Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: edgeR

https://packages.ecosyste.ms/registries/bioconductor.org/packages/edgeR

Empirical Analysis of Digital Gene Expression Data in R
3 versions
Latest release: about 1 year ago
166 dependent packages
2,704,225 downloads total

Papers Mentioning edgeR 6,568

10.1186/s13059-016-1137-3
Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
Cited by: 106
Author(s): Xuan Li, Emily Speranza, César Muñoz‐Fontela, Sam Haldenby, Natasha Y. Rickett, Isabel García-Dorival, Yongxiang Fang, Yper Hall, Elsa Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny, Nichola Rockliffe, E. Diane Williamson, Thomas R. Laws, N’Faly Magassouba, David A. Matthews, Stephan Günther, Andrew R. Cossins, Armand Sprecher, John H. Connor, Miles W. Carroll, Julian A. Hiscox
Software Mentions: 4
Published: almost 8 years ago
10.18632/oncotarget.10052
Network-based identification of microRNAs as potential pharmacogenomic biomarkers for anticancer drugs
Cited by: 71
Author(s): Jie Li, Kecheng Lei, Zengrui Wu, Weihua Li, Guixia Liu, Jianwen Liu, Feixiong Cheng, Yun Tang
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pone.0141910
Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?
Cited by: 25
Author(s): Shanrong Zhao, Li Xi, Baohong Zhang
Software Mentions: 4
Published: about 9 years ago
10.3390/ijms21218333
Transcriptional Effects of Psychoactive Drugs on Genes Involved in Neurogenesis
Cited by: 7
Author(s): Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Trang T. T. Truong, Zoe Liu, Bruna Panizzutti, Mark F. Richardson, Laura J. Gray, Michael Berk, Olivia Dean, Ken Walder
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pone.0071462
Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 11 years ago
10.18632/aging.202780
circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathway
Cited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0169648
The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and Is Counteracted by the HBV X Protein Shortly after Infection
Cited by: 107
Author(s): Congrong Niu, Christine M. Livingston, Li Li, Rudolf K. F. Beran, Stéphane Daffis, Dhivya Ramakrishnan, Dara Burdette, Leanne Peiser, Eduardo Salas, Hilario J. Ramos, Mei Yu, Guofeng Cheng, Michel Strubin, William E. Delaney, Simon P. Fletcher
Software Mentions: 4
Published: almost 8 years ago
10.7717/peerj.7107
Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
Cited by: 8
Author(s): Juchuanli Tu, Xiaolu Li, Jianjun Wang
Software Mentions: 4
Published: over 5 years ago
10.1186/s13059-016-1088-8
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Cited by: 214
Author(s): Duane D. McKenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung‐Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K. Childers, Christopher P. Childers, Dave J. Clarke, Lorna Cohen, Jeffery P. Demuth, Huyen Dinh, Harshavardhan Doddapaneni, Amanda Dolan, Jian J. Duan, Shannon Dugan, Markus Friedrich, Karl M. Glastad, Michael A. D. Goodisman, Stéphanie Haddad, Yi Han, Daniel Hughes, Panagiotis Ioannidis, J. Spencer Johnston, Jeffery W. Jones, Leslie A. Kuhn, D. R. Lance, Chien Yueh Lee, Sandra L. Lee, Han Lin, Jeremy A. Lynch, Armin P. Moczek, Shwetha C. Murali, Donna M. Muzny, David R. Nelson, Subba Reddy Palli, Kristen A. Panfilio, Dan Pers, Monica F. Poelchau, Honghu Quan, Jiaxin Qu, Anandasankar Ray, Joseph P. Rinehart, Hugh M. Robertson, Richard L. Roehrdanz, Andrew J. Rosendale, Seunggwan Shin, Christian Silva, Alex S. Torson, Iris M. Vargas Jentzsch, John H. Werren, Kim C. Worley, George D. Yocum, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: about 8 years ago
10.1155/2015/621690
The Impact of Normalization Methods on RNA-Seq Data Analysis
Cited by: 81
Author(s): Joanna Zyprych-Walczak, Alicja Szabelska, Luiza Handschuh, Katarzyna Górczak, Kamila Klamecka, Marek Figlerowicz, Idzi Siatkowski
Software Mentions: 4
Published: almost 10 years ago
10.3390/ijms20225710
The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAirTM) and in Human Bronchial Epithelial Cells (BEAS-2B)
Cited by: 13
Author(s): Pavel Rőssner, Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Hasmik Margaryan, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka
Software Mentions: 4
Published: about 5 years ago
10.1186/s13059-016-0947-7
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
Cited by: 858
Author(s): Aaron T. L. Lun, Karsten Bach, John C. Marioni
Software Mentions: 4
Published: over 8 years ago
10.1186/s12862-017-1087-8
Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria
Cited by: 21
Author(s): Melania Abrahamian, Meenakshi S. Kagda, Audrey M. V. Ah‐Fong, Howard S. Judelson
Software Mentions: 4
Published: about 7 years ago
10.1186/s12864-016-2646-x
A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species
Cited by: 25
Author(s): Montserrat Torres-Oliva, Isabel Almudí, Alistair P. McGregor, Nico Posnien
Software Mentions: 4
Published: over 8 years ago
10.1128/mSystems.00215-21
Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation
Cited by: 5
Author(s): Marlène S Birk, Rina Ahmed-Begrich, Stefan Tran, Alexander K. W. Elsholz, Christian K. Frese, Emmanuelle Charpentier
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0157022
SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: over 8 years ago
10.3389/fonc.2020.576615
Integrated Analysis of Distant Metastasis-Associated Genes and Potential Drugs in Colon Adenocarcinoma
Cited by: 6
Author(s): Min Wu, Weiyang Lou, Meng Lou, Peifen Fu, Xiaofang Yu
Software Mentions: 4
Published: about 4 years ago
10.1111/acel.13178
The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders
Cited by: 27
Author(s): Michelle M. Denomme, Mary E. Haywood, Jason C. Parks, William B. Schoolcraft, Mandy G. Katz‐Jaffe
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.ppat.1009132
Memory like NK cells display stem cell like properties after Zika virus infection
Cited by: 8
Author(s): Weshely Kujur, Oscar Murillo, Sitaramaraju Adduri, Ramakrishna Vankayalapati, Nagarjun V. Konduru, Sachin Mulik
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12864-016-2618-1
Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage
Cited by: 107
Author(s): Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Sotelo‐Silveira, Adriana Geisinger
Software Mentions: 4
Published: over 8 years ago
10.1186/1471-2164-15-899
Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season
Cited by: 40
Author(s): Ran Di, Jianning He, Shuhui Song, Dongmei Tian, Qiuyue Liu, Xiaojun Liang, Qing Ma, Min Sun, Jiandong Wang, Wenming Zhao, G. L. Cao, Jinxin Wang, Ziyin Yang, Ying Ge, Mingxing Chu
Software Mentions: 4
Published: about 10 years ago
10.1186/s12885-021-07911-8
Construction of the optimization prognostic model based on differentially expressed immune genes of lung adenocarcinoma
Cited by: 6
Author(s): Yuanliang Zhai, Bin Zhao, Yuzhen Wang, Lina Li, Jingjin Li, Li Xu, Linhan Chang, Qian Chen, Zhijun Liao
Software Mentions: 4
Published: almost 4 years ago
10.3390/genes12020203
Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia
Cited by: 8
Author(s): Marnie J. Hodge, Sara de las Heras‐Saldana, Sally J. Rindfleish, Cyril Stephen, Sameer D. Pant
Software Mentions: 4
Published: almost 4 years ago
10.1186/s13059-015-0843-6
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
Cited by: 291
Author(s): Wei Li, Johannes Köster, Xu Han, Chen Hao Chen, Tengfei Xiao, Jun S. Liu, Myles Brown, X. Shirley Liu
Software Mentions: 4
Published: about 9 years ago
10.3390/ijms21082800
Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Cited by: 13
Author(s): Xi Wu, Yang Yang, Chaoyue Zhong, Yin Guo, Tengyu Wei, Shuisheng Li, Haoran Lin, Xiaochun Liu
Software Mentions: 4
Published: over 4 years ago
10.7554/eLife.47013
An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans
Cited by: 27
Author(s): Murilo Delgobo, Daniel A G B Mendes, Edgar Kozlova, Edroaldo Lummertz da Rocha, Gabriela F. Rodrigues-Luiz, Lucas Mascarin, Greicy Brisa Malaquias Dias, Daniel de Oliveira Patricio, Tim Dierckx, Maíra A. Bicca, G Bretton, Yonne Karoline Tenório de Menezes, Márick R Starick, Darcita Büerger Rovaris, Joanita Del Moral, Daniel Santos Mansur, Johan Van Weyenbergh, André Báfica
Software Mentions: 4
Published: about 5 years ago
10.7717/peerj.11820
Clinical and prognostic relevance of <i>CXCL12</i> expression in acute myeloid leukemia
Cited by: 2
Author(s): Shi-sen Wang, Zi‐jun Xu, Yue Jin, Ji‐chun Ma, Pei‐hui Xia, Xiang‐mei Wen, Zhen-wei Mao, Lin Jiang, Jun Qian
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-021-07729-5
The holobiont transcriptome of teneral tsetse fly species of varying vector competence
Cited by: 3
Author(s): Miguel Medina Munoz, Caitlyn Brenner, Dylan Richmond, Noah Spencer, Rita V. M. Rio
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.ppat.1009552
Intraspecific variation in immune gene expression and heritable symbiont density
Cited by: 8
Author(s): Holly L. Nichols, Elliott B. Goldstein, Omid Saleh Ziabari, Benjamin J. Parker
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-015-0590-8
Field pathogenomics reveals the emergence of a diverse wheat yellow rust population
Cited by: 175
Author(s): Amelia Hubbard, Clare M. Lewis, Kentaro Yoshida, Ricardo H. Ramírez-González, C. de Vallavieille‐Pope, Jane Thomas, Sophien Kamoun, R. A. Bayles, Cristóbal Uauy, Diane G. O. Saunders
Software Mentions: 4
Published: almost 10 years ago
10.1186/s12864-016-3345-3
TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq
Cited by: 6
Author(s): Cole M. McQueen, Canaan Whitfield-Cargile, Kranti Konganti, Glenn P. Blodgett, Scott V. Dindot, Noah D. Cohen
Software Mentions: 4
Published: about 8 years ago
10.7554/eLife.04235
Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: about 10 years ago
10.3390/pathogens8040183
Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.ppat.1009785
Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART
Cited by: 9
Author(s): Michael J. Corley, Carlo Sacdalan, Alina P.S. Pang, Nitiya Chomchey, Nisakorn Ratnaratorn, Victor Valcour, Eugène Kroon, Kyu S. Cho, Andrew C. Belden, Donn Colby, Merlin L. Robb, Denise C. Hsu, Serena Spudich, Robert Paul, Sandhya Vasan, Lishomwa C. Ndhlovu, Rv study groups
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-014-0554-4
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
Cited by: 1,433
Author(s): Wei Li, Xu Han, Tengfei Xiao, Le Cong, Michael I. Love, Feng Zhang, Rafael A. Irizarry, Jun S. Liu, Myles Brown, X Shirley Liu
Software Mentions: 4
Published: about 10 years ago
10.3390/ijms21124470
Differences between Well-Differentiated Neuroendocrine Tumors and Ductal Adenocarcinomas of the Pancreas Assessed by Multi-Omics Profiling
Cited by: 8
Author(s): Teresa Starzyńska, Jakub Karczmarski, Agnieszka Paziewska, Maria Kulecka, Katarzyna Kuśnierz, Natalia Żeber‐Lubecka, Filip Ambrożkiewicz, Michał Mikula, Beata Kos‐Kudła, Jerzy Ostrowski
Software Mentions: 4
Published: over 4 years ago
10.3389/fmicb.2019.01015
Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere
Cited by: 48
Author(s): Xin Qian, Hanzhou Li, Yong-Long Wang, Bian Wu, Mingsong Wu, Liang Chen, Xingchun Li, Ying Zhang, Xiangping Wang, Miaomiao Shi, Yong Zheng, Liang‐Dong Guo, Dianxiang Zhang
Software Mentions: 4
Published: over 5 years ago
10.1186/s12885-018-4757-z
Association of tamoxifen resistance and lipid reprogramming in breast cancer
Cited by: 98
Author(s): Susanne Hultsch, Matti Kankainen, Lassi Paavolainen, Ruusu-Maaria Kovanen, Elina Ikonen, Sara Kangaspeska, Vilja Pietiäinen, Olli Kallioniemi
Software Mentions: 4
Published: over 6 years ago
10.1186/2045-3701-2-26
Statistical methods for identifying differentially expressed genes in RNA-Seq experiments
Cited by: 43
Author(s): Zhide Fang, Jeffrey A. Martin, Zhong Wang
Software Mentions: 4
Published: almost 13 years ago
10.1186/s13071-021-04597-6
Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector
Cited by: 5
Author(s): Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Software Mentions: 4
Published: almost 4 years ago
10.1186/s13059-014-0410-6
Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pone.0164766
RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: about 8 years ago
10.1371/journal.pone.0164461
Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA
Cited by: 40
Author(s): M. Malvisi, Fiorentina Palazzo, Nicola Morandi, Barbara Lazzari, J. L. Williams, G. Pagnacco, Giulietta Minozzi
Software Mentions: 4
Published: about 8 years ago
10.1186/s12885-020-6513-4
Immunogenomic pathways associated with cytotoxic lymphocyte infiltration and survival in colorectal cancer
Cited by: 8
Author(s): Yuanyuan Shen, Yue Guan, Justin Hummel, Chi‐Ren Shyu, Jonathan B. Mitchem
Software Mentions: 4
Published: almost 5 years ago
10.1371/journal.pone.0190456
Mitochondrial DNA depletion by ethidium bromide decreases neuronal mitochondrial creatine kinase: Implications for striatal energy metabolism
Cited by: 18
Author(s): Emily B. Warren, Aidan Aicher, Joshua P. Fessel, Christine Konradi
Software Mentions: 4
Published: almost 7 years ago
10.3390/ijms21124453
YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: over 4 years ago
10.1186/gb-2013-14-2-r15
Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta
Cited by: 217
Author(s): Stephen R. Fairclough, Zehua Chen, Eric M. Kramer, Qiandong Zeng, Sarah Young, Hugh M. Robertson, Emina Begović, Daniel J. Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B. Franz Lang, Brian J. Haas, Chad Nusbaum, Nicole King
Software Mentions: 4
Published: almost 12 years ago
10.1186/gb-2013-14-11-r131
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs
Cited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: almost 12 years ago
10.1371/journal.pone.0115964
A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
Cited by: 12
Author(s): Asta Laiho, Laura L. Elo
Software Mentions: 4
Published: almost 10 years ago
10.1371/journal.pone.0188264
Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts
Cited by: 25
Author(s): Aimy Sebastian, Nicholas R. Hum, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Gabriela G. Loots
Software Mentions: 4
Published: about 7 years ago
10.1186/s12865-021-00428-6
Transcriptomics of type 2 diabetic and healthy human neutrophils
Cited by: 8
Author(s): Sarah E. Kleinstein, Jamison McCorrison, A. Razzaque Ahmed, Hatice Hastürk, Thomas E. Van Dyke, Marcelo Freire
Software Mentions: 4
Published: over 3 years ago
10.1186/s13071-019-3534-4
Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens
Cited by: 15
Author(s): Charles Li, Xianghe Yan, Hyun S. Lillehoj, Seong-Hwan Oh, Liheng Liu, Zhifeng Sun, Changqin Gu, Youngsub Lee, Zhezi Xianyu, Hongyan Zhao
Software Mentions: 4
Published: over 5 years ago
10.1186/gb-2014-15-2-r32
KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Cited by: 112
Author(s): Benjamin L. Kidder, Gangqing Hu, Keji Zhao
Software Mentions: 4
Published: almost 11 years ago
10.3390/cancers12123786
Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures
Cited by: 9
Author(s): Sofia Karkampouna, Maria Rosaria De Filippo, Charlotte K.Y. Ng, Irena Klima, Eugenio Zoni, Martin Spahn, Frank Stein, Per Haberkant, George N. Thalmann, Marianna Kruithof-de Julio
Software Mentions: 4
Published: about 4 years ago
10.3389/fendo.2019.00840
Role of MicroRNAs in the Regulation of Subcutaneous White Adipose Tissue in Individuals With Obesity and Without Type 2 Diabetes
Cited by: 17
Author(s): Olga Brovkina, А Г Никитин, Д. С. Ходырев, Ekaterina A. Shestakova, Igor A. Sklyanik, Anna S. Panevina, Iurii Stafeev, Mikhail Menshikov, Anastasiya A. Kobelyatskaya, Anatoliy Yurasov, V. S. Fedenko, Yu I Yashkov, М. В. Шестакова
Software Mentions: 4
Published: about 5 years ago
10.1186/s12864-021-07592-4
RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish
Cited by: 8
Author(s): Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries
Software Mentions: 4
Published: over 3 years ago
10.1186/s12916-021-01925-6
Glycolysis-associated lncRNAs identify a subgroup of cancer patients with poor prognoses and a high-infiltration immune microenvironment
Cited by: 17
Author(s): Kuo Hao Ho, Tzu Wen Huang, Chwen Ming Shih, Yi Ting Lee, Ann Jeng Liu, Peng Hsu Chen, Ku Chung Chen
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12872-020-01838-x
Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Cited by: 4
Author(s): Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu
Software Mentions: 4
Published: almost 4 years ago
10.1186/gb-2012-13-10-r88
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Cited by: 72
Author(s): Alok K. Tewari, Galip Gürkan Yardımcı, Yoichiro Shibata, Nathan C. Sheffield, Lingyun Song, Barry S. Taylor, Stoyan Georgiev, Gerhard A. Coetzee, Uwe Ohler, Terrence S. Furey, Gregory E. Crawford, Phillip G. Febbo
Software Mentions: 4
Published: almost 13 years ago
10.1038/s41598-019-41843-5
Different bacterial and viral pathogens trigger distinct immune responses in a globally invasive ant
Cited by: 20
Author(s): Philip J. Lester, Kaitlin H. Buick, James W. Baty, Antoine Felden, John Haywood
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0166862
Drosophila DDX3/Belle Exerts Its Function Outside of the Wnt/Wingless Signaling Pathway
Cited by: 1
Author(s): Fabian H. Jenny, Konrad Basler
Software Mentions: 4
Published: almost 8 years ago
10.1371/journal.pone.0114461
Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium Infection
Cited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: about 10 years ago
10.1128/mSystems.00596-19
Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics
Cited by: 7
Author(s): Matthew Chung, Laura Teigen, Silvia Libro, Robin E. Bromley, Dustin Olley, Nikhil Kumar, Lisa Sadzewicz, Luke J. Tallon, Anup Mahurkar, Jeremy M. Foster, Michelle L. Michalski, Julie C. Dunning Hotopp
Software Mentions: 4
Published: about 5 years ago
10.18632/oncotarget.11788
Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics
Cited by: 64
Author(s): Zhibo Qu, Jingang Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qi Feng, Joy M. Raison, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: over 8 years ago
10.1186/s12864-016-2952-3
Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response
Cited by: 46
Author(s): Marcos Paolinelli, José Manuel Villalobos-Escobedo, Philippe E. Rolshausen, Alfredo Herrera-Estrella, Clara E. Galindo-Sánchez, José Fabricio López-Hernández, Rufina Hernández-Martínez
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pone.0125224
An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data
Cited by: 31
Author(s): Nysia I. George, John F. Bowyer, Nathaniel M. Crabtree, Ching‐Wei Chang
Software Mentions: 4
Published: over 9 years ago
10.1534/genetics.120.303460
Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in <i>Drosophila pseudoobscura</i>
Cited by: 16
Author(s): Zachary L. Fuller, Spencer Koury, Christopher J. Leonard, Randee E. Young, Kobe Ikegami, Jonathan Westlake, Stephen Richards, Stephen W. Schaeffer, Nitin Phadnis
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0123569
XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine
Cited by: 5
Author(s): Asoke K. Talukder, Shashidhar Ravishankar, Krittika Sasmal, Santhosh Gandham, Jyothsna Prabhukumar, Prahalad Achutharao, Debmalya Barh, Francesco Blasi
Software Mentions: 4
Published: over 9 years ago
10.18632/aging.103083
Nudix hydrolase 1 is a prognostic biomarker in hepatocellular carcinoma
Cited by: 6
Author(s): Qifeng Ou, Ning Ma, Zhenzhen Yu, Rongchang Wang, Yucheng Hou, Ziming Wang, Fan Chen, Wen Li, Jiong Bi, Jiachi Ma, Longjuan Zhang, Shan Qiao, Xiaohui Huang
Software Mentions: 4
Published: over 4 years ago
10.18632/oncotarget.27488
MAGE-A inhibit apoptosis and promote proliferation in multiple myeloma through regulation of BIM and p21Cip1
Cited by: 10
Author(s): Anna Mei, Kaity Tung, Jessie Han, Deepak Perumal, Alessandro Laganà, Jonathan J. Keats, Daniel Auclair, Ajai Chari, Sundar Jagannath, Samir Parekh, Hearn Jay Cho
Software Mentions: 4
Published: almost 5 years ago
10.1186/s12859-018-2261-8
Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0230566
Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease
Cited by: 35
Author(s): Elena Buglo, Evan Sarmiento, Nicole Belliard Martuscelli, David W. Sant, Matt C. Danzi, A. Jeanine Abrams, Julia E. Dallman, Stephan Züchner
Software Mentions: 4
Published: over 4 years ago
10.1534/genetics.118.301515
PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in <i>Arabidopsis thaliana</i>
Cited by: 17
Author(s): Tohru Kanno, Peter Venhuizen, Wen Teng, Wen-Dar Lin, Phebe Chiou, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: about 6 years ago
10.1080/15476286.2020.1777768
Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples
Cited by: 10
Author(s): Fabiola Curion, Adam E. Handel, Moustafa Attar, Giuseppe Gallone, Rory Bowden, M Z Cader, Michael B. Clark
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0238420
Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma
Cited by: 1
Author(s): Wenjing Zhang, Shuai Xu, Laner Shi, Zhangzhi Zhu, Xinying Xie
Software Mentions: 4
Published: over 4 years ago
10.1098/rsos.200517
Brain microRNAs among social and solitary bees
Cited by: 12
Author(s): Karen M. Kapheim, Beryl M. Jones, Eirik Søvik, Eckart Stolle, Robert M. Waterhouse, Guy Bloch, Yehuda Ben‐Shahar
Software Mentions: 4
Published: over 4 years ago
10.3389/fncel.2021.629279
Validation of Induced Microglia-Like Cells (iMG Cells) for Future Studies of Brain Diseases
Cited by: 24
Author(s): Atoshi Banerjee, Yujie Lu, Kenny Do, Travis Mize, Xiaogang Wu, Xiangning Chen, Jingchun Chen
Software Mentions: 4
Published: over 3 years ago
10.1186/s12862-017-1103-z
De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus
Cited by: 11
Author(s): Alexey Moskalev, Anna V. Kudryavtseva, Alexander S. Graphodatsky, Violetta R. Beklemisheva, Natalia A. Serdyukova, Konstantin V. Krutovsky, Vadim V. Sharov, Ivan V. Kulakovskiy, Andrey S. Lando, Artem S. Kasianov, Dmitry A. Kuzmin, Yuliya A. Putintseva, Sergey Feranchuk, Mikhail Shaposhnikov, Vadim E. Fraifeld, Dmitri Toren, А. В. Снежкина, Vasily Sitnik
Software Mentions: 4
Published: about 7 years ago
10.1186/s12864-016-3070-y
The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets
Cited by: 27
Author(s): Pablo Ivan Pereira Ramos, Márlon Grégori Flores Custódio, Guadalupe del Rosario Quispe Saji, Thiago Bérgamo Cardoso, Gisele Lucchetti da Silva, Graziela Braun, Willames M. B. S. Martins, Raquel Girardello, Ana Tereza Ribeiro de Vasconcelos, Elmer Fernández, Ana Cristina Gales, Marisa Fabiana Nicolás
Software Mentions: 4
Published: about 8 years ago
10.1128/mSystems.00284-18
Systems-Level Analysis of Oxygen Exposure in <i>Zymomonas mobilis</i> : Implications for Isoprenoid Production
Cited by: 22
Author(s): Julia Martien, Alexander S. Hebert, David Stevenson, Matthew Regner, Daven B. Khana, Joshua J. Coon, Daniel Amador‐Noguez
Software Mentions: 4
Published: almost 6 years ago
10.1128/mSystems.00038-18
Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation
Cited by: 66
Author(s): Andrea Söllinger, Alexander Tøsdal Tveit, Morten Poulsen, Samantha Joan Noel, Mia M. Bengtsson, Jörg Bernhardt, Anne Louise Frydendahl Hellwing, Peter Lund, Katharina Riedel, Christa Schleper, Ole Højberg, Tim Urich
Software Mentions: 4
Published: over 6 years ago
10.1186/1471-2164-14-S1-S9
Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information
Cited by: 2
Author(s): Ellis Patrick, Michael Buckley, David M. Lin, Jean Yee Hwa Yang
Software Mentions: 4
Published: almost 12 years ago
10.1186/s12263-018-0594-6
Studying microbial functionality within the gut ecosystem by systems biology
Cited by: 30
Author(s): Bastian Hornung, Vítor A. P. Martins dos Santos, Hauke Smidt, Peter J. Schaap
Software Mentions: 4
Published: almost 7 years ago
10.26508/lsa.201900535
The molecular clock protein Bmal1 regulates cell differentiation in mouse embryonic stem cells
Cited by: 12
Author(s): Amador Gallardo, Ana Rodríguez Molina, Helena G Asenjo, Jordi Martorell-Marugán, Rosa Montes, Verónica Ramos-Mejía, Antonio Sánchez–Pozo, Pedro Carmona-Sáez, Lourdes López-Onieva, David Landeira
Software Mentions: 4
Published: over 4 years ago
10.18632/aging.202950
Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer’s disease etiopathogenesis
Cited by: 13
Author(s): Laura Madrid, Sonia Moreno‐Grau, Shahzad Ahmad, Antonio González‐Pérez, Itziar de Rojas, Rui Xia, Pamela Victoria Martino Adami, Pablo García‐González, Luca Kleineidam, Qiong Yang, Vincent Damotte, Joshua C. Bis, Fuensanta Noguera-Perea, Céline Bellenguez, Xueqiu Jian, Juan Marín-Muñoz, Benjamin Grenier‐Boley, Adela Orellana, M. Arfan Ikram, Philippe Amouyel, Claudia L. Satizábal, Alzheimer’s Disease Neuroimaging Initiative, Luis Miguel Real, Carmen Antúnez-Almagro, Anita L. DeStefano, Alfredo Cabrera-Socorro, Rebecca Sims, Cornelia M. van Duijn, Eric Boerwinkle, Alfredo Ramı́rez, Myriam Fornage, Jean‐Charles Lambert, Julie Williams, Sudha Seshadri, Janina S. Ried, Agustín Ruiz, María Eugenia Sáez
Software Mentions: 4
Published: over 3 years ago
10.1186/1748-7188-7-5
A normalization strategy for comparing tag count data
Cited by: 72
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
Software Mentions: 4
Published: over 12 years ago
10.1186/s12864-020-07327-x
Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO2 during early development
Cited by: 5
Author(s): Juliet M. Wong, Gretchen E. Hofmann
Software Mentions: 4
Published: almost 4 years ago
10.3390/ijms20143480
Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-019-5530-7
Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus
Cited by: 17
Author(s): Sara de las Heras‐Saldana, Ki Yong Chung, Seung Hwan Lee, Cedric Gondro
Software Mentions: 4
Published: almost 6 years ago
10.18632/oncotarget.12180
The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
Cited by: 72
Author(s): Florian Finkernagel, Silke Reinartz, Sonja Lieber, Till Adhikary, Annika Wortmann, Nathalie Hoffmann, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 4
Published: about 8 years ago
10.1186/s12864-015-2114-z
Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
Cited by: 9
Author(s): Gareth D. Weedall, Helen Irving, Margaret Hughes, Charles S. Wondji
Software Mentions: 4
Published: about 9 years ago
10.1186/s12916-020-01605-x
Circulating mRNAs are differentially expressed in pregnancies with severe placental insufficiency and at high risk of stillbirth
Cited by: 23
Author(s): Natalie J. Hannan, Owen Stock, Rebecca Spencer, Clare Whitehead, Anna L. David, Katie Groom, Scott Petersen, Amanda Henry, Joanne Said, Sean Seeho, Stefan C. Kane, Lavinia Gordon, Sally Beard, Kantaraja Chindera, Smita T. Karegodar, Richard Hiscock, Natasha Pritchard, Tu’uhevaha J Kaitu’u-Lino, Susan Walker, Stephen Tong
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pone.0081809
Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
Cited by: 55
Author(s): Antheia Kissopoulou, Jon Jonasson, Tomas Lindahl, Abdimajid Osman
Software Mentions: 4
Published: about 11 years ago
10.1371/journal.pone.0166944
Transcriptomic Analysis Shows Decreased Cortical Expression of NR4A1, NR4A2 and RXRB in Schizophrenia and Provides Evidence for Nuclear Receptor Dysregulation
Cited by: 23
Author(s): Susan M. Corley, Shan-Yuan Tsai, Marc R. Wilkins, Cynthia Shannon Weickert
Software Mentions: 4
Published: about 8 years ago
10.1186/s12864-016-2403-1
RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations
Cited by: 20
Author(s): Edin Hamzić, Rikke Brødsgaard Kjærup, Núria Mach, Guilietta Minozzi, Francesco Strozzi, V. Gualdi, J. L. Williams, Jun Chen, Eva Wattrang, Bart Buitenhuis, Helle R. Juul‐Madsen, Tina Sørensen Dalgaard
Software Mentions: 4
Published: almost 9 years ago
10.3390/cancers13030548
Identification of RCC Subtype-Specific microRNAs–Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data
Cited by: 11
Author(s): Arkadiusz Kajdasz, Weronika Majer, Katarzyna Kluzek, Jacek Sobkowiak, Tomasz Milecki, Natalia Derebecka, Zbigniew Kwias, Hans A.R. Bluyssen, Joanna Wesoły
Software Mentions: 4
Published: almost 4 years ago
10.1098/rsob.200253
The role of antioxidants in restoring MAPK 14 and a DNA damage marker level following autophagy suppression
Cited by: 3
Author(s): Abdalla Elbialy
Software Mentions: 4
Published: about 4 years ago
10.18632/aging.102820
Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma
Cited by: 22
Author(s): Feiwen Deng, Chen Dong, Xiaoli Wei, Shilin Lu, Xuan Luo, Jincan He, Junting Liu, Tiebao Meng, Anli Yang, Huanwei Chen
Software Mentions: 4
Published: almost 5 years ago
10.1128/mSphere.00231-18
Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes
Cited by: 28
Author(s): Gregory A. DeIulio, Li Guo, Yong Zhang, Jonathan M. Goldberg, H. Corby Kistler, Lijun Ma
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-017-3809-0
Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data
Cited by: 20
Author(s): Susan A. Yoon, Dougu Nam
Software Mentions: 4
Published: over 7 years ago