bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s13059-020-02072-6

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Cited by: 7
Author(s): Guy Karlebach, Peter J. Hansen, Diogo Veiga, Robin Steinhaus, Daniel Daniš, Sheng Li, Olga Anczuków, Peter N. Robinson
Software Mentions: 8
Published: over 6 years ago

10.1038/s41419-021-03525-x

Loss of retinoic acid receptor-related receptor alpha (Rorα) promotes the progression of UV-induced cSCC
Cited by: 6
Author(s): Guolong Zhang, Guorong Yan, Fu Zhuo, Yuhao Wu, Fei Wu, Zhe Zheng, Shiji Fang, Ying Gao, Xiao Bao, Yeqiang Liu, Xiuli Wang, Sibo Zhu
Software Mentions: 8
Published: over 5 years ago

10.3389/fimmu.2021.617592

Phenotypic and Epigenetic Adaptations of Cord Blood CD4+ T Cells to Maternal Obesity
Cited by: 11
Author(s): Suhas Sureshchandra, Norma Mendoza, Allen Jankeel, Randall M. Wilson, Nicole Marshall, Ilhem Messaoudi
Software Mentions: 8
Published: over 5 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: over 5 years ago

10.1038/s41598-021-94732-1

A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes
Cited by: 22
Author(s): Tanya Grancharova, Kaytlyn A. Gerbin, Alexander Rosenberg, Charles M. Roco, Joy Arakaki, Colette M DeLizo, Stephanie Q. Dinh, Rory Donovan-Maiye, Matthew Hirano, Angelique M. Nelson, Joyce Tang, Julie A. Theriot, Calysta Yan, Vilas Menon, Sean P. Palecek, Georg Seelig, Ruwanthi N. Gunawardane
Software Mentions: 8
Published: over 5 years ago

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: over 5 years ago

10.3389/fpls.2018.00108

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Cited by: 61
Author(s): Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Élie Maza
Software Mentions: 8
Published: over 8 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 5 years ago

10.3389/fgene.2018.00588

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data
Cited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: almost 8 years ago

10.1038/s41419-021-03552-8

Transcriptional profiling reveals the transcription factor networks regulating the survival of striatal neurons
Cited by: 12
Author(s): Lin Yang, 智慧蘇, Zi-Wu Wang, Zhenmeiyu Li, Zicong Shang, Heng Du, Shuai Liu, Dashi Qi, Zhengang Yang, Zhejun Xu, Zhuangzhi Zhang
Software Mentions: 8
Published: over 5 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

10.12688/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: about 8 years ago

10.1371/journal.pone.0248889

Lung gene expression and single cell analyses reveal two subsets of idiopathic pulmonary fibrosis (IPF) patients associated with different pathogenic mechanisms
Cited by: 10
Author(s): Jozsef Karman, Jing Wang, Corneliu Bodea, Sherry Cao, Marc C. Levesque
Software Mentions: 8
Published: over 5 years ago

10.1155/2020/5843874

Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney
Cited by: 1
Author(s): Xiaoqing Wang, Xiangyu Wu, Tianyou Li, Meng Cui, Lichao Zhu, Gang Wang, Feng Guo
Software Mentions: 8
Published: about 6 years ago

10.1186/s13059-020-02038-8

Personalized and graph genomes reveal missing signal in epigenomic data
Cited by: 25
Author(s): Cristian Groza, Tony Kwan, Nicole Soranzo, Tomi Pastinen, Guillaume Bourque
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2020.00805

Prognostic lncRNA, miRNA, and mRNA Signatures in Papillary Thyroid Carcinoma
Cited by: 8
Author(s): Kun Wang, Jing Xu, Lu Zhao, Shiyang Liu, Chen‐Guang Liu, Lin Zhang
Software Mentions: 8
Published: over 6 years ago

10.3390/ijms21103591

Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant Soybean
Cited by: 8
Author(s): Adrienne N. Moran Lauter, Lindsay Rutter, Dianne Cook, Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 8
Published: over 6 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: over 5 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: almost 8 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: over 9 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: almost 6 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/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: 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: about 9 years ago

10.3390/bios3030238

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: over 13 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: about 9 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

10.1155/2021/2628824

A Potential ceRNA Network for Neurological Damage in Preterm Infants
Cited by: 7
Author(s): Hui‐Zi Jin, Xinlan Liang, Zhenyu Cai
Software Mentions: 7
Published: about 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: over 5 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

10.1002/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: almost 8 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

10.1038/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: over 5 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: about 7 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: over 12 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: over 5 years ago

10.1042/BSR20204340

TIGIT-related transcriptome profile and its association with tumor immune microenvironment in breast cancer
Cited by: 8
Author(s): Qin Zhang, Chaowei Gao, Jianqiang Shao, Zunyi Wang
Software Mentions: 7
Published: over 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.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: over 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: 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: about 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

10.3390/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

10.1186/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: about 5 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: almost 9 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: over 9 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: 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: over 7 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: almost 11 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: over 6 years ago

10.1371/journal.pone.0219723

Sex-dependent and -independent transcriptional changes during haploid phase gametogenesis in the sugar kelp Saccharina latissima
Cited by: 10
Author(s): Gareth A. Pearson, Neusa Martins, Pedro M Madeira, Ester Á. Serrão, Inka Bartsch
Software Mentions: 7
Published: about 7 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: almost 7 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

10.3390/ijms21134727

Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies
Cited by: 16
Author(s): Maximilian Fuchs, Fabian Philipp Kreutzer, Lorenz A. Kapsner, Saskia Mitzka, Annette Just, Filippo Perbellini, Cesare M. Terracciano, Xiaoyan Ke, Robert Geffers, Christian Bogdan, Hans‐Ulrich Prokosch, Jan Fiedler, Thomas Thum, Meik Kunz
Software Mentions: 7
Published: over 6 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: over 6 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/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: almost 6 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: 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: over 9 years ago

10.1038/s41416-019-0571-x

Prognosis and modulation mechanisms of COMMD6 in human tumours based on expression profiling and comprehensive bioinformatics analysis
Cited by: 24
Author(s): Mi Yang, Weiqiang Huang, Yaling Sun, Huazhen Liang, Min Chen, Xixi Wu, Xiaoqing Wang, Longshan Zhang, Xiaobin Cheng, Yu Fan, Hua Pan, Longhua Chen, Jian Guan
Software Mentions: 7
Published: about 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

10.7717/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: almost 7 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: about 10 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: about 6 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

10.3389/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

10.1186/1471-2105-16-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: about 11 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: about 6 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

10.1186/s12864-020-06888-1

A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples
Cited by: 6
Author(s): Huamei Li, Ingo G. H. Schmidt‐Wolf, Wenglong Ming, Xiao Sun, Hongde Liu
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-019-2599-6

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
Cited by: 189
Author(s): Tianyu Wang, Boyang Li, Craig E. Nelson, Sheida Nabavi
Software Mentions: 7
Published: almost 8 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

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: over 9 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: over 6 years ago

10.1186/s12859-017-1974-4

CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates
Cited by: 14
Author(s): Joel Zi-Bin Low, Tsung Fei Khang, Martti T. Tammi
Software Mentions: 7
Published: almost 9 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: over 5 years ago

10.1186/s12864-021-07593-3

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Cited by: 23
Author(s): Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Software Mentions: 7
Published: over 5 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

10.7554/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: over 6 years ago

10.3389/fgene.2021.678436

Development of an Immune-Related LncRNA Prognostic Signature for Glioma
Cited by: 8
Author(s): Yudong Cao, Hecheng Zhu, Jun Tan, Yin Wu, Quanwei Zhou, Zhaoqi Xin, Zhaoping Wu, Zhipeng Jiang, Youwei Guo, Yirui Kuang, Can Li, Ming Zhao, Xingjun Jiang, Jian Peng, Chao Ren
Software Mentions: 7
Published: over 5 years ago

10.18632/aging.103999

CCL5-dependent mast cell infiltration into the tumor microenvironment in clear cell renal cell carcinoma patients
Cited by: 12
Author(s): Tianjie Liu, Qing Xia, Haibao Zhang, Zixi Wang, Wenjie Yang, Xiao Gu, Tao Hou, Yule Chen, Xinqi Pei, Guodong Zhu, Dalin He, Lei Li, Shan Xu
Software Mentions: 7
Published: almost 6 years ago

10.3389/fgene.2019.00292

Identification of Long Non-coding and Messenger RNAs Differentially Expressed Between Primary and Metastatic Melanoma
Cited by: 16
Author(s): Lichang Sun, Zhiguang Guan, Shanshan Wei, Rui Tan, Pengfei Li, Yan Liu
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-020-73391-8

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
Cited by: 36
Author(s): Meaghan L. Pimsler, Kennan Oyen, James D. Herndon, Jason M. Jackson, James P. Strange, Michael E. Dillon, Jeffrey D. Lozier
Software Mentions: 7
Published: about 6 years ago

10.3389/fgene.2021.702695

Identification and Elucidation of the Protective isomiRs in Lung Cancer Patient Prognosis
Cited by: 1
Author(s): Fu-Mei Hsieh, Su-Ting Lai, Ming-Fong Wu, Chen-Ching Lin
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2105-14-262

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Cited by: 30
Author(s): Yingtao Bi, Ramana V. Davuluri
Software Mentions: 7
Published: about 13 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

10.1242/dmm.049068

A mechanism linking perinatal 2,3,7,8 tetrachlorodibenzo-p-dioxin exposure to lower urinary tract dysfunction in adulthood
Cited by: 4
Author(s): Anne E. Turco, S. G. Oakes, Kimberly P. Keil Stietz, Cheryl L. Dunham, Diya B. Joseph, Thrishna S Chathurvedula, Nicholas M Girardi, Andrew J. Schneider, Joseph Gawdzik, Celeste M Sheftel, Peiqing Wang, Zunyi Wang, Dale E. Bjorling, William A. Ricke, Weiping Tang, Laura Hernández, Janet R. Keast, Adrian D. Bonev, Matthew D Grimes, Douglas W. Strand, Nathan R. Tykocki, Robyn L Tanguay, Richard E. Peterson, Chad M. Vezina
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-018-5390-6

Stability of methods for differential expression analysis of RNA-seq data
Cited by: 14
Author(s): Bingqing Lin, Zhen Pang
Software Mentions: 7
Published: almost 8 years ago

10.3390/microorganisms8101505

Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents
Cited by: 3
Author(s): Antônio Victor Campos Coelho, Romero Marinho de Moura, Sérgio Crovella
Software Mentions: 7
Published: about 6 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: over 7 years ago

10.1186/1471-2164-15-452

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
Cited by: 52
Author(s): Arun Kommadath, Hua Bao, Adriano S. Arantes, Graham Plastow, Christopher K. Tuggle, Shawn M. D. Bearson, Le Luo Guan, Paul Stothard
Software Mentions: 7
Published: over 12 years ago

10.15252/emmm.202013180

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1
Cited by: 21
Author(s): George Sflomos, Laura Battista, Patrick Aouad, Fabio De Martino, Valentina Scabia, Athina Stravodimou, Ayyakkannu Ayyanan, Assia Ifticene‐Treboux, Philipp Bücher, Maryse Fiche, Giovanna Ambrosini, Cathrin Brisken, Rls
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2164-15-702

Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves
Cited by: 58
Author(s): Adrienne N. Moran Lauter, Gregory A. Peiffer, Tao Yin, Steven A. Whitham, Dianne Cook, Randy C. Shoemaker, Michelle A. Graham
Software Mentions: 7
Published: about 12 years ago

10.1186/s40168-021-01013-0

animalcules: interactive microbiome analytics and visualization in R
Cited by: 16
Author(s): Yue Zhao, Anthony Federico, Tyler Faits, Solaiappan Manimaran, Daniel Segrè, Stefano Monti, W. Evan Johnson
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-017-4304-3

Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence
Cited by: 71
Author(s): Hana Hall, Patrick S Medina, Daphne A. Cooper, Spencer E. Escobedo, Jeremiah Rounds, Kaelan J. Brennan, Christopher Vincent, Pedro Miura, R. W. Doerge, Vikki M. Weake
Software Mentions: 7
Published: almost 9 years ago

10.1038/srep30794

Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry
Cited by: 33
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 7
Published: over 10 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: almost 11 years ago

10.1186/s12864-019-6308-7

Human gene expression variability and its dependence on methylation and aging
Cited by: 23
Author(s): Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12885-020-06777-6

The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers
Cited by: 11
Author(s): Stephany Orjuela, Mirco Menigatti, Peter Schraml, Patryk Kambakamba, Mark D. Robinson, Giancarlo Marra
Software Mentions: 7
Published: over 6 years ago

10.1186/s12864-018-4934-0

Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola
Cited by: 30
Author(s): Xiaofei Liang, Shengping Shang, Qiuyue Dong, Bo Wang, Rong Zhang, Mark L. Gleason, Guangyu Sun
Software Mentions: 7
Published: over 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568