bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.7554/eLife.64317

Evolutionary shifts in taste coding in the fruit pest Drosophila suzukii
Cited by: 33
Author(s): Hany K.M. Dweck, Gaëlle J.S. Talross, Wanyue Wang, John R. Carlson
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-019-5887-7

Refinement of breast cancer molecular classification by miRNA expression profiles
Cited by: 59
Author(s): Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao H. Saal, Åke Borg, Johan Vallon-Christerson, Carlos Rovira
Software Mentions: 5
Published: over 5 years ago

10.1186/s13293-021-00368-1

Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies
Cited by: 16
Author(s): José F. Català-Senent, Marta R. Hidalgo, Marina Berenguer, Gopanandan Parthasarathy, Harmeet Malhi, Pablo Malmierca-Merlo, María de la Iglesia-Vayá, Francisco García‐García
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.61257

Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length
Cited by: 30
Author(s): Mirna Marinić, Katelyn Mika, Sravanthi Chigurupati, Vincent J. Lynch
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.53948

Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling
Cited by: 14
Author(s): Y. Claire, John C. Marioni, Gillian M. Griffiths, Alison F. Richard
Software Mentions: 5
Published: over 4 years ago

10.1111/acel.13280

Modeling the human aging transcriptome across tissues, health status, and sex
Cited by: 23
Author(s): Maxim N. Shokhirev, Adiv A. Johnson
Software Mentions: 5
Published: about 4 years ago

10.3389/fcimb.2016.00136

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection
Cited by: 22
Author(s): Caroline Poyntner, Barbara Blasi, Elsa Arcalís, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.15657

An integrative transcriptomic atlas of organogenesis in human embryos
Cited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.60100

Sequential perturbations to mouse corticogenesis following in utero maternal immune activation
Cited by: 15
Author(s): Cesar P Canales, Myka L. Estes, Karol Cichewicz, Kartik Angara, John Paul Aboubechara, Scott A. Cameron, Kathryn Prendergast, Linda Su-Feher, Iva Zdilar, Ellie J Kreun, Emma C Connolly, Jin Myeong Seo, Jack B Goon, Kathleen Farrelly, Tyler W. Stradleigh, Deborah van der List, Lori Haapanen, Judy Van de Water, Daniel Vogt, A. Kimberley McAllister, A. Nord
Software Mentions: 5
Published: almost 4 years ago

10.18632/aging.102923

Integrative analysis of DNA methylation and gene expression reveals distinct hepatocellular carcinoma subtypes with therapeutic implications
Cited by: 10
Author(s): Xiaowen Huang, Chen Yang, Jilin Wang, Tiantian Sun, Hua Xiong
Software Mentions: 5
Published: over 4 years ago

10.1093/molbev/msaa110

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
Cited by: 10
Author(s): Rosa Fernández, Marina Marcet‐Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-015-2040-0

Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study
Cited by: 27
Author(s): Philip Shaw, Sastra Chaotheing, Pavita Kaewprommal, Jittima Piriyapongsa, Chayaphat Wongsombat, Nattida Suwannakitti, Pongpisid Koonyosying, Chairat Uthaipibull, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-020-6665-2

The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice
Cited by: 37
Author(s): Lei Xu, Anil Surathu, Isaac Raplee, Ashok Chockalingam, Sharron Stewart, Lacey Walker, Leonard Sacks, Vikram Patel, Zhihua Li, Rodney Rouse
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.6499

Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure
Cited by: 5
Author(s): Zhenguo Xu, Zhilong Jia, Jianxin Shi, Zeyu Zhang, Xiaojian Gao, Qi Jia, Bohan Liu, Jixuan Liu, Chunlei Liu, Xiaojing Zhao, Kunlun He
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-016-1248-6

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
Cited by: 11
Author(s): Lydia Müller, Daniel Gerighausen, Mariam R. Farman, Dirk Zeckzer
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.65574

KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism
Cited by: 16
Author(s): Anthony A Ruberto, Aline Gréchez-Cassiau, Sabrina Guérin, Luc Martin, Johana S. Revel, Mohamed Mehiri, Malayannan Subramaniam, Franck Delaunay, Michèle Teboul
Software Mentions: 5
Published: over 3 years ago

10.1093/bioinformatics/btz089

How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana
Cited by: 9
Author(s): Kimon Froussios, Nicholas J. Schurch, Katarzyna Mackinnon, Marek Gierliński, Céline Duc, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: over 3 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 4 years ago

10.1007/s00395-021-00887-3

LncRNA LncHrt preserves cardiac metabolic homeostasis and heart function by modulating the LKB1-AMPK signaling pathway
Cited by: 24
Author(s): Ning Liu, Masaharu Kataoka, Yingchao Wang, Linbin Pu, Xiaoxuan Dong, Xuyang Fu, Feng Zhang, Feng Gao, Tian Liang, Jianqiu Pei, Changchen Xiao, Qiongzi Qiu, TingTing Hong, Qiming Chen, Jing Zhao, Long‐Guan Zhu, Junhua He, Xiaoyun Hu, Yu Nie, Wei Zhu, Hong Yu, Douglas B. Cowan, Xinyang Hu, Jianan Wang, Dazhi Wang, Jinghai Chen
Software Mentions: 5
Published: over 3 years ago

10.1128/mSystems.00053-18

Balances: a New Perspective for Microbiome Analysis
Cited by: 173
Author(s): Javier Rivera Pinto, J. J. Egozcue, Vera Pawlowsky‐Glahn, Roger Paredes, Marc Noguera‐Julian, M. Luz Calle
Software Mentions: 5
Published: over 6 years ago

10.1128/mBio.03042-19

Quantitative Framework for Model Evaluation in Microbiology Research Using Pseudomonas aeruginosa and Cystic Fibrosis Infection as a Test Case
Cited by: 83
Author(s): Daniel M. Cornforth, Frances L. Diggle, Jeffrey A. Melvin, Jennifer M. Bomberger, Marvin Whiteley
Software Mentions: 5
Published: almost 5 years ago

10.3389/fcell.2021.684643

Development of an Individualized Ubiquitin Prognostic Signature for Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Yue Wu, Xi Zhang, Wa Xian, Huan Feng, Bintao Hu, Zhiyao Deng, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Jihong Liu, Tao Wang
Software Mentions: 5
Published: over 3 years ago

10.1128/mBio.01193-19

Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host
Cited by: 23
Author(s): Brad Griesenauer, Tuan M. Tran, Kate R. Fortney, Diane M. Janowicz, Paula A. Johnson, Hongyu Gao, Stephen Barnes, Landon Wilson, Yunlong Liu, Stanley M. Spinola
Software Mentions: 5
Published: over 5 years ago

10.3390/toxins13080552

Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells
Cited by: 4
Author(s): Ilse Vanhoutte, Caroline De Tender, Kristel Demeyere, Mohamed F. Abdallah, Sarah Ommeslag, Pieter Vermeir, Sarah De Saeger, Jane Debode, Evelyne Meyer, Siska Croubels, Kris Audenaert, Leen De Gelder
Software Mentions: 5
Published: over 3 years ago

10.1186/s13229-020-00359-w

IGF-1 treatment causes unique transcriptional response in neurons from individuals with idiopathic autism
Cited by: 17
Author(s): Sara B. Linker, Ana Paula Mendes, Maria C. Marchetto
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-021-84667-y

Neuron-specific spinal cord translatomes reveal a neuropeptide code for mouse dorsal horn excitatory neurons
Cited by: 15
Author(s): Rebecca R Das Gupta, Louis Scheurer, Paweł Pelczar, Hendrik Wildner, Hanns Ulrich Zeilhofer
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-019-2969-0

Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models
Cited by: 24
Author(s): Marina Esteban-Medina, María Peña‐Chilet, Carlos Loucera, Joaquı́n Dopazo
Software Mentions: 5
Published: over 5 years ago

10.1186/s13100-018-0138-z

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis
Cited by: 33
Author(s): Gavin Pereira, Laura Sánchez, Paul Schaughency, Alejandro Rubio-Roldán, Justin Choi, Evarist Planet, Ranjan Batra, Priscilla Turelli, Didier Trono, Lyle W. Ostrow, John Ravits, Haig H. Kazazian, Sarah J. Wheelan, Sara R. Heras, Jens Mayer, José L. García‐Pérez, John Goodier
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-021-84194-w

Antisense oligonucleotide development for the selective modulation of CYP3A5 in renal disease
Cited by: 2
Author(s): Kevin A. Lidberg, Andrew J. Annalora, Marija Jozic, Daniel J. Elson, Lu Wang, Theo K. Bammler, Susanne Ramm, Maria Beatriz Monteiro, Jonathan Himmelfarb, Carol S. Marcus, Patrick L. Iversen, Edward J. Kelly
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-06809-2

Gene expression predictions and networks in natural populations supports the omnigenic theory
Cited by: 22
Author(s): Aurélien Chateigner, Marie-Claude Lesage-Descauses, Odile Rogier, Véronique Jorge, Jean‐Charles Leplé, Véronique Brunaud, Christine Paysant‐Le Roux, Ludivine Soubigou‐Taconnat, Marie‐Laure Martin‐Magniette, Leopoldo Sánchez, Vincent Segura
Software Mentions: 5
Published: over 4 years ago

10.3389/fcell.2021.624711

Single-Cell RNA Sequencing With Combined Use of Bulk RNA Sequencing to Reveal Cell Heterogeneity and Molecular Changes at Acute Stage of Ischemic Stroke in Mouse Cortex Penumbra Area
Cited by: 22
Author(s): Kang Guo, Jianing Luo, Dayun Feng, Lin Wu, Xin Wang, Xia Li, Kai Tao, Xun Wu, Wenxing Cui, Yijie He, Bing Wang, Zhenwei Zhao, Zhiguo Zhang
Software Mentions: 5
Published: almost 4 years ago

10.15252/emmm.202013328

Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients
Cited by: 11
Author(s): Mirko Signorelli, Mitra Ebrahimpoor, Olga Veth, Kristina Hettne, Nisha Verwey, R. García-Rodríguez, Christa L Tanganyika-deWinter, Luz Berenice López-Hernández, Rosa Escobar Cedillo, Benjamín Gómez-D́iaz, Ólafur Þ. Magnússon, Hailiang Mei, Roula Tsonaka, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-74748-9

Dynamic changes in the brain protein interaction network correlates with progression of Aβ42 pathology in Drosophila
Cited by: 6
Author(s): Harry M. Scholes, Adam Cryar, Fiona Kerr, David Sutherland, Lee A. Gethings, Johannes P.C. Vissers, Jonathan G. Lees, Christine A. Orengo, Linda Partridge, Konstantinos Thalassinos
Software Mentions: 5
Published: about 4 years ago

10.1186/s12862-019-1572-3

The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish
Cited by: 4
Author(s): Mauricio Losilla, David Luecke, Jason R. Gallant
Software Mentions: 5
Published: almost 5 years ago

10.1242/dmm.040147

Dynamic MAPK signaling activity underlies a transition from growth arrest to proliferation in Drosophila scribble mutant tumors
Cited by: 17
Author(s): Tiantian Ji, Lina Zhang, Mingxi Deng, Shan Huang, Jiguang Wang, Tri Pham, Andrew A. Smith, Varun Sridhar, Clemens Cabernard, Yan Yan
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-74705-6

Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method
Cited by: 5
Author(s): Marta Lucchetta, Marco Pellegrini
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-021-07517-1

Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri
Cited by: 1
Author(s): Valérie Ducret, Adam Richards, Mathieu Videlier, Thibault Scalvenzi, Karen Moore, Konrad Paszkiewicz, Camille Bonneaud, Nicolas Pollet, Anthony Herrel
Software Mentions: 5
Published: over 3 years ago

10.15252/emmm.202012105

Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s disease
Cited by: 23
Author(s): Rafael Alcalá-Vida, Marta Garcia‐Forn, Carla Castany‐Pladevall, Jordi Creus-Muncunill, Yoko Itō, Enrique Blanco, Arantxa Golbano, Kilian Crespí-Vázquez, Aled Parry, Guy Slater, Shamith A. Samarajiwa, Sandra Peiró, Luciano Di Croce, Masashi Narita, Esther Pérez‐Navarro
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-76769-w

GIANT: galaxy-based tool for interactive analysis of transcriptomic data
Cited by: 8
Author(s): Jimmy Vandel, Céline Gheeraert, Bart Staels, Jérôme Eeckhoute, Philippe Lefèbvre, Julie Dubois-Chevalier
Software Mentions: 5
Published: about 4 years ago

10.1155/2021/8895723

Identification and Construction of a Long Noncoding RNA Prognostic Risk Model for Stomach Adenocarcinoma Patients
Cited by: 14
Author(s): Zhiqiang Zha, Peiling Zhang, Dailing Li, Guolong Liu, Lin Lü
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12859-017-1780-z

Local sequence and sequencing depth dependent accuracy of RNA-seq reads
Cited by: 9
Author(s): Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng, Feifei Xiao
Software Mentions: 5
Published: over 7 years ago

10.1007/s00424-021-02582-7

Abnormal neonatal sodium handling in skin precedes hypertension in the SAME rat
Cited by: 2
Author(s): L. J. Mullins, Jessica R. Ivy, Mairi Ward, Olav Tenstad, Helge Wiig, Kento Kitada, Jonathan Manning, Natalia Rakova, Dominik N. Müller, John J. Mullins
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-72511-8

Burn resuscitation strategy influences the gut microbiota-liver axis in swine
Cited by: 11
Author(s): Wayne Muraoka, Jose C. Granados, Belinda I. Gómez, Susannah E. Nicholson, Kevin K. Chung, Jeffrey W. Shupp, James A. Bynum, Michael A. Dubick, David M. Burmeister
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-76991-6

Salivary microbiome composition changes after bariatric surgery
Cited by: 11
Author(s): Mária Džunková, Róbert Lipták, Barbora Vlková, Roman Gardlík, M Cierny, Andrés Moya, Peter Celec
Software Mentions: 5
Published: about 4 years ago

10.1177/1759091419843393

Global Brain Transcriptome Analysis of a Tpp1 Neuronal Ceroid Lipofuscinoses Mouse Model
Cited by: 11
Author(s): Miriam S. Domowicz, Wen-Ching Chan, Patricia Claudio-Vázquez, Judith Henry, Christopher B. Ware, Jorge Andrade, Glyn Dawson, Nancy B. Schwartz
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2020.588041

Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy
Cited by: 3
Author(s): Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2105-15-S9-S6

BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data
Cited by: 10
Author(s): Jin Gu, Wang Xiao, Leena Halakivi-Clarke, Robert Clarke, Jianhua Xuan
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-020-67690-3

Transcriptomic analysis of the mechanisms of alleviating renal interstitial fibrosis using the traditional Chinese medicine Kangxianling in a rat model
Cited by: 13
Author(s): Yufeng Jiang, Yaohan Zhu, Timing Zhen, Jie Li, Kaichen Xing, Liqun He, Sibo Zhu
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-020-00966-y

Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation
Cited by: 10
Author(s): Rajesh Kaushal, Peng Li, Sunil Kumar Singh, Mengrui Zhang, Xinlian Zhang, Juan Ignacio Vílchez, Zhen Wang, Danxia He, Yu Ye, Suhui Lv, Zhongtian Xu, Rafael J. L. Morcillo, Wei Wang, Wei-Chang Huang, Paul W. Paré, Chun‐Peng Song, Jian‐Kang Zhu, Renyi Liu, Wenxuan Zhong, Ping Ma, Huiming Zhang
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12863-018-0660-5

Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression
Cited by: 45
Author(s): I‐Hsuan Lin, Junn-Liang Chang, Kate Hua, Wan-Chen Huang, Ming Hsu, Yifan Chen
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-015-1739-2

De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil
Cited by: 20
Author(s): Bree K. Yednock, Timothy J. Sullivan, Joseph E. Neigel
Software Mentions: 5
Published: over 9 years ago

10.1016/j.devcel.2020.11.013

Diverse Routes toward Early Somites in the Mouse Embryo
Cited by: 40
Author(s): Carolina Guibentif, J. B. Griffiths, Iván Imaz-Rosshandler, Shila Ghazanfar, Jennifer Nichols, Valerie Wilson, Berthold Göttgens, John C. Marioni
Software Mentions: 5
Published: almost 4 years ago

10.1186/s40168-017-0237-y

Normalization and microbial differential abundance strategies depend upon data characteristics
Cited by: 1,253
Author(s): Sophie Weiss, Zhenjiang Zech Xu, Shyamal D. Peddada, Amir Almasi‐Hashiani, Kyle Bittinger, Antonio González, Catherine Lozupone, Jesse Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde, Rob Knight
Software Mentions: 5
Published: almost 8 years ago

10.1002/mbo3.1146

Deeper below the surface—transcriptional changes in selected genes of Clostridium beijerinckii in response to butanol shock
Cited by: 5
Author(s): Petra Patáková, Jan Kolek, Katerina Jureckova, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Ivo Provazník
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-63275-2

Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model
Cited by: 9
Author(s): Flávio Lichtenstein, Asif Iqbal, Sonia Elisabete Alves de Lima Will, Rosemary Viola Bösch, Carlos DeOcesano-Pereira, Maurício Barbugiani Goldfeder, Roger Chammas, Carlos Eduardo Madureira Trufen, Kátia L.P. Morais, Jean Gabriel de Souza, Renato José Mendonça Natalino, Inácio L.M. Junqueira-de-Azevedo, Milton Yutaka Nishiyama-Jr, Úrsula Castro de Oliveira, F Alves, Jaqueline Mayara Araujo, Aline Ramos Maia Lobba, Ana Marisa Chudzinski‐Tavassi
Software Mentions: 5
Published: over 4 years ago

10.1016/j.tranon.2021.101107

3D heterospecies spheroids of pancreatic stroma and cancer cells demonstrate key phenotypes of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Xinyuan Liu, Beate Gündel, Xidan Li, Jianping Liu, Andrew N. Wright, Matthias Löhr, Gustav Arvidsson, Rainer Heuchel
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-021-01037-6

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis
Cited by: 15
Author(s): Jessica Dittmer, Robert M. Brucker
Software Mentions: 5
Published: over 3 years ago

10.1186/s13075-015-0544-2

Transcriptome analysis of ageing in uninjured human Achilles tendon
Cited by: 61
Author(s): Mandy J. Peffers, Yongxiang Fang, Kathleen Cheung, Tim Koh Jia Wei, Peter Clegg, Helen L. Birch
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13100-021-00236-0

Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa
Cited by: 26
Author(s): Guillaume Wos, Rimjhim Roy Choudhury, Filip Kolář, Christian Parisod
Software Mentions: 5
Published: almost 4 years ago

10.1186/s40168-021-01129-3

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)
Cited by: 7
Author(s): Wodan Ling, Ni Zhao, Anna Plantinga, Lenore J. Launer, Anthony A. Fodor, Katie A. Meyer, Michael C. Wu
Software Mentions: 5
Published: over 3 years ago

10.1186/s12863-020-00852-4

Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs
Cited by: 9
Author(s): Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto, W. L. Flowers
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-36768-4

Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
Cited by: 10
Author(s): Stefan Wyder, Michael T. Raissig, Ueli Grossniklaus
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12859-019-3324-1

Lag penalized weighted correlation for time series clustering
Cited by: 8
Author(s): Thevaa Chandereng, Anthony Gitter
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-019-39318-8

Identifying Windows of Susceptibility by Temporal Gene Analysis
Cited by: 9
Author(s): Kristin P. Bennett, Elisabeth M. Brown, Hannah De los Santos, Matthew Poegel, Thomas R. Kiehl, Evan W. Patton, Spencer Norris, Sally Temple, John S. Erickson, Deborah L. McGuinness, Nathan C. Boles
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-36471-4

Astrocytoma progression scoring system based on the WHO 2016 criteria
Cited by: 12
Author(s): Zhen-Hang Li, Yanlei Guan, Qiang Liu, Yao Wang, Run Cui, Yunjie Wang
Software Mentions: 5
Published: almost 6 years ago

10.1101/2020.04.24.059527

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

10.1038/s41598-018-33718-y

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Cited by: 40
Author(s): Yongpeng Li, Xing Fu, Meicheng Zhao, Wei Zhang, Bo Li, Diaoguo An, Junming Li, Aimin Zhang, Renyi Liu, Xigang Liu
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-019-5496-5

OMICfpp: a fuzzy approach for paired RNA-Seq counts
Cited by: 1
Author(s): Alberto Berral-González, Ángela L. Riffo‐Campos, Guillermo Ayala
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-015-2135-7

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish
Cited by: 27
Author(s): Candida Vaz, Choon Wei Wee, Gek Ping Serene Lee, Philip W. Ingham, Vivek Tanavde, Sinnakaruppan Mathavan
Software Mentions: 5
Published: about 9 years ago

10.3389/fcell.2021.664178

Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos
Cited by: 0
Author(s): Jin Sun, Weisheng Zheng, Wenqiang Liu, Xiaochen Kou, Yanhong Zhao, Zehang Liang, Lu Wang, Zihao Zhang, Jing Xiao, Rui Gao, Shaorong Gao, Cizhong Jiang
Software Mentions: 5
Published: over 3 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: over 6 years ago

10.1128/AEM.02992-18

Characterizing the Key Agents in a Disease-Suppressed Soil Managed by Reductive Soil Disinfestation
Cited by: 33
Author(s): Liang Liang Liu, Xinqi Huang, Jun Zhao, Jinbo Zhang, Zucong Cai
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-27078-w

Global miRNA expression profile reveals novel molecular players in aneurysmal subarachnoid haemorrhage
Cited by: 19
Author(s): Kátia de Paiva Lopes, Tatiana Vinasco-Sandoval, Ricardo Assunção Vialle, Fernando Mendes Paschoal, Vanessa Albuquerque Paschoal Aviz Bastos, Edson Bor‐Seng‐Shu, Manoel Jacobsen Teixeira, Elizabeth Sumi Yamada, Pablo Diego do Carmo Pinto, Amanda Ferreira Vidal, André M. Ribeiro-dos-Santos, Fabiano Cordeiro Moreira, Sidney Emanuel Batista dos Santos, Eric Homero Albuquerque Paschoal, Ândrea Ribeiro‐dos‐Santos
Software Mentions: 5
Published: over 6 years ago

10.1186/s12885-021-08362-x

Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours
Cited by: 2
Author(s): Bhavya Dhaka, Radhakrishnan Sabarinathan
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-29993-4

Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver
Cited by: 10
Author(s): José P. Silva, Derek Van Booven
Software Mentions: 5
Published: over 6 years ago

10.1186/s12934-015-0226-4

An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture
Cited by: 17
Author(s): Bat-Erdene Jugder, Zhiliang Chen, Darren Tan Tek Ping, Hélène Lebhar, Jeffrey Welch, Christopher P. Marquis
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-021-07937-z

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments
Cited by: 13
Author(s): Stephanie De Vos, Stéphane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, Thomas Van Leeuwen, Tim De Meyer, Gilbert Van Stappen, Yves Van de Peer, Peter Bossier
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-68949-5

Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages
Cited by: 10
Author(s): Viviane Yumi Baba, Adrian F. Powell, Suzana Tiemi Ivamoto, Luiz Filipe Protásio Pereira, André Luís Laforga Vanzela, Renata Mussoi Giacomin, Susan R. Strickler, Lukas A. Mueller, Rosana Rodrigues, Leandro Simões Azeredo Gonçalves
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-015-0146-x

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Cited by: 91
Author(s): Yue Jiang, Xuejian Xiong, Jayne S. Danska, John Parkinson
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12864-015-2174-0

Extensive variation between tissues in allele specific expression in an outbred mammal
Cited by: 67
Author(s): Amanda J. Chamberlain, Christy J. Vander Jagt, Ben J. Hayes, Majid Khansefid, L. C. Marett, Catriona A. Millen, Thuy Thi Thu Nguyen, Michael E. Goddard
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-019-5511-x

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
Cited by: 35
Author(s): Kirti Shekhawat, Hugh-G. Patterton, Florian F. Bauer, Mathabatha Evodia Setati
Software Mentions: 5
Published: almost 6 years ago

10.1038/srep37393

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer
Cited by: 84
Author(s): Stephan H. Bernhart, Helene Kretzmer, Lesca M. Holdt, Frank Jühling, Ole Ammerpohl, Anke Bergmann, Bernd H. Northoff, Gero Doose, Reiner Siebert, Peter F. Stadler, Steve Hoffmann
Software Mentions: 5
Published: about 8 years ago

10.3390/metabo10020066

EFMviz: A COBRA Toolbox Extension to Visualize Elementary Flux Modes in Genome-Scale Metabolic Models
Cited by: 6
Author(s): Chaitra Sarathy, Martina Kutmon, Michael Lenz, Michiel E. Adriaens, Chris T. Evelo, Ilja C. W. Arts
Software Mentions: 5
Published: almost 5 years ago

10.1128/AEM.00338-19

Wood Modification by Furfuryl Alcohol Resulted in a Delayed Decomposition Response in Rhodonia ( Postia ) placenta
Cited by: 13
Author(s): Inger Skrede, Monica Hongrø Solbakken, Jaqueline Hess, Carl Gunnar Fossdal, Olav A. Hegnar, Gry Alfredsen
Software Mentions: 5
Published: over 5 years ago

10.1038/srep29647

Tracking Cancer Genetic Evolution using OncoTrack
Cited by: 4
Author(s): Asoke K. Talukder, Mahima Agarwal, Kenneth H. Buetow, Patrice Denèfle
Software Mentions: 5
Published: over 8 years ago

10.1038/srep25668

Etiology matters – Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy
Cited by: 76
Author(s): Konrad J. Dębski, Asla Pitkänen, Noora Puhakka, Anna Bot, Ishant Khurana, K N Harikrishnan, Mark Ziemann, Antony Kaspi, Assam El‐Osta, Katarzyna Łukasiuk, Katja Kobow
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-015-2246-1

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: about 9 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: over 8 years ago

10.1080/21655979.2020.1862527

The underlying molecular mechanism and identification of transcription factor markers for laryngeal squamous cell carcinoma
Cited by: 8
Author(s): Bin-Yu Mo, Guosheng Li, Su-Hua Huang, Wei-Ying He, Lu Xie, Zhu‐Xin Wei, Ya-Si Su, Liang Yue, Li Yang, Ya Cheng, Wei Dai, Run Lin
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0236586

Transcriptome analysis of contrasting resistance to herbivory by Empoasca fabae in two shrub willow species and their hybrid progeny
Cited by: 5
Author(s): Wanyan Wang, Craig H. Carlson, Lawrence B. Smart, John E. Carlson
Software Mentions: 5
Published: over 4 years ago

10.1177/1177932219860817

Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data
Cited by: 10
Author(s): Takayuki Osabe, Kentaro Shimizu, Koji Kadota
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0214833

Disparate effects of antibiotic-induced microbiome change and enhanced fitness in Daphnia magna
Cited by: 27
Author(s): Asa Motiei, Björn Brindefalk, Martin Ogonowski, Rehab El-Shehawy, Paulina Pastuszek, Karin Ek, Birgitta Liewenborg, Klas I. Udekwu, Elena Gorokhova
Software Mentions: 5
Published: almost 5 years ago

10.1093/bioinformatics/btaa1063

ProkSeq for complete analysis of RNA-Seq data from prokaryotes
Cited by: 8
Author(s): A. K. M. Firoj Mahmud, Nicolas Delhomme, Soumyadeep Nandi, Maria Fällman
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0159182

LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates
Cited by: 6
Author(s): Jungsoo Gim, Sungho Won, Taesung Park
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0105097

Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance
Cited by: 64
Author(s): Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gómez-Chiarri
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-018-25748-3

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9
Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: over 6 years ago

10.7717/peerj.3797

Variance component testing for identifying differentially expressed genes in RNA-seq data
Cited by: 3
Author(s): Sheng Yang, Fang Shao, Weiwei Duan, Yang Zhao, Feng Chen
Software Mentions: 5
Published: over 7 years ago

10.1093/bioinformatics/btaa1009

glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data
Cited by: 89
Author(s): Constantin Ahlmann-Eltze, Wolfgang Huber
Software Mentions: 5
Published: about 4 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568