bioconductor: EBSeq | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago

10.3390/cancers12040948

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility
Cited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: over 4 years ago

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: almost 10 years ago

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: almost 8 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: about 9 years ago

10.3389/fcimb.2021.687607

Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis Infections
Cited by: 1
Author(s): María Adelaida Gómez, Ashton T. Belew, Adriana Navas, Mariana Rosales-Chilama, Julieth Murillo, Laura A. L. Dillon, Theresa A Alexander, Álvaro José Martínez-Valencia, Najib M. El-Sayed
Software Mentions: 12
Published: about 3 years ago

10.1371/journal.pone.0190152

RNA-Seq differential expression analysis: An extended review and a software tool
Cited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: almost 7 years ago

10.1016/j.csbj.2015.08.004

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis
Cited by: 73
Author(s): Daniel Spies, Constance Ciaudo
Software Mentions: 11
Published: almost 10 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: over 8 years ago

10.1016/j.csbj.2021.05.040

Robustness of differential gene expression analysis of RNA-seq
Cited by: 31
Author(s): Alexey Stupnikov, Caitríona E. McInerney, Kienan I. Savage, Stuart McIntosh, Frank Emmert‐Streib, Richard D. Kennedy, Manuel Salto-Tellez, Kevin M. Prise, Darragh G. McArt
Software Mentions: 11
Published: almost 4 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: almost 5 years ago

10.1186/s12859-016-1386-x

Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes
Cited by: 0
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 11
Published: almost 8 years ago

10.1186/s12864-019-6181-4

Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)
Cited by: 12
Author(s): Jianjun Fu, Wenbin Zhu, Lanmei Wang, Ming Luo, Fei Song, Zaijie Dong
Software Mentions: 10
Published: about 5 years ago

10.3389/fnmol.2017.00045

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation
Cited by: 4
Author(s): Sanjeev V. Namjoshi, Kimberly F. Raab‐Graham
Software Mentions: 10
Published: over 7 years ago

10.1038/s41598-020-76881-x

Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
Cited by: 81
Author(s): Luis A. Corchete, Elizabeta A. Rojas, Diego Alonso-López, Javier De Las Rivas, Norma C. Gutiérrez, F.J. Burguillo
Software Mentions: 10
Published: about 4 years ago

10.7554/eLife.43257

Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures
Cited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Software Mentions: 10
Published: over 5 years ago

10.1186/s12859-017-1498-y

Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysis
Cited by: 15
Author(s): Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano
Software Mentions: 10
Published: almost 8 years ago

10.7554/eLife.36187

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Cited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: about 6 years ago

10.3389/fpls.2020.01269

Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening
Cited by: 27
Author(s): Beatriz Ester García-Gómez, David Ruiz, J. Salazar, M. Rubio, Pedro J. Martínez-García, Pedro Martínez‐Gómez
Software Mentions: 9
Published: over 4 years ago

10.1186/s12864-015-1676-0

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies
Cited by: 14
Author(s): Chengcai Chu, Zhiming Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley, Mingyu Liang, Pengyuan Liu, Yan Lu
Software Mentions: 9
Published: over 9 years ago

10.1186/1471-2164-16-S7-S14

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Cited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: over 9 years ago

10.1371/journal.pone.0220518

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
Cited by: 4
Author(s): Albert Fradera-Sola, Ann Thomas, Dagmara Gasior, John A. Harper, Matthew J. Hegarty, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 9
Published: over 5 years ago

10.1186/s13059-015-0702-5

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Cited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: over 9 years ago

10.1186/s12864-020-6534-z

Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni
Cited by: 17
Author(s): Lijun Lu, Eric S. Loker, Si-Ming Zhang, Sarah Kay Buddenborg, Lijing Bu
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0153782

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
Cited by: 11
Author(s): Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban
Software Mentions: 8
Published: over 8 years ago

10.1186/s12864-016-2848-2

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
Cited by: 21
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 8
Published: over 8 years ago

10.1186/1471-2105-14-91

A comparison of methods for differential expression analysis of RNA-seq data
Cited by: 725
Author(s): Charlotte Soneson, Mauro Delorenzi
Software Mentions: 7
Published: over 11 years ago

10.1186/s12864-019-6415-5

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex
Cited by: 19
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Michael E. Pfrender, James Brown, John K. Colbourne, Leda Mirbahai
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12859-021-04198-1

Comparative evaluation of full-length isoform quantification from RNA-Seq
Cited by: 12
Author(s): Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens, Gregory R. Grant
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-16-S9-S2

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis
Cited by: 17
Author(s): Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Calogero, Francesca Zolezzi
Software Mentions: 7
Published: over 9 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: almost 11 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 6 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 11 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 11 years ago

10.1038/s42003-021-02095-0

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Cited by: 28
Author(s): Mariana Galvão Ferrarini, Avantika Lal, Rita Rebollo, Andreas J. Gruber, Andrea Guarracino, Itziar Martinez Gonzalez, Taylor Floyd, Daniel Siqueira de Oliveira, Justin Shanklin, Ethan Beausoleil, Taneli Pusa, Brett E. Pickett, Vanessa Aguiar‐Pulido
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pntd.0008780

Genomic and transcriptional analysis of genes containing fibrinogen and IgSF domains in the schistosome vector Biomphalaria glabrata, with emphasis on the differential responses of snails susceptible or resistant to Schistosoma mansoni
Cited by: 8
Author(s): Lijun Lu, Eric S. Loker, Coen M. Adema, Si-Ming Zhang, Lijing Bu
Software Mentions: 6
Published: about 4 years ago

10.1186/s13068-018-1116-x

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
Cited by: 54
Author(s): Shihui Yang, Jessica M. Vera, Jeff Grass, Giannis Savvakis, Oleg V. Moskvin, Yongqiang Yang, Sean J. McIlwain, Yucai Lyu, Irene Zinonos, Alexander S. Hebert, Joshua J. Coon, Donna M. Bates, Trey K. Sato, Steven D. Brown, Michael E. Himmel, Min Zhang, Robert Landick, Katherine M. Pappas, Yaoping Zhang
Software Mentions: 6
Published: over 6 years ago

10.1186/s12864-021-07437-0

Transcriptomics analysis of Toxoplasma gondii-infected mouse macrophages reveals coding and noncoding signatures in the presence and absence of MyD88
Cited by: 7
Author(s): Kayla L. Menard, Lijing Bu, Eric Denkers
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-019-6375-9

Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics
Cited by: 27
Author(s): Yanchao Xu, Richard Odongo Magwanga, Xiaomin Yang, Dingsha Jin, Xiaoyan Cai, Yuqing Hou, Yangyang Wei, Kunbo Wang, Fang Liu
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12859-015-0664-3

Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications
Cited by: 5
Author(s): Fang Yu, Ming Hui Chen, Lynn Kuo, Heather Talbott, John S. Davis
Software Mentions: 6
Published: over 9 years ago

10.1186/1471-2164-15-S10-S7

LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data
Cited by: 16
Author(s): Bingqing Lin, Lifeng Zhang, Xin Chen
Software Mentions: 6
Published: almost 10 years ago

10.1186/s12864-016-3020-8

RNA-Seq analysis of seasonal and individual variation in blood transcriptomes of healthy managed bottlenose dolphins
Cited by: 27
Author(s): Jeanine S. Morey, Marion G. Neely, Denise Lunardi, Paul E. Anderson, Lori H. Schwacke, Michelle R. Campbell, Frances M. Van Dolah
Software Mentions: 6
Published: about 8 years ago

10.3389/fimmu.2019.01463

Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats
Cited by: 17
Author(s): Sajad A. Wani, Anamika Sahu, Raja Ishaq Nabi Khan, Awadh Bihari Pandey, Shikha Saxena, Neelima Hosamani, Waseem Akram Malla, Dheeraj Chaudhary, Sonam Kanchan, V. K. Sah, Kaushal Kishor Rajak, D. Muthuchelvan, Bina Mishra, Ashok Kumar Tiwari, Aditya Prasad Sahoo, Basavaraj Sajjanar, Yash Pal Singh, Ravi Kumar Gandham, Bishnu Prasad Mishra, Raj Kumar Singh
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-018-19984-w

Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage
Cited by: 51
Author(s): Jun Wang, Zhu Jun, Yadong Zhang, Fangjun Fan, Wenqi Li, Fangquan Wang, Zhong WeiGong, Cailin Wang, Jie Yang
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2020.575488

Integrated Analysis of Transcriptome and Secretome From Umbilical Cord Mesenchymal Stromal Cells Reveal New Mechanisms for the Modulation of Inflammation and Immune Activation
Cited by: 18
Author(s): Mónica Cruz-Barrera, Nathalia Flórez-Zapata, Nicolás Lemus-Diaz, Carlos O. Medina, Cristian Camilo Galindo, Lorena-Xiomara González-Acero, Luz Correa, Bernardo Camacho, Jens Gruber, Gustavo Salguero
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.49673

Rbfox1 up-regulation impairs BDNF-dependent hippocampal LTP by dysregulating TrkB isoform expression levels
Cited by: 25
Author(s): Francesco Tomassoni-Ardori, Gianluca Fulgenzi, Jodi Becker, Colleen Barrick, Mary Ellen Palko, Skyler Kuhn, Vishal N. Kopardé, Maggie Cam, Sudhirkumar Yanpallewar, Shalini Oberdoerffer, Lino Tessarollo
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms20143543

Sex-Dimorphic Behavioral Alterations and Altered Neurogenesis in U12 Intron Splicing-Defective Zrsr1 Mutant Mice
Cited by: 9
Author(s): Francisco Alén, Isabel Gómez-Redondo, Patricia Rivera, Juan Suárez, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Serafín Pérez‐Cerezales, Keiko Horiuchi, Laura Orío, Fernando Rodríguez de Fonseca, Alfonso Gutiérrez‐Adán
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2105-15-S9-S6

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

10.1093/bib/bbz018

CAFU: a Galaxy framework for exploring unmapped RNA-Seq data
Cited by: 11
Author(s): Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jinxin Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma
Software Mentions: 5
Published: over 5 years ago

10.1186/s13058-019-1230-0

Elacestrant (RAD1901) exhibits anti-tumor activity in multiple ER+ breast cancer models resistant to CDK4/6 inhibitors
Cited by: 44
Author(s): Hemang Patel, Nianjun Tao, Kyung Min Lee, Mariela Huerta, Heike Arlt, Tara Mullarkey, Steven Troy, Carlos L. Arteaga, Teeru Bihani
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-017-3673-y

Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Cited by: 95
Author(s): Jenna Kropp Schmidt, José A. Carrillo, Hadjer Namous, Daniels Alyssa, Sana M. Salih, Jiuzhou Song, Hasan Khatib
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2164-15-917

Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut
Cited by: 37
Author(s): Matan Shelomi, W. Cameron Jasper, Joel Atallah, Lynn S. Kimsey, Brian R. Johnson
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pbio.2006347

Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation
Cited by: 33
Author(s): Mingming Zhao, Jaimy Joy, Weiqiang Zhou, Supriyo De, William H. Wood, Kevin G. Becker, Hongkai Ji, Ranjan Sen
Software Mentions: 5
Published: about 6 years ago

10.1177/1177932219860817

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

10.7717/peerj.3797

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

10.1186/s12859-017-1897-0

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12870-017-1108-1

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription
Cited by: 17
Author(s): Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.ppat.1005168

The White-Nose Syndrome Transcriptome: Activation of Anti-fungal Host Responses in Wing Tissue of Hibernating Little Brown Myotis
Cited by: 90
Author(s): Kenneth A. Field, Joseph S. Johnson, Thomas M. Lilley, Sophia Reeder, Elizabeth J. Rogers, Melissa Behr, DeeAnn M. Reeder
Software Mentions: 4
Published: about 9 years ago

10.1186/s12920-020-0659-4

Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer
Cited by: 16
Author(s): Chai-Jin Lee, Hongryul Ahn, Dabin Jeong, Minwoo Pak, Ji Hwan Moon, Sun Kim
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-016-2950-5

The influence of trematode parasite burden on gene expression in a mammalian host
Cited by: 9
Author(s): Bhagya K. Wijayawardena, Dennis J. Minchella, J. Andrew DeWoody
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-015-2277-7

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome
Cited by: 42
Author(s): Erik A. Visser, Jill L. Wegrzyn, Emma T. Steenkmap, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-016-3130-3

Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera)
Cited by: 15
Author(s): Gladys K. Andino, Michael Gribskov, Denis L. Anderson, Jay D. Evans, Greg J. Hunt
Software Mentions: 4
Published: about 8 years ago

10.3390/genes9090431

Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots
Cited by: 16
Author(s): Gabriela Machaj, Hamed Bostan, Alicja Macko-Podgórni, Massimo Iorizzo, Dariusz Grzebelus
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.8301

Bioinformatics profiling identifies seven immune-related risk signatures for hepatocellular carcinoma
Cited by: 9
Author(s): Feng Xue, Lixue Yang, Binghua Dai, Hui Xue, Lei Zhang, Ruowen Ge, Ying Sun
Software Mentions: 4
Published: over 4 years ago

10.1186/s12862-018-1288-9

Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers
Cited by: 16
Author(s): Bette Hecox-Lea, David B. Mark Welch
Software Mentions: 4
Published: almost 6 years ago

10.3389/fimmu.2019.03065

Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells
Cited by: 17
Author(s): Jessica Vázquez, Deborah Chasman, Gladys López, Chanel T. Tyler, Irene M. Ong, Aleksandar K. Stanic
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2017.00944

Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers
Cited by: 43
Author(s): Tommy Harding, Andrew J. Roger, Alastair G. B. Simpson
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2016.00225

Extending the R Library PROPER to Enable Power Calculations for Isoform-Level Analysis with EBSeq
Cited by: 2
Author(s): Amadou Thierno Gaye
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0131504

A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2021.695699

Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone
Cited by: 3
Author(s): Shaozhen Liu, Qiong Yang, Yue Chen, Qing Liu, Weiwei Wang, Jing Song, Yao Zheng, Wenzhong Liu
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2019.01081

Characterization of Hepatocellular Carcinoma Cell Lines Using a Fractionation-Then-Sequencing Approach Reveals Nuclear-Enriched HCC-Associated lncRNAs
Cited by: 12
Author(s): Elaine Chow, Jizhou Zhang, Hao Qin, Ting‐Fung Chan
Software Mentions: 4
Published: about 5 years ago

10.1111/rssc.12213

A Bayesian Model Selection Approach for Identifying Differentially Expressed Transcripts from RNA Sequencing Data
Cited by: 5
Author(s): Panagiotis Papastamoulis, Magnus Rattray
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-019-5832-9

A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis
Cited by: 23
Author(s): Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xin Yan, Xinxin Geng
Software Mentions: 4
Published: over 5 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

10.1038/s41598-021-96055-7

Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR
Cited by: 6
Author(s): Gilbert O. Silveira, Murilo Sena Amaral, Helena S. Coelho, Lucas F. Maciel, Adriana S. A. Pereira, Giovanna G. O. Olberg, Patrícia A. Miyasato, Eliana Nakano, Sérgio Verjovski-Almeida
Software Mentions: 4
Published: over 3 years ago

10.1002/ece3.1720

The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development
Cited by: 34
Author(s): Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson, Timothy A. Linksvayer
Software Mentions: 4
Published: about 9 years ago

10.1002/ece3.3133

Transcriptomic differentiation underlying marine‐to‐freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)
Cited by: 17
Author(s): Lily C. Hughes, Gustavo M. Somoza, Bryan Nguyen, James P. Bernot, Mariano González‐Castro, Juan Martín Díaz de Astarloa, Guillermo Ortı́
Software Mentions: 4
Published: over 7 years ago

10.1128/mBio.02302-20

Identification of Zinc-Dependent Mechanisms Used by Group B Streptococcus To Overcome Calprotectin-Mediated Stress
Cited by: 27
Author(s): Lindsey R. Burcham, Yoann Le Breton, Jana N. Radin, Brady L. Spencer, Liwen Deng, Aurélia Hiron, Monica Ransom, Jéssica da C. Mendonça, Ashton T. Belew, Najib M. El-Sayed, Kevin S. McIver, Thomas E. Kehl-Fie, Kelly S. Doran
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12885-020-07513-w

Ovarian cancer cells direct monocyte differentiation through a non-canonical pathway
Cited by: 5
Author(s): Kaitlin C. Fogg, Andrew Miller, Ying Liu, Will Flanigan, Alyssa Walker, Amy O'Shea, Christina Kendziorski, Pamela K. Kreeger
Software Mentions: 4
Published: about 4 years ago

10.1099/acmi.0.000082

Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways
Cited by: 2
Author(s): K. S. Solanki, Ravikumar Gandham, Prasad Thomas, Pallab Chaudhuri
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-015-0623-z

MetaDiff: differential isoform expression analysis using random-effects meta-regression
Cited by: 7
Author(s): Jia Cheng, Weihua Guan, Amy Yang, Rui Xiao, W.H. Wilson Tang, Christine S. Moravec, Kenneth B. Margulies, Thomas P. Cappola, Mingyao Li, Chun G Li
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-019-2074-6

Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species
Cited by: 37
Author(s): Ying Hong, Jian Shi, Shanshan Zhang, Gesang Pingcuo, Shuo Wang, Fan Zhao, Yongning Cui, Xiuli Zeng
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-017-4141-4

Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes
Cited by: 3
Author(s): Billy T. Lau, Hanlee P. Ji
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-020-61007-0

De novo transcriptome of the diatom Cylindrotheca closterium identifies genes involved in the metabolism of anti-inflammatory compounds
Cited by: 21
Author(s): Ali Murat Elagoz, Luca Ambrosino, Chiara Lauritano
Software Mentions: 3
Published: over 4 years ago

10.1186/s12870-020-02586-y

De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites
Cited by: 9
Author(s): Guolin Zhou, Ping Zhu
Software Mentions: 3
Published: about 4 years ago

10.1038/srep18470

Genome-wide analysis of microRNAs identifies the lipid metabolism pathway to be a defining factor in adipose tissue from different sheep
Cited by: 37
Author(s): Xiangyang Miao, Qingmiao Luo, Xiaoqiong Qin, Yuntao Guo
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-020-70673-z

Unique molecular signatures of antiviral memory CD8+ T cells associated with asymptomatic recurrent ocular herpes
Cited by: 2
Author(s): Swayam Prakash, Subhransu Roy, Ruchi Srivastava, Pierre-Gregoire A Coulon, Nisha R Dhanushkodi, Hawa Vahed, Allen Jankeel, Roger Geertsema, Cassandra Amezquita, Lan Nguyễn, Ilhem Messaoudi, Amanda M. Burkhardt, Lbachir BenMohamed
Software Mentions: 3
Published: over 4 years ago

10.3390/ani10040681

Comprehensive Transcriptional Changes in the Liver of Kanglang White Minnow (Anabarilius grahami) in Response to the Infection of Parasite Ichthyophthirius multifiliis
Cited by: 3
Author(s): Ying Qiu, Yanhui Yin, Zhiqiang Ruan, Yu Gao, Chao Bian, Jieming Chen, Xiaoai Wang, Xiaofu Pan, Jing Yang, Qiong Shi, Weixing Jiang
Software Mentions: 3
Published: over 4 years ago

10.1038/hortres.2017.5

Differential gene expression analysis of ‘Chili’ (Pyrus bretschneideri) fruit pericarp with two types of bagging treatments
Cited by: 22
Author(s): Yuling Wang, Xinfu Zhang, Ran Wang, Ying-Xin Bai, Chenglian Liu, Yuan Yang, Yingjie Yang, Shaolan Yang
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.1828

The myogenic electric organ ofSternopygus macrurus: a non-contractile tissue with a skeletal muscle transcriptome
Cited by: 10
Author(s): Matthew Pinch, Robert Güth, Manoj P. Samanta, Alexander Chaidez, Graciela A. Unguez
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-015-0873-9

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Cited by: 34
Author(s): Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stefan Krebs, Gustav Steinhoff, Róbert Dávid, Olaf Wolkenhauer
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0140032

Modeling Exon-Specific Bias Distribution Improves the Analysis of RNA-Seq Data
Cited by: 1
Author(s): Xuejun Liu, Li Zhang, Songcan Chen
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0157783

De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction
Cited by: 15
Author(s): Chen Wu, Ross N. Crowhurst, Alice B. Dennis, Victoria Twort, Shanlin Liu, Richard D. Newcomb, Howard A. Ross, Thomas R. Buckley
Software Mentions: 3
Published: over 8 years ago

10.1093/jxb/erw386

Post-transcriptional regulation of photosynthetic genes is a key driver of C4leaf ontogeny
Cited by: 15
Author(s): Niklaus Fankhauser, Sylvain Aubry
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2018.02591

Transcriptome and Resistance-Related Genes Analysis of Botrytis cinerea B05.10 Strain to Different Selective Pressures of Cyprodinil and Fenhexamid
Cited by: 8
Author(s): Xuegui Wang, Changwei Gong, Yun Zhao, Litao Shen
Software Mentions: 3
Published: about 6 years ago

10.3389/fpls.2017.01233

Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry
Cited by: 76
Author(s): Irina Ionescu, Gregorio López‐Ortega, Meike Burow, Almudena Bayo-Canha, Alexander Junge, Oliver Gericke, Birger Lindberg Møller, Raquel Sánchez‐Pérez
Software Mentions: 3
Published: over 7 years ago

Projects: bioconductor: EBSeq

Papers Mentioning EBSeq 261