bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-92913-6

Ganoderma lucidum promotes sleep through a gut microbiota-dependent and serotonin-involved pathway in mice
Cited by: 14
Author(s): Chunyan Yao, Zhiyuan Wang, Huiyong Jiang, Yan Ren, Qin Huang, Yin Wang, Hui Xie, Ying Zou, Ying Yu, Longxian Lv
Software Mentions: 8
Published: about 5 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: almost 11 years ago

10.1371/journal.pone.0232271

Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data
Cited by: 20
Author(s): Bukyung Baik, Susan A. Yoon, Dougu Nam
Software Mentions: 8
Published: over 6 years ago

10.3390/cancers12010045

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma
Cited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: over 6 years ago

10.3390/cancers12030756

Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid
Cited by: 23
Author(s): Mariah M. Hoffman, Jessica S. Zylla, Somshuvra Bhattacharya, Kristin Calar, Timothy W. Hartman, Ratan D. Bhardwaj, W. Keith Miskimins, Pilar de la Puente, Etienne Z. Gnimpieba, Shanta M. Messerli
Software Mentions: 8
Published: over 6 years ago

10.3390/cancers13122955

PLEK2, RRM2, GCSH: A Novel WWOX-Dependent Biomarker Triad of Glioblastoma at the Crossroads of Cytoskeleton Reorganization and Metabolism Alterations
Cited by: 10
Author(s): Żaneta Kałuzińska, Damian Kołat, Andrzej K. Bednarek, Elżbieta Płuciennik
Software Mentions: 8
Published: about 5 years ago

10.1038/s41598-017-13731-3

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation
Cited by: 16
Author(s): Mahdi Golkaram, Jaeshin Jang, Stefan Hellander, Kenneth S. Kosik, Linda R. Petzold
Software Mentions: 8
Published: almost 9 years ago

10.1038/s41598-017-06929-y

A systems approach to a spatio-temporal understanding of the drought stress response in maize
Cited by: 64
Author(s): Zhenyan Miao, Zhaoxue Han, Ting Zhang, Siyuan Chen, Chuang Ma
Software Mentions: 8
Published: about 9 years ago

10.3390/cancers13071561

NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma
Cited by: 19
Author(s): Haitang Yang, Sean Hall, Beibei Sun, Liang Zhao, Yanyun Gao, Ralph A. Schmid, Swee T. Tan, Ren‐Wang Peng, Feng Yao
Software Mentions: 8
Published: over 5 years ago

10.3389/fcimb.2018.00326

In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages
Cited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: almost 8 years ago

10.1186/s12870-019-2182-3

A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference
Cited by: 9
Author(s): Enrique Ostria‐Gallardo, Giovanni Larama, Graciela Berríos, Ana Fallard, Ana Gutiérrez-Moraga, Ingo Ensminger, León A. Bravo
Software Mentions: 8
Published: over 6 years ago

10.1186/s13059-018-1435-z

RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellum
Cited by: 152
Author(s): Chunhui Ma, Mengqi Chang, Hongyi Lv, Zhiwei Zhang, Weilong Zhang, Xue He, Gaolang Wu, Shuaiyang Zhao, Yao Zhang, Di Wang, Xufei Teng, Chunying Liu, Qing Li, Arne Klungland, Yamei Niu, Shuhui Song, Wei‐Min Tong
Software Mentions: 8
Published: about 8 years ago

10.1038/s41598-021-93570-5

Three dimensional modeling of biologically relevant fluid shear stress in human renal tubule cells mimics in vivo transcriptional profiles
Cited by: 18
Author(s): Emily J. Ross, Emily R. Gordon, Hanna Sothers, Roshan Darji, Oakley Baron, Dustin W. Haithcock, Balabhaskar Prabhakarpandian, Kapil Pant, R Myers, Sara J. Cooper, Nancy J. Cox
Software Mentions: 8
Published: about 5 years ago

10.3389/fonc.2020.535985

Biomarker Discovery for the Carcinogenic Heterogeneity Between Colon and Rectal Cancers Based on lncRNA-Associated ceRNA Network Analysis
Cited by: 24
Author(s): Xin Qi, Yuxin Lin, Xingyun Liu, Jiajia Chen, Bairong Shen
Software Mentions: 8
Published: almost 6 years ago

10.1126/sciadv.abd3311

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell
Cited by: 64
Author(s): Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, KM Keller, Karin Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C. P. Holstege, Michelle L. Tas, Marc H. W. A. Wijnen, Max M. van Noesel, Ignacio del Valle, Giuseppe Barone, Reinier van der Linden, Catriona Duncan, John Anderson, John C. Achermann, Muzlifah Haniffa, Sarah A. Teichmann, Dyanne Rampling, Neil J. Sebire, Xiaoling He, Ronald R. de Krijger, Roger A. Barker, Kerstin B. Meyer, Ömer Bayraktar, Karin Straathof, Jan J. Molenaar, Sam Behjati
Software Mentions: 8
Published: over 5 years ago

10.12688/f1000research.13196.2

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Cited by: 42
Author(s): Yunshun Chen, Bhupinder Pal, Jane E. Visvader, Gordon K. Smyth
Software Mentions: 8
Published: almost 8 years ago

10.3389/fcell.2021.681745

Comprehensive Analysis of the Immune Infiltrates and PD-L1 of m6A RNA Methylation Regulators in Hepatocellular Carcinoma
Cited by: 9
Author(s): Yali Xu, Xueling He, Junjian Deng, Lin Xiong, Yue Li, Xiaoyu Zhang, Wenliang Chen, Xin Liu, Ximing Xu
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pgen.1009294

Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling
Cited by: 4
Author(s): Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yihua Chen, Fu‐Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L. Hwang, Yi-Hsien Su, Jr-Kai Yu
Software Mentions: 7
Published: over 5 years ago

10.1016/j.gpb.2018.07.007

Deciphering Brain Complexity Using Single-cell Sequencing
Cited by: 50
Author(s): Quanhua Mu, Yiyun Chen, Jiguang Wang
Software Mentions: 7
Published: about 7 years ago

10.3390/cancers12030690

Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo
Cited by: 17
Author(s): Nicholas R. Hum, Aimy Sebastian, Sean F. Gilmore, Wei He, Kelly A. Martin, Aubree Hinckley, Karen Dubbin, Monica L. Moya, Elizabeth K. Wheeler, Matthew A. Coleman, Gabriela G. Loots
Software Mentions: 7
Published: over 6 years ago

10.5808/GI.2019.17.1.e6

Statistical Analysis of Metagenomics Data
Cited by: 147
Author(s): M. Luz Calle
Software Mentions: 7
Published: over 7 years ago

10.1038/s41437-019-0251-x

Genetic and genomic analysis of the seed-filling process in maize based on a logistic model
Cited by: 14
Author(s): Yin Su, Pengcheng Li, Yongsheng Xu, Jun Li, Tiantian Yang, Jie Wei, Shaohang Xu, Junjie Yu, Huiying Fang, Li Xue, Dejun Hao, Zefeng Yang, Chenwu Xu
Software Mentions: 7
Published: about 7 years ago

10.3389/fnins.2021.600462

Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson’s Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1
Cited by: 10
Author(s): Linjing Shen, Changliang Wang, Liang Chen, Garry Wong
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-021-02372-5

Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1
Cited by: 11
Author(s): Claudia Vivori, Panagiotis Papasaikas, Ralph Stadhouders, Bruno Di Stefano, Anna Ribó Rubio, Clara Berenguer Balaguer, Serena Francesca Generoso, Anna Mallol, José Luis Sardina, Bernhard Payer, Thomas Graf, Juan Valcárcel
Software Mentions: 7
Published: about 5 years ago

10.1002/glia.23767

Transcriptional profiling of microglia; current state of the art and future perspectives
Cited by: 72
Author(s): Emma Gerrits, Yang Heng, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 7
Published: over 6 years ago

10.12688/f1000research.9005.3

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Cited by: 297
Author(s): Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Tian Li, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 7
Published: over 7 years ago

10.12688/f1000research.11290.1

Gene length and detection bias in single cell RNA sequencing protocols
Cited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: over 9 years ago

10.1186/s13059-020-02087-z

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance
Cited by: 34
Author(s): Flora D’Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca Berrens, Junbin Qian, Paweł Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Jonathan De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N. Savvides, M. Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-021-02466-0

Acute depletion of CTCF rewires genome-wide chromatin accessibility
Cited by: 26
Author(s): Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu, Chunliang Li
Software Mentions: 7
Published: almost 5 years ago

10.1093/gbe/evab144

CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation
Cited by: 17
Author(s): Galen Martin, Danelle Seymour, Brandon S. Gaut
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2020.00995

Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography
Cited by: 31
Author(s): Xin Zhou, Jinting Wang, Z.F. Zhang, Wei Li, Wen Chen, Lei Cai
Software Mentions: 7
Published: about 6 years ago

10.1186/s12920-020-00808-8

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
Cited by: 11
Author(s): Timothy A. McCaffrey, Georges St. Laurent, Dmitry Shtokalo, Денис Антонец, Yuri Vyatkin, Dan Jones, Eleanor Battison, Joel T. Nigg
Software Mentions: 7
Published: almost 6 years ago

10.3389/fpls.2019.01313

A Bioinformatics Guide to Plant Microbiome Analysis
Cited by: 45
Author(s): Rares Calin Lucaciu, Claus Pelikan, Samuel M. Gerner, Christos Zioutis, Stephan Köstlbacher, Harald Marx, Craig W. Herbold, Hannes Schmidt, Thomas Rattei
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pgen.1009763

Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
Cited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13059-019-1912-z

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel
Cited by: 14
Author(s): Michael Frochaux, Maroun Bou Sleiman, Vincent Gardeux, Riccardo Dainese, Brian Hollis, Maria Litovchenko, Virginie Braman, Tommaso Andreani, Dani Osman, Bart Deplancke
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-019-1862-5

scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
Cited by: 225
Author(s): José Alquicira-Hernández, Anuja Sathe, Hanlee P. Ji, Quan Nguyen, Joseph E. Powell
Software Mentions: 7
Published: over 6 years ago

10.12688/f1000research.7016.2

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data
Cited by: 16
Author(s): Aaron T. L. Lun
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.ppat.1005438

Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
Cited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.ppat.1009130

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles
Cited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1005930

Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects
Cited by: 36
Author(s): Erica Hildebrand, Sue Biggins
Software Mentions: 7
Published: over 10 years ago

10.1093/bib/bbz126

Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-016-0940-1

A benchmark for RNA-seq quantification pipelines
Cited by: 146
Author(s): Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri D. Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, Rafael A. Irizarry
Software Mentions: 7
Published: over 10 years ago

10.3390/ijms221910451

Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance
Cited by: 1
Author(s): Stephanie Schaarschmidt, Ulrike Glaubitz, Alexander Erban, Joachim Kopka, Ellen Zuther
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12920-020-0695-0

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain
Cited by: 20
Author(s): Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
Software Mentions: 7
Published: over 6 years ago

10.3390/genes11101165

OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
Cited by: 21
Author(s): Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu
Software Mentions: 7
Published: almost 6 years ago

10.7717/peerj.8206

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Cited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: over 6 years ago

10.3390/e21030242

A Method Based on Differential Entropy-Like Function for Detecting Differentially Expressed Genes Across Multiple Conditions in RNA-Seq Studies
Cited by: 1
Author(s): Zhuo Wang, Shuilin Jin, Chiping Zhang
Software Mentions: 7
Published: over 7 years ago

10.3389/fimmu.2019.00488

The Association Between Vitamin D and Multiple Sclerosis Risk: 1,25(OH)2D3 Induces Super-Enhancers Bound by VDR
Cited by: 24
Author(s): Ming Lu, Bennet J McComish, Kathryn P. Burdon, Bruce Taylor, Heinrich Körner
Software Mentions: 7
Published: over 7 years ago

10.1002/ece3.4756

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata
Cited by: 9
Author(s): Martin Helmkampf, M. Renee Bellinger, Monika Frazier, Misaki Takabayashi
Software Mentions: 7
Published: over 7 years ago

10.1002/jev2.12127

Inflammasome‐induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses
Cited by: 26
Author(s): Christina F. Budden, Linden J. Gearing, Romina Kaiser, Lena Standke, Paul J. Hertzog, Eicke Latz
Software Mentions: 7
Published: about 5 years ago

10.1038/s41419-020-2477-1

Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 6 years ago

10.1002/ece3.3234

The other white‐nose syndrome transcriptome: Tolerant and susceptible hosts respond differently to the pathogen Pseudogymnoascus destructans
Cited by: 21
Author(s): Christina M. Davy, Michael E. Donaldson, Craig K. R. Willis, Barry J. Saville, L. McGuire, Heather W. Mayberry, Alana Wilcox, Gudrun Wibbelt, Vikram Misra, Trent K. Bollinger, Christopher J. Kyle
Software Mentions: 7
Published: about 9 years ago

10.3390/genes12081179

Dysregulation of Synaptic Signaling Genes Is Involved in Biology of Uterine Leiomyoma
Cited by: 2
Author(s): Jovan Krsteski, Mario Gorenjak, Igor But, Maja Pakiž, Uroš Potočnik
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.59610

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Cited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: about 6 years ago

10.3390/ijms22094917

The Cellular Composition of Bovine Coccygeal Intervertebral Discs: A Comprehensive Single-Cell RNAseq Analysis
Cited by: 24
Author(s): Martina Caliò, Benjamin Gantenbein, Marcel Egli, Lucy Poveda, Fabian Ille
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-014-0465-4

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
Cited by: 84
Author(s): Belinda Phipson, Alicia Oshlack
Software Mentions: 7
Published: almost 12 years ago

10.3389/fimmu.2020.585168

Distinct Age-Related Epigenetic Signatures in CD4 and CD8 T Cells
Cited by: 40
Author(s): Bin Hu, Rohit R. Jadhav, Claire E. Gustafson, Sabine Le Saux, Zhongde Ye, Xuanying Li, Lu Tian, Cornelia M. Weyand, Jörg J. Goronzy
Software Mentions: 7
Published: over 5 years ago

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: about 5 years ago

10.15252/embr.201642378

Linear ubiquitination by <scp>LUBEL</scp> has a role in Drosophila heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: almost 10 years ago

10.1016/j.ccell.2020.08.016

Metabolic Imaging Detects Resistance to PI3Kα Inhibition Mediated by Persistent FOXM1 Expression in ER+ Breast Cancer
Cited by: 35
Author(s): Susana Ros, Alan J. Wright, Paula D’Santos, De‐En Hu, Robin Hesketh, Yaniv Lubling, Dimitra Georgopoulou, Giulia Lerda, Dominique‐Laurent Couturier, Pedram Razavi, Rapahel Pelossof, Ankita Batra, Elizabeth Mannion, David Y. Lewis, Alistair Martin, Richard D. Baird, Mafalda Oliveira, Leonora W. de Boo, Sabine C. Linn, Maurizio Scaltriti, Oscar M. Rueda, Alejandra Bruna, Carlos Caldas, Kevin M. Brindle
Software Mentions: 7
Published: almost 6 years ago

10.7717/peerj.10836

Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry
Cited by: 9
Author(s): Kerri L. Steenwerth, Ian Arthur Morelan, Ruby J. Stahel, Rosa Figueroa‐Balderas, Dario Cantu, Jungmin Lee, Ron C. Runnebaum, Amisha T. Poret-Peterson
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-018-1438-9

UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Cited by: 80
Author(s): Wenan Chen, Yán Li, John Easton, David Finkelstein, Gang Wu, Xiang Chen
Software Mentions: 7
Published: about 8 years ago

10.1016/j.isci.2021.102870

Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance
Cited by: 14
Author(s): Katharina Gapp, Guillermo E. Parada, Fridolin Groß, Alberto Corcoba, Jasmine Kaur, Evelyn Grau, Martin Hemberg, Johannes Bohacek, Eric A. Miska
Software Mentions: 7
Published: about 5 years ago

10.3390/genes11040400

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant
Cited by: 7
Author(s): Alexandre Rêgo, Samridhi Chaturvedi, Amy L. Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-021-93509-w

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation
Cited by: 9
Author(s): Muhammad Munir Iqbal, Michael Serralha, Parwinder Kaur, David Martino
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2020.619404

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I
Cited by: 18
Author(s): Abdellah Barakate, Jamie Orr, Miriam Schreiber, Isabelle Colas, Dominika Lewandowska, Nicola McCallum, Malcolm Macaulay, Jenny Morris, Mikel Arrieta, Pete E. Hedley, Luke Ramsay, Robbie Waugh
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2020.566579

Bioinformatics Analysis Discovers Microtubular Tubulin Beta 6 Class V (TUBB6) as a Potential Therapeutic Target in Glioblastoma
Cited by: 12
Author(s): Lan Jiang, Xiaolong Zhu, Hui Yang, Tianbing Chen, Kun Lv
Software Mentions: 7
Published: almost 6 years ago

10.1093/bib/bbt086

Comparison of software packages for detecting differential expression in RNA-seq studies
Cited by: 317
Author(s): Fatemeh Seyednasrollah, Asta Laiho, Laura L. Elo
Software Mentions: 7
Published: over 12 years ago

10.1534/g3.114.011759

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: about 12 years ago

10.3389/fpls.2021.684192

Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation From Its Location Outside the Nucleus
Cited by: 7
Author(s): Rachelle A. Lapham, Lan‐Ying Lee, Eder Xhako, Esteban Gañán Gómez, V. M. Nivya, Stanton B. Gelvin
Software Mentions: 7
Published: about 5 years ago

10.3389/fpls.2021.639631

Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca
Cited by: 11
Author(s): Piotr M. Kopec, Katarzyna Mikołajczyk, E. Jajor, A. Perek, Joanna Nowakowska, Christian Obermeier, Harmeet Singh Chawla, M. Korbas, I. Bartkowiak-Broda, Wojciech M. Karłowski
Software Mentions: 7
Published: over 5 years ago

10.1186/s12920-021-01081-z

Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma
Cited by: 2
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 7
Published: almost 5 years ago

10.3389/fpls.2021.661361

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks
Cited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2019.01581

Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
Cited by: 24
Author(s): Tomás Carrasco-Valenzuela, Claudia Muñoz-Espinoza, Aníbal Riveros, Romina Pedreschi, Pere Arús, Reinaldo Campos-Vargas, Claudio Meneses
Software Mentions: 7
Published: over 6 years ago

10.3389/fgene.2017.00062

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods
Cited by: 92
Author(s): Alessandra Dal Molin, Giacomo Baruzzo, Barbara Di Camillo
Software Mentions: 7
Published: about 9 years ago

10.3389/fgene.2021.684002

Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity
Cited by: 5
Author(s): Junjie Liu, Wei Lv, Shuling Li, Jingwen Deng
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41598-019-52584-w

Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data
Cited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41598-019-46412-4

Host–symbiont combinations dictate the photo-physiological response of reef-building corals to thermal stress
Cited by: 62
Author(s): Kenneth D. Hoadley, Allison M. Lewis, Drew C. Wham, D. Tye Pettay, Chris Grasso, Robin T. Smith, Dustin W. Kemp, Todd C. LaJeunesse, Mark E. Warner
Software Mentions: 7
Published: about 7 years ago

10.1038/s41598-021-87234-7

Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model
Cited by: 9
Author(s): Sk Md Mosaddek Hossain, Aanzil Akram Halsana, Lutfunnesa Khatun, Sumanta Ray, Anirban Mukhopadhyay
Software Mentions: 7
Published: over 5 years ago

10.12688/f1000research.17145.2

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors
Cited by: 35
Author(s): Ashis Saha, Alexis Battle
Software Mentions: 7
Published: over 7 years ago

10.3389/fonc.2021.674394

Comprehensive Analysis of Cyclin Family Gene Expression in Colon Cancer
Cited by: 12
Author(s): Jieling Li, Liyuan Zhou, Ying Liu, Lingzhi Yang, Dayi Jiang, Kuan Li, Shouqi Xie, Wang Xiao, Shaoxiang Wang
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: over 6 years ago

10.3389/fonc.2020.01409

Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma
Cited by: 43
Author(s): Yin Wu, Xingjun Jiang, Jun Tan, Zhaoqi Xin, Quanwei Zhou, Chaohong Zhan, Xianyong Fu, Zhaoping Wu, Youwei Guo, Zhipeng Jiang, Chao Ren, Guihua Tang
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-017-14366-0

Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor Cells
Cited by: 10
Author(s): Christina Sollinger, Jacquelyn Lillis, Jeffrey Malik, Michael Getman, Christoph Pröschel, Laurie A. Steiner
Software Mentions: 7
Published: almost 9 years ago

10.3389/fonc.2021.734873

DNA Methylation Regulator-Meditated Modification Patterns Define the Distinct Tumor Microenvironment in Lung Adenocarcinoma
Cited by: 3
Author(s): Dejian Yuan, Zehong Wei, Yicheng Wang, Cheng Fang, Yujie Zeng, Yang Li, Shangyu Zhang, Jianbo Li, Renkuan Tang
Software Mentions: 7
Published: almost 5 years ago

10.3390/cancers12082310

Systematic Analysis of Aberrant Biochemical Networks and Potential Drug Vulnerabilities Induced by Tumor Suppressor Loss in Malignant Pleural Mesothelioma
Cited by: 15
Author(s): Haitang Yang, Duo Xu, Yang Zhang, Feng Yao, Heng Zhao, Ralph A. Schmid, Ren‐Wang Peng
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-017-18435-2

Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys
Cited by: 32
Author(s): Pål Trosvik, Eli Knispel Rueness, Eric J. de Muinck, Amera Moges, Addisu Mekonnen
Software Mentions: 7
Published: over 8 years ago

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: over 12 years ago

10.3390/cancers12071788

Characterization of Glycolysis-Associated Molecules in the Tumor Microenvironment Revealed by Pan-Cancer Tissues and Lung Cancer Single Cell Data
Cited by: 44
Author(s): Jinjia Wei, Kaitang Huang, Zixi Chen, Meiling Hu, Yunmeng Bai, Shudai Lin, Hongli Du
Software Mentions: 7
Published: about 6 years ago

10.3389/fonc.2020.00061

The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma
Cited by: 18
Author(s): Yu Liu, Li-Yu Wang, Hengchang Liu, Chunxiang Li, Jie He
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-017-02932-5

Transcriptomic analysis of short-fruit 1 (sf1) reveals new insights into the variation of fruit-related traits in Cucumis sativus
Cited by: 25
Author(s): Lina Wang, Chuanai Cao, Shuangshuang Zheng, Haiyang Zhang, Panjing Liu, Qian Ge, Jingrui Li, Zhonghai Ren
Software Mentions: 7
Published: about 9 years ago

10.3389/fcell.2020.576996

Development and Validation of a Novel DNA Methylation-Driven Gene Based Molecular Classification and Predictive Model for Overall Survival and Immunotherapy Response in Patients With Glioblastoma: A Multiomic Analysis
Cited by: 9
Author(s): Zihao Wang, Lu Gao, Xiaopeng Guo, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 7
Published: almost 6 years ago

10.26508/lsa.201800085

Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells
Cited by: 29
Author(s): Constantine Mylonas, Peter Tessarz
Software Mentions: 7
Published: about 8 years ago

10.3390/cancers13092126

Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential
Cited by: 7
Author(s): Syuzo Kaneko, Toutai Mitsuyama, Kouya Shiraishi, Noriko Ikawa, Kanto Shozu, Ai Dozen, Hidenori Machino, Ken Asada, Masaaki Komatsu, Asako Kukita, Kenbun Sone, Hiroshi Yoshida, Noriko Motoi, Shinya Hayami, Yutaka Yoneoka, Tomoyasu Kato, Takashi Kohno, Toru Natsume, Gottfried von Keudell, Vassiliki Saloura, Hiroki Yamaue, Ryuji Hamamoto
Software Mentions: 7
Published: over 5 years ago

10.3389/fonc.2021.657094

LINC01977 Promotes Breast Cancer Progression and Chemoresistance to Doxorubicin by Targeting miR-212-3p/GOLM1 Axis
Cited by: 12
Author(s): Zheng Li, Yaming Li, Xiaolong Wang, Yiran Liang, Dan Luo, Dianwen Han, Chen Li, Tong Chen, Hanwen Zhang, Ying Liu, Zekun Wang, Bing Chen, Limin Wang, Wenjing Zhao, Qifeng Yang
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-017-10853-6

The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: almost 9 years ago

10.1186/s13059-020-02082-4

Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells
Cited by: 22
Author(s): Juli Liu, Sheng Liu, Hongyu Gao, Lei Han, Xun Chu, Sheng Yi, Weinian Shou, Yue Wang, Yunlong Liu, Jun Wan, Lei Yang
Software Mentions: 7
Published: about 6 years ago

10.1186/1471-2105-16-S11-S4

Epiviz: a view inside the design of an integrated visual analysis software for genomics
Cited by: 3
Author(s): Florin Chelaru, Héctor Corrada Bravo
Software Mentions: 7
Published: almost 11 years ago

10.1002/1878-0261.12911

LncRNA NKX2‐1‐AS1 promotes tumor progression and angiogenesis via upregulation of SERPINE1 expression and activation of the VEGFR‐2 signaling pathway in gastric cancer
Cited by: 39
Author(s): Fei Teng, Ju‐Xiang Zhang, Yi Chen, Xiaodong Shen, Chang Su, Yanjiao Guo, Pu‐Hua Wang, Chencheng Shi, Ming Lei, Yiou Cao, Shao‐Qun Liu
Software Mentions: 7
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568