregory A. Wray
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-017-16472-5

Identification of a histone family gene signature for predicting the prognosis of cervical cancer patients
Cited by: 42
Author(s): Xiaofang Li, Run Tian, Hugh Gao, Yongkang Yang, Bryan R.G. Williams, Michael P. Gantier, Nigel A.J. McMillan, Dakang Xu, Yiqun Hu, Yue Gao
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-019-6247-3

Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts
Cited by: 13
Author(s): Vinicius Vilperte, Calin Rares Lucaciu, Heidi Halbwirth, Robert Boehm, Thomas Rattei, Thomas Debener
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-16930-0

MALE STERILE6021 (MS6021) is required for the development of anther cuticle and pollen exine in maize
Cited by: 27
Author(s): Youhui Tian, Senlin Xiao, Juan Liu, Yamuna Somaratne, Hua Zhang, Mingming Wang, Huairen Zhang, Li Zhao, Huabang Chen
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-17140-4

Transcriptome analysis of watermelon (Citrullus lanatus) fruits in response to Cucumber green mottle mosaic virus (CGMMV) infection
Cited by: 41
Author(s): Xiaodong Li, Mengnan An, Zihao Xia, Xiaojiao Bai, Yuanhua Wu
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-016-2680-8

Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level
Cited by: 60
Author(s): Jordane Despres, Evelyne Forano, Pascale Lepercq, Sophie Comtet-Marre, Grégory Jubelin, Christophe Chambon, Carl J. Yeoman, Margret E. Berg Miller, Christopher J. Fields, Eric C. Martens, Nicolas Terrapon, Bernard Henrissat, Bryan A. White, Pascale Mosoni
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-4053-3

Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.)
Cited by: 26
Author(s): Ming Li, Zhaoxu Liang, Shikun He, Yuan Zeng, Yan Ji, Fang Wei, Kai–Chao Wu, Guanyu Wang, Ning Xia, Wang LunWang, Song Li, Huachun Tan, Feiquan Tan
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.46551

NRG1 is a critical regulator of differentiation in TP63-driven squamous cell carcinoma
Cited by: 9
Author(s): Ganapati V. Hegde, Cecile de la Cruz, Jennifer M. Giltnane, Lisa Crocker, Avinashnarayan Venkatanarayan, Gabriele Schaefer, Debra Dunlap, Joerg D. Hoeck, Robert Piskol, Florian Gnad, Zora Modrušan, Frédéric J. de Sauvage, Christian W. Siebel, Erica Jackson
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-015-2219-4

Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei)
Cited by: 59
Author(s): J. Peng, Pinyuan Wei, Bin Zhang, Yang Zhao, Dingyuan Zeng, Xiuli Chen, Ming Li, Xiaohan Chen
Software Mentions: 1
Published: almost 11 years ago

10.1186/s13072-015-0013-9

Modelling the conditional regulatory activity of methylated and bivalent promoters
Cited by: 7
Author(s): David Budden, Daniel Hurley, Edmund J. Crampin
Software Mentions: 1
Published: about 11 years ago

10.1002/cam4.2097

Circulating PD‐1 (+) cells may participate in immune evasion in peripheral T‐cell lymphoma and chidamide enhance antitumor activity of PD‐1 (+) cells
Cited by: 10
Author(s): Wei Zhang, Haorui Shen, Yan Zhang, Wei Wang, Shaoxuan Hu, Dongmei Zou, Daobin Zhou
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-17751-x

The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis
Cited by: 34
Author(s): Diana A. Aguilar-Ayala, Laurentijn Tilleman, Filip Van Nieuwerburgh, Dieter Deforce, Juan Carlos Palomino, Peter Vandamme, Jorge A. González-y-Merchand, Anandi Martin
Software Mentions: 1
Published: over 8 years ago

10.1096/fj.201701558R

Macrophage‐derived extracellular vesicles mediate smooth muscle hyperplasia: role of altered miRNA cargo in response to HIV infection and substance abuse
Cited by: 45
Author(s): Himanshu Sharma, Mahendran Chinnappan, Stuti Agarwal, Pranjali Dalvi, Sumedha Gunewardena, Amy O’Brien-Ladner, Navneet K. Dhillon
Software Mentions: 1
Published: over 8 years ago

10.1186/s12863-021-00973-4

Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes
Cited by: 9
Author(s): Lin Yuan, Kun Pan, Yonghui Li, Bo Yi, Bingmiao Gao
Software Mentions: 1
Published: about 5 years ago

10.3390/nu10111721

The Effect of Dietary Mushroom Agaricus bisporus on Intestinal Microbiota Composition and Host Immunological Function
Cited by: 25
Author(s): Gloria Solano‐Aguilar, Saebyeol Jang, Sukla Lakshman, Richi Gupta, Ethiopia Beshah, Masoumeh Sikaroodi, Bryan T. Vinyard, Aleksey Molokin, Patrick M. Gillevet, Joseph F. Urban
Software Mentions: 1
Published: almost 8 years ago

10.1002/2211-5463.13059

Quantitative comparison of the mRNA content of human iPSC‐derived motor neurons and their extracellular vesicles
Cited by: 4
Author(s): Kentaro Otake, Keiko Adachi-Tominari, Hiroaki Nagai, Masayo Saito, Osamu Sano, Yoshihiko Hirozane, Hidehisa Iwata
Software Mentions: 1
Published: over 5 years ago

10.1002/advs.201901341

Selective Killing of Cancer Cells by Nonplanar Aromatic Hydrocarbon‐Induced DNA Damage
Cited by: 14
Author(s): Yan Zhou, Fuwei Gan, Yuanliang Zhang, Xiaozhen He, Chengshuo Shen, Huibin Qiu, Peifeng Liu
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-021-07751-7

Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis
Cited by: 9
Author(s): Tejaswi Yarra, Kirti Ramesh, Mark Blaxter, Anne Hüning, Frank Melzner, Melody S. Clark
Software Mentions: 1
Published: about 5 years ago

10.1289/ehp.1408188

Effects of the Endocrine-Disrupting Chemical DDT on Self-Renewal and Differentiation of Human Mesenchymal Stem Cells
Cited by: 53
Author(s): Amy L. Strong, Zhenzhen Shi, Michael J. Strong, David F. Miller, Douglas B. Rusch, Aaron Buechlein, Erik K. Flemington, John A. McLachlan, Kenneth P. Nephew, Matthew E. Burow, Bruce A. Bunnell
Software Mentions: 1
Published: over 11 years ago

10.3390/ijms17010012

Identification of the Avian Pasteurella multocida phoP Gene and Evaluation of the Effects of phoP Deletion on Virulence and Immunogenicity
Cited by: 16
Author(s): Kangpeng Xiao, Qing Liu, Xueyan Liu, Yunlong Hu, Xinxin Zhao, Qingke Kong
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms17030283

Physiological Investigation and Transcriptome Analysis of Polyethylene Glycol (PEG)-Induced Dehydration Stress in Cassava
Cited by: 73
Author(s): Lili Fu, Zehong Ding, Bingying Han, Wei Hu, Yajun Li, Jiaming Zhang
Software Mentions: 1
Published: over 10 years ago

10.1186/s12940-017-0288-3

Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment
Cited by: 18
Author(s): Zhao‐Xi Wang, Birgit Claus Henn, Chaolong Wang, Yongyue Wei, Su Li, Ryan Sun, Han Chen, Peter J. Wagner, Quan Lu, Xihong Lin, Robert O. Wright, David C. Bellinger, Molly L. Kile, Maitreyi Mazumdar, Martha María Téllez‐Rojo, Lourdes Schnaas, David C. Christiani
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-017-3664-z

Medium term water deficit elicits distinct transcriptome responses in Eucalyptus species of contrasting environmental origin
Cited by: 16
Author(s): Antanas Spokevicius, Josquin Tibbits, Philippe Rigault, Marc-Alexandre Nolin, Caroline Müller, Andrew Merchant
Software Mentions: 1
Published: over 9 years ago

10.1186/s12863-020-00893-9

A novel mouse model expressing human forms for complement receptors CR1 and CR2
Cited by: 6
Author(s): Harriet M. Jackson, Kate E. Foley, Rita O’Rourke, Timothy M. Stearns, Dina Fathalla, B. Paul Morgan, Gareth R. Howell
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms17050689

Genome-Wide Transcriptome Profiling of Mycobacterium smegmatis MC2 155 Cultivated in Minimal Media Supplemented with Cholesterol, Androstenedione or Glycerol
Cited by: 10
Author(s): Qun Li, Fanglan Ge, Yunya Tan, Guangxiang Zhang, Wei Li
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2156-15-S2-S6

Male-specific phosphorylated SR proteins in adult flies of the Mediterranean Fruitfly Ceratitis capitata
Cited by: 4
Author(s): Giuseppe Saccone, Christos Louis, Hongyou Zhang, Valeria Petrella, Michele Di Natale, Maria Perri, Marco Salvemini
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12863-016-0439-5

C14orf132 gene is possibly related to extremely low birth weight
Cited by: 3
Author(s): Airi Tiirats, Triin Viltrop, Margit Nõukas, Ene Reimann, Andres Salumets, Sulev Kõks
Software Mentions: 1
Published: almost 10 years ago

10.18632/aging.203235

miR-30a-5p suppresses lung squamous cell carcinoma via ATG5 - mediated autophagy
Cited by: 15
Author(s): Jichen Yang, Sunyin Rao, Run Cao, Shouyong Xiao, Xin Cui, Lianhua Ye
Software Mentions: 1
Published: about 5 years ago

10.1186/s40478-019-0739-x

c-MYC overexpression induces choroid plexus papillomas through a T-cell mediated inflammatory mechanism
Cited by: 5
Author(s): Ashirwad Merve, Xinyu Zhang, Nicola Pomella, Serena Acquati, Joerg D. Hoeck, Anaëlle Dumas, Gabriel Rosser, Yichen Li, Jennie N. Jeyapalan, Silvia Vicenzi, Qianhai Fan, Zeng Jie Yang, Arianna Sabò, Denise Sheer, Axel Behrens, Silvia Marino
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2180-14-31

Hyperexpression of α-hemolysin explains enhanced virulence of sequence type 93 community-associated methicillin-resistant Staphylococcus aureus
Cited by: 46
Author(s): Kyra Chua, Ian R. Monk, Ya-Hsun Lin, Torsten Seemann, Kellie L. Tuck, Jessica L. Porter, Justin Stepnell, Geoffrey W. Coombs, John K. Davies, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 1
Published: over 12 years ago

10.1186/s12940-020-00666-y

Epigenome-wide association study for pesticide (Permethrin and DEET) induced DNA methylation epimutation biomarkers for specific transgenerational disease
Cited by: 12
Author(s): Jennifer L. M. Thorson, Daniel Beck, Millissia Ben Maamar, Eric Nilsson, Michael K. Skinner
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12863-020-00862-2

RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers
Cited by: 3
Author(s): Hellenn Cardoso Oliveira, A. M. G. Ibelli, Simone Eliza Facioni Guimarães, Maurício Egídio Cantão, J. de O. Peixoto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2021.598296

TRPM2, PDLIM5, BCL3, CD14, GBA Genes as Feasible Markers for Premature Coronary Heart Disease Risk
Cited by: 9
Author(s): Kriengchai Prasongsukarn, Wilanee Dechkhajorn, Surachet Benjathummarak, Yaowapa Maneerat
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms17050690

Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction
Cited by: 19
Author(s): Hyungtaek Jung, Byung-Ha Yoon, Woo Jin Kim, Dong-Wook Kim, David A. Hurwood, Russell E. Lyons, Krishna R. Salin, Heui‐Soo Kim, Ilseon Baek, Vincent Chand, Peter B. Mather
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-017-18607-0

Differentially expressed microRNAs between cattleyak and yak testis
Cited by: 23
Author(s): Cheng Xu, Shan Wu, Wangsheng Zhao, TserangDonko Mipam, Jingbo Liu, Wenjing Liu, Chuanping Yi, Mujahid Ali Shah, Shumin Yu, Xin Cai
Software Mentions: 1
Published: over 8 years ago

10.1186/s12863-018-0700-1

Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium
Cited by: 8
Author(s): Lijun Wu, Tao Liu, Yongsheng Xu, Wenjie Chen, Baolong Liu, Lianquan Zhang, Dengcai Liu, Huaigang Zhang, Bo Zhang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-021-07402-x

Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum
Cited by: 6
Author(s): Akeem Owolabi Taiwo, Lincoln A. Harper, Mark Derbyshire
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.01377

Data Mining and Expression Analysis of Differential lncRNA ADAMTS9-AS1 in Prostate Cancer
Cited by: 39
Author(s): Jiahui Wan, Jiangbo Shu, Ying Jiang, Wei Ma, Xiuli Wang, Zikang He, Rongjun Cui
Software Mentions: 1
Published: over 6 years ago

10.1007/s00497-021-00413-4

Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development
Cited by: 20
Author(s): Zhaodong Hao, Zhongjuan Zhang, Daoquan Xiang, Prakash Venglat, Jinhui Chen, Peng Gao, Raju Datla, Dolf Weijers
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-19200-9

Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin
Cited by: 37
Author(s): Laura Stirm, Peter Huypens, Steffen Sass, Richa Batra, Louise Fritsche, Sara Y. Brucker, Harald Abele, Anita M. Hennige, Fabian J. Theis, Johannes Beckers, Martin Hrabé de Angelis, Andreas Fritsche, Hans‐Ulrich Häring, Harald Staiger
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms17101612

Elevated Expression of Calpain-4 Predicts Poor Prognosis in Patients with Gastric Cancer after Gastrectomy
Cited by: 5
Author(s): Peike Peng, Lingqiang Min, Shushu Song, Junjie Zhao, Lili Li, Caiting Yang, Miaomiao Shao, Mingming Zhang, Hao Wu, Jie Zhang, Can Li, Xuefei Wang, Hongshan Wang, Jing Qin, Yuanyuan Ruan, Jianxin Gu
Software Mentions: 1
Published: almost 10 years ago

10.1093/eep/dvaa022

Effect of concentration and duration of particulate matter exposure on the transcriptome and DNA methylome of bronchial epithelial cells
Cited by: 12
Author(s): Steven K. Huang, Priya Tripathi, Lada A. Koneva, Raymond G. Cavalcante, N. Craig, Anne M. Scruggs, Maureen A. Sartor, Furong Deng, Yahong Chen
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.00847

Differences in DNA Methylation Between Disease-Resistant and Disease-Susceptible Chinese Tongue Sole (Cynoglossus semilaevis) Families
Cited by: 13
Author(s): Yunji Xiu, Changwei Shao, Ying Zhu, Yangzhen Li, Tian Gan, Wenteng Xu, Francesc Piferrer, Songlin Chen
Software Mentions: 1
Published: almost 7 years ago

10.1093/eep/dvy026

Fatherhood alters gene expression within the MPOA
Cited by: 7
Author(s): Adele M. H. Seelke, Jessica Bond, Trent C Simmons, Nikhil Joshi, Matthew L. Settles, Danielle S. Stolzenberg, Mijke Rhemtulla, Karen L. Bales
Software Mentions: 1
Published: almost 8 years ago

10.3389/fgene.2020.00452

DNA Methylation and Demethylation Are Regulated by Functional DNA Methyltransferases and DnTET Enzymes in Diuraphis noxia
Cited by: 8
Author(s): Pieter H. du Preez, Kelly Breeds, N. Francois V. Burger, Hendrik Willem Swiegers, Johannes Christoff Truter, Anna‐Maria Botha
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-016-3059-6

RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response
Cited by: 6
Author(s): Andrea Prunotto, Brian J. Stevenson, Corinne Berthonneche, Fanny Schüpfer, Jacques S. Beckmann, Fabienne Maurer, Sven Bergmann
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-015-2268-8

Transcriptome profiling and validation of gene based single nucleotide polymorphisms (SNPs) in sorghum genotypes with contrasting responses to cold stress
Cited by: 55
Author(s): Ratan Chopra, Gloria Burow, Chad Hayes, Yves Emendack, Zhanguo Xin, John J. Burke
Software Mentions: 1
Published: almost 11 years ago

10.1002/ece3.7581

Comparative transcriptomics of albino and warningly‐coloured caterpillars
Cited by: 4
Author(s): Juan A. Galarza
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-19837-6

Persistent activation of interlinked type 2 airway epithelial gene networks in sputum-derived cells from aeroallergen-sensitized symptomatic asthmatics
Cited by: 15
Author(s): Anya C. Jones, Niamh M. Troy, Elisha White, Elysia M. Hollams, Alexander M. Gout, Kak-Ming Ling, Anthony Kicic, Stephen M. Stick, Peter D. Sly, Patrick G. Holt, Graham L. Hall, Anthony Bosco
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms17111951

Transcriptome Analysis of mRNA and miRNA in Somatic Embryos of Larix leptolepis Subjected to Hydrogen Treatment
Cited by: 15
Author(s): Yali Liu, Sang‐Mi Han, Xiangming Ding, Xinmin Li, Lifeng Zhang, Wanfeng Li, Haiyan Xu, Zhexin Li, Qi Liu
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-018-19954-2

Different milk diets have substantial effects on the jejunal mucosal immune system of pre-weaning calves, as demonstrated by whole transcriptome sequencing
Cited by: 18
Author(s): H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Rosemarie Weikard, Christa Kühn
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2019.00521

De novo Assembly and Characterization of the Floral Transcriptomes of Two Varieties of Melastoma malabathricum
Cited by: 4
Author(s): Tao Zheng, Yang Lin, Longping Wang, Qing Lin, Xiuxiang Lin, Zhendong Chen, Zhenping Lin
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2020.568017

Analysis and Screening of Reproductive Long Non-coding RNAs Through Genome-Wide Analyses of Goat Endometrium During the Pre-attachment Phase
Cited by: 12
Author(s): Linjun Hong, Qun Hu, Xupeng Zang, Yanshe Xie, Chunmei Zhou, Xian Zou, Yaokun Li, Ming Deng, Yongqing Guo, Guangbin Liu, Dewu Liu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12862-019-1362-y

Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation
Cited by: 6
Author(s): Kristin Franke, Isabell Karl, Tonatiuh Peña Centeno, Barbara Feldmeyer, Christian Lassek, Vicencio Oostra, Katharina Riedel, Mario Stanke, Christopher W. Wheat, Klaus Fischer
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2148-13-165

Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei
Cited by: 14
Author(s): Jianbo Yuan, Xiaojun Zhang, Cheng-Zhang Liu, Jiankai Wei, Fuhua Li, Jianhai Xiang
Software Mentions: 1
Published: about 13 years ago

10.3389/fgene.2021.696956

A Novel Computational Framework to Predict Disease-Related Copy Number Variations by Integrating Multiple Data Sources
Cited by: 5
Author(s): Yandan Lin, Tao Sun, Jing Zhao, Zhen Shen
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-019-5741-y

Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq
Cited by: 35
Author(s): Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Yongzhu Liu, Ming Huang, Gangyi Yang, Hong Liu, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 1
Published: over 7 years ago

10.1186/s12862-015-0322-4

Genetic variation of transgenerational plasticity of offspring germination in response to salinity stress and the seed transcriptome of Medicago truncatula
Cited by: 52
Author(s): Wendy Vu, Peter L. Chang, Ken S. Moriuchi, Maren Friesen
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-021-07566-6

Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)
Cited by: 2
Author(s): Duo Chen, Peiyao Yan, Yanping Guo
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.635429

KRT18 Modulates Alternative Splicing of Genes Involved in Proliferation and Apoptosis Processes in Both Gastric Cancer Cells and Clinical Samples
Cited by: 8
Author(s): Biao Chen, Ximing Xu, Dandan Lin, Xin Chen, Yali Xu, Xin Liu, Weiguo Dong
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2021.710143

Low-Dose Radiation Can Cause Epigenetic Alterations Associated With Impairments in Both Male and Female Reproductive Cells
Cited by: 8
Author(s): Chi Tim Leung, Yi Cheng Yang, K.N. Yu, Nathan Tam, Ting‐Fung Chan, Xiao Lin, Richard Yuen Chong Kong, Jill Man Ying Chiu, Anson Wong, Wing Yiu Lui, Karen Wing Yee Yuen, Keng Po Lai, Rudolf S.S. Wu
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-3891-3

Small RNA fragments derived from multiple RNA classes – the missing element of multi-omics characteristics of the hepatitis C virus cell culture model
Cited by: 16
Author(s): Paulina Jackowiak, Anna Hojka-Osińska, Anna Philips, Agnieszka Żmieńko, Lucyna Budzko, Patrick Maillard, Agata Budkowska, Marek Figlerowicz
Software Mentions: 1
Published: about 9 years ago

10.1007/s11103-017-0594-8

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene
Cited by: 35
Author(s): Larissa Arrais Guimarães, Ana Paula Zotta Mota, Ana Cláudia Guerra Araújo, Lúcio Flávio de Alencar Figueiredo, Bruna Medeiros Pereira, Mario Alfredo de Passos Saraiva, Raquel Bispo Silva, Etienne G. J. Danchin, P. M. Guimarães, Ana Cristina Miranda Brasileiro
Software Mentions: 1
Published: over 9 years ago

10.1186/s12866-016-0739-y

Identification of the crp gene in avian Pasteurella multocida and evaluation of the effects of crp deletion on its phenotype, virulence and immunogenicity
Cited by: 17
Author(s): Xinxin Zhao, Qing Liu, Kangpeng Xiao, Yunlong Hu, Xueyan Liu, Yanyan Li, Qingke Kong
Software Mentions: 1
Published: about 10 years ago

10.1002/ece3.7889

Transcriptomic response of <i>Daphnia magna</i> to nitrogen‐ or phosphorus‐limited diet
Cited by: 3
Author(s): Zhimeng Xu, Yingdong Li, Meng Li, Hongbin Liu
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.103772

ARHGEF11 promotes proliferation and epithelial-mesenchymal transition of hepatocellular carcinoma through activation of &#x3B2;-catenin pathway
Cited by: 9
Author(s): Dingjun Hao, Zexin Zhu, Xu Lin, Xing Chen, Xuefeng Li, Tian Lan, Wei Li, Kefei Yuan, Yong Zeng
Software Mentions: 1
Published: almost 6 years ago

10.3389/fgene.2021.610501

Comprehensive Analysis of Survival-Related lncRNAs, miRNAs, and mRNAs Forming a Competing Endogenous RNA Network in Gastric Cancer
Cited by: 11
Author(s): Yanjie Zhao, Heng Zhang, Qiang Ju, Xinmei Li, Yuxin Zheng
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-4284-3

Transcriptome sequencing and analysis of zinc-uptake-related genes in Trichophyton mentagrophytes
Cited by: 7
Author(s): Xinke Zhang, Pengxiu Dai, Yongping Gao, Xiaohua Gong, Hao Cui, Yipeng Jin, Yihua Zhang
Software Mentions: 1
Published: almost 9 years ago

10.3389/fgene.2021.704778

GH Overexpression Alters Spermatic Cells MicroRNAome Profile in Transgenic Zebrafish
Cited by: 4
Author(s): William Borges Domingues, Tony Silveira, Leandro S. Nunes, Eduardo B. Blödorn, Augusto Schneider, Carine Dahl Corcine, Antônio Sérgio Varela, Izani Bonel Acosta, Mateus Tavares Kütter, Gonzalo Greif, Carlos Robello, Danillo Pinhal, Luís Fernando Marins, Vinicius F. Campos
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-020-6521-4

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism
Cited by: 7
Author(s): Wenkai Hui, Fei Zhao, Jingyan Wang, Xiaoyang Chen, Jue-Wei Li, Yu Zhong, Hongyun Liu, Junxing Zheng, Liangzhen Zhang, Qingmin Que, Aimin Wu, Wei Gong
Software Mentions: 1
Published: over 6 years ago

10.15252/embr.202051660

Plasmodium transcription repressor AP2‐O3 regulates sex‐specific identity of gene expression in female gametocytes
Cited by: 21
Author(s): Zhenkui Li, Huiting Cui, Jiepeng Guan, Cong Liu, Zhengang Yang, Jing Yuan
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2017.00114

Triportheus albus Cope, 1872 in the Blackwater, Clearwater, and Whitewater of the Amazon: A Case of Phenotypic Plasticity?
Cited by: 15
Author(s): José Deney Alves Araújo, Andrea Ghelfi, Adalberto Luı́s Val
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-15-492

Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development
Cited by: 63
Author(s): David Fernando Plaza, Chi Feng Lin, Niels Sebastiaan Johannes van der Velden, Markus Aebi, Markus Künzler
Software Mentions: 1
Published: about 12 years ago

10.1002/cam4.3963

Pivotal factors associated with the immunosuppressive tumor microenvironment and melanoma metastasis
Cited by: 21
Author(s): Chuan Zhang, Dan Dang, Lele Cong, Hongyan Sun, Xianling Cong
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-018-21525-4

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations
Cited by: 35
Author(s): Brooke R. Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth W. Slettedahl, Douglas W. Mahoney, Nikolaos Vasmatzis, Hang Xu, Min‐Soo Kim, Matthew A. Bockol, Daniel R. O’Brien, Diane E. Grill, Nathaniel D. Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth A. Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas C. Smyrk, Ann L. Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David A. Ahlquist, Lisa A. Boardman
Software Mentions: 1
Published: over 8 years ago

10.1002/pld3.74

Developmental dynamics of stem starch accumulation in <i>Sorghum bicolor</i>
Cited by: 19
Author(s): Brian McKinley, Anna L. Casto, William L. Rooney, John E. Mullet
Software Mentions: 1
Published: about 8 years ago

10.1186/s12870-020-02638-3

Comparative transcriptome analysis suggests convergent evolution of desiccation tolerance in Selaginella species
Cited by: 8
Author(s): Gerardo Alejo‐Jacuinde, Sandra Isabel González-Morales, Araceli Oropeza-Aburto, June Simpson, Luis Herrera-Estrella
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12866-016-0695-6

In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study
Cited by: 36
Author(s): Yijuan Xu, Raluca Maltesen, Lone Heimann Larsen, Henrik Carl Schønheyder, Vang Quy Le, Jeppe Lund Nielsen, Per Halkjær Nielsen, Trine Rolighed Thomsen, Kåre Lehmann Nielsen
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-018-21371-4

Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy
Cited by: 28
Author(s): María Carolina Gallego Iradi, Judy C. Triplett, James Thomas, Rachel Davila, Anthony M Crown, Hilda Brown, Jada Lewis, Maurice S. Swanson, Guilian Xu, Edgardo Rodríguez-Lebrón, David R. Borchelt
Software Mentions: 1
Published: over 8 years ago

10.1186/s12861-017-0147-z

Transcriptome profiling reveals expression signatures of cranial neural crest cells arising from different axial levels
Cited by: 23
Author(s): Rachael Lumb, Sam Buckberry, Genevieve A. Secker, David Lawrence, Quenten Schwarz
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.70564

Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories
Cited by: 19
Author(s): DeElegant Robinson, Michael Place, James Hose, Adam Jochem, Audrey P. Gasch
Software Mentions: 1
Published: about 5 years ago

10.15252/embr.201744853

The dynamic recruitment of <scp>TRBP</scp> to neuronal membranes mediates dendritogenesis during development
Cited by: 22
Author(s): Anna Antoniou, Sharof Khudayberdiev, Agata Idziak, Silvia Bicker, Ralf Jacob, Gerhard Schratt
Software Mentions: 1
Published: over 8 years ago

10.1016/j.xplc.2021.100164

The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen
Cited by: 25
Author(s): Dangping Luo, José C. Huguet‐Tapia, R. Taylor Raborn, Frank F. White, Volker Brendel, Bing Yang
Software Mentions: 1
Published: over 5 years ago

10.1007/s00299-015-1822-9

Transcriptome sequencing reveals the roles of transcription factors in modulating genotype by nitrogen interaction in maize
Cited by: 20
Author(s): Qiuyue Chen, Zhipeng Liu, Baobao Wang, Xufeng Wang, Jinsheng Lai, Feng Tian
Software Mentions: 1
Published: about 11 years ago

10.1186/s12861-015-0054-0

Development of the follicular basement membrane during human gametogenesis and early folliculogenesis
Cited by: 66
Author(s): A. Marijne Heeren, Liesbeth van Iperen, Daniëlle B Klootwijk, Ana de Melo Bernardo, Matthias S Roost, Maria M Gomes Fernandes, L. A. Louwe, Carina G. J. M. Hilders, Frans M. Helmerhorst, Lucette Aj van der Westerlaken, Susana M. Chuva de Sousa Lopes
Software Mentions: 1
Published: over 11 years ago

10.1186/s12870-018-1428-9

Comprehensive transcriptome analysis reveals genes in response to water deficit in the leaves of Saccharum narenga (Nees ex Steud.) hack
Cited by: 33
Author(s): Xihui Liu, Ronghua Zhang, Hesheng Ou, Yiyun Gui, Jizhen Wei, Hui Zhou, Huachun Tan, Yang–Rui Li
Software Mentions: 1
Published: almost 8 years ago

10.18632/aging.203157

Immune infiltration-related N6-methyladenosine RNA methylation regulators influence the malignancy and prognosis of endometrial cancer
Cited by: 19
Author(s): Jian Ma, Di Yang, Xiaolong Ma
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2020.00583

The Construction and Comprehensive Prognostic Analysis of the LncRNA-Associated Competitive Endogenous RNAs Network in Colorectal Cancer
Cited by: 8
Author(s): Wei Li, Weifang Yu, Xia Jiang, Xian Gao, Guiqi Wang, Xiaojing Jin, Zhenze Zhao, Yuegeng Liu
Software Mentions: 1
Published: about 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568