bioconductor: NOISeq | Projects | Ecosyste.ms: Papers

10.1186/s13059-016-0881-8

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

10.3389/fgene.2019.00499

ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Cited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 5 years ago

10.1371/journal.pone.0256196

Finding differentially expressed sRNA-Seq regions with srnadiff
Cited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: about 3 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

10.1371/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

10.1186/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

10.1016/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

10.1186/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

10.1038/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: almost 4 years ago

10.1186/s13059-018-1466-5

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
Cited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: over 6 years ago

10.3389/fgene.2019.00279

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: over 5 years ago

10.1186/1471-2164-16-S6-S3

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
Cited by: 54
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Matteo Pallocca, Ernesto Picardi, Anna Maria D’Erchia, Raffaele Calogero, Tiziana Castrignanò, Graziano Pesole
Software Mentions: 9
Published: over 9 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: about 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

10.1038/s41598-020-77201-z

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae
Cited by: 3
Author(s): José Córdoba-Caballero, Pedro Seoane, Fernando M. Jabato, James R. Perkins, Manuel Manchado, M. Gonzalo Claros
Software Mentions: 9
Published: almost 4 years ago

10.1177/2515841419835460

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
Cited by: 6
Author(s): Nicholas Owen, Mariya Moosajee
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12870-019-1679-0

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Cited by: 34
Author(s): Alejandro Sanz-Carbonell, Maria Carmen Marqués, Alexander Bustamante, Mario A. Fares, Guillermo Rodrigo, Gustavo Gómez
Software Mentions: 9
Published: over 5 years ago

10.12688/f1000research.27868.3

WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
Cited by: 5
Author(s): Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Software Mentions: 9
Published: over 3 years ago

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 4 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: about 9 years ago

10.1038/s41597-020-00696-8

Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients
Cited by: 10
Author(s): Antonio Federico, Veera Hautanen, Nils Christian, Andreas Kremer, Angela Serra, Dario Greco
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0125000

From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Cited by: 6
Author(s): Jilong Li, Jie Hou, Sun Liang, Jordan Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, C. Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
Software Mentions: 8
Published: over 9 years ago

10.1155/2015/789516

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Cited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: almost 10 years ago

10.1186/1471-2105-14-219

TCC: an R package for comparing tag count data with robust normalization strategies
Cited by: 394
Author(s): Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota
Software Mentions: 8
Published: over 11 years ago

10.1186/s12864-019-6162-7

Transcriptome analysis of the differential effect of the NADPH oxidase gene RbohB in Phaseolus vulgaris roots following Rhizobium tropici and Rhizophagus irregularis inoculation
Cited by: 11
Author(s): Citlali Fonseca-García, Alejandra E. Zayas, Jesús Montiel, Noreide Nava, Federico Sánchez, Carmen Quinto
Software Mentions: 7
Published: about 5 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

10.1186/1471-2105-14-262

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

10.1186/s12864-018-4896-2

Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands
Cited by: 8
Author(s): Panagiotis Moulos, Αλέξανδρος Αλεξανδράτος, Ioannis Nellas, Skarlatos G. Dedos
Software Mentions: 7
Published: over 6 years ago

10.1186/s12967-021-02936-w

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
Cited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Software Mentions: 7
Published: over 3 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 6 years ago

10.1371/journal.pgen.1009294

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

10.3389/fpls.2019.01645

Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply
Cited by: 15
Author(s): Paula Pongrac, Sina Fischer, Jacqueline Thompson, G. M. Wright, Philip J. White
Software Mentions: 7
Published: almost 5 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 7 years ago

10.1038/s41598-020-79296-w

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon
Cited by: 6
Author(s): Andrea M. Makkay, Artemis S. Louyakis, Nikhil Ram-Mohan, Uri Gophna, J. Peter Gogarten, R. Thane Papke
Software Mentions: 7
Published: almost 4 years ago

10.1242/dmm.039297

Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development
Cited by: 10
Author(s): Christopher Nash, Nadia Boufaied, Dunarel Badescu, Yu Chang Wang, Miltiadis Paliouras, Mark Trifiro, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-017-3938-5

A permutation-based non-parametric analysis of CRISPR screen data
Cited by: 26
Author(s): Gaoxiang Jia, Xinlei Wang, Guanghua Xiao
Software Mentions: 7
Published: over 7 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

10.1038/sdata.2016.73

Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands
Cited by: 7
Author(s): Panagiotis Moulos, Martina Samiotaki, George Panayotou, Skarlatos G. Dedos
Software Mentions: 6
Published: about 8 years ago

10.1186/s12859-020-3399-8

iSeqQC: a tool for expression-based quality control in RNA sequencing
Cited by: 15
Author(s): Gaurav Kumar, Adam Ertel, George J. Feldman, Joan Kupper, Paolo Fortina
Software Mentions: 6
Published: over 4 years ago

10.1186/s12920-019-0513-8

Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine
Cited by: 7
Author(s): Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Francesca Vitali, Helen Hao Zhang, Yves A. Lussier
Software Mentions: 6
Published: over 5 years ago

10.3389/fgene.2019.00904

Advances and Challenges in Metatranscriptomic Analysis
Cited by: 217
Author(s): Migun Shakya, Chien‐Chi Lo, Patrick Chain
Software Mentions: 6
Published: about 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

10.1002/pld3.159

The HAC1 histone acetyltransferase promotes leaf senescence and regulates the expression of ERF022
Cited by: 28
Author(s): Will E. Hinckley, Keykhosrow Keymanesh, Jaime Cordova, Judy A. Brusslan
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1007869

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer
Cited by: 8
Author(s): Magali Richard, Clémentine Decamps, Florent Chuffart, Élisabeth Brambilla, Sophie Rousseaux, Saadi Khochbin, Daniel Jost
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-021-82156-w

Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy
Cited by: 23
Author(s): Wellison J. S. Diniz, Matthew S Crouse, Robert A. Cushman, Kyle J McLean, J. S. Caton, Carl R Dahlen, Lawrence P. Reynolds, Alison K Ward
Software Mentions: 6
Published: almost 4 years ago

10.3389/fimmu.2021.729217

Timing of Transcriptomic Peripheral Blood Mononuclear Cell Responses of Sheep to Fasciola hepatica Infection Differs From Those of Cattle, Reflecting Different Disease Phenotypes
Cited by: 4
Author(s): Dagmara A. Niedziela, Amalia Naranjo‐Lucena, Verónica Molina-Hernández, John A. Browne, Á. Martínez-Moreno, J. Pérez, David E. MacHugh, Grace Mulcahy
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pcbi.1005515

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
Cited by: 17
Author(s): Andreas Tuerk, Gregor Wiktorin, Serhat Güler
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-017-16685-8

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics
Cited by: 7
Author(s): Nadia Boufaied, Christopher Nash, Annie Rochette, Anthony K. Smith, Brigid Orr, O. Cathal Grace, Yu Chang Wang, Dunarel Badescu, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 6
Published: almost 7 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

10.3390/genes12030385

Maternal Vitamin and Mineral Supplementation and Rate of Maternal Weight Gain Affects Placental Expression of Energy Metabolism and Transport-Related Genes
Cited by: 25
Author(s): Wellison J. S. Diniz, Lawrence P. Reynolds, P. P. Borowicz, Alison K Ward, Kevin K. Sedivec, Kacie L McCarthy, Cierrah J Kassetas, Friederike Baumgaertner, James D Kirsch, Sheri T. Dorsam, Tammi L Neville, J Chris Forcherio, Ronald Scott, J. S. Caton, Carl R Dahlen
Software Mentions: 5
Published: over 3 years ago

10.1093/gbe/evz280

Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae)
Cited by: 2
Author(s): Laramie L. Lindsey, Roy N. Platt, C. Douglas Phillips, David A. Ray, Robert D. Bradley
Software Mentions: 5
Published: almost 5 years ago

10.3390/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: about 4 years ago

10.1186/s13059-014-0527-7

The importance of study design for detecting differentially abundant features in high-throughput experiments
Cited by: 12
Author(s): Huaien Luo, Juntao Li, Burton Kuan Hui Chia, Paul Robson, Niranjan Nagarajan
Software Mentions: 5
Published: almost 10 years ago

10.18632/oncotarget.23206

Coagulation cascade and complement system in systemic lupus erythematosus
Cited by: 19
Author(s): Yan Liang, Shangbo Xie, Changhao Wu, Yuan Hu, Qin Zhang, Si Li, Yin‐Guang Fan, Rui‐Xue Leng, Hai‐Feng Pan, Huabao Xiong, Dong‐Qing Ye
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.42819

Shank3 modulates sleep and expression of circadian transcription factors
Cited by: 56
Author(s): Ashley M Ingiosi, Hannah Schoch, Taylor Wintler, Kristan G. Singletary, Dario Righelli, Leandro Gabriel Roser, E Medina, Davide Risso, Marcos G. Frank, Lucı́a Peixoto
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0124564

Differential Gene Expression Reveals Candidate Genes for Drought Stress Response in Abies alba (Pinaceae)
Cited by: 45
Author(s): David Behringer, Heike Zimmermann, Birgit Ziegenhagen, Sascha Liepelt
Software Mentions: 5
Published: over 9 years ago

10.3390/ijms21186488

Lipid Stores and Lipid Metabolism Associated Gene Expression in Porcine and Bovine Parthenogenetic Embryos Revealed by Fluorescent Staining and RNA-seq
Cited by: 16
Author(s): Arkadiusz Kajdasz, Ewelina Warzych, Natalia Derebecka, Zofia E. Madeja, D. Lechniak, Joanna Wesoły, Piotr Pawlak
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2164-15-141

Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation
Cited by: 40
Author(s): Wang Shou, Tomasz Furmanek, Harald Kryvi, Christel Krossøy, Geir K. Totland, Sindre Grotmol, Anna Wargelius
Software Mentions: 5
Published: over 10 years ago

10.1136/jitc-2020-001657

Regorafenib enhances antitumor immunity via inhibition of p38 kinase/Creb1/Klf4 axis in tumor-associated macrophages
Cited by: 52
Author(s): Da-Liang Ou, Chia Wei Chen, Chia‐Lang Hsu, Chih‐Hung Chung, Zi Rui Feng, Bin Shyun Lee, Ann Lii Cheng, Muh Hwa Yang, Chiun Hsu
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-66759-3

The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia
Cited by: 6
Author(s): Ximena Gómez‐Maqueo, Diana Soriano, Noé Velázquez-Rosas, Sandra Alvarado-López, Karina Jiménez‐Durán, María Del Mar Garciadiego, Alicia Gamboa‐deBuen
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2019.01427

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
Cited by: 11
Author(s): Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe‐Fadrosh, Paul Dijkstra, Brian P. Hedlund
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-017-17460-5

Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple
Cited by: 22
Author(s): Jiabin Wang, Zhiying Li, Ming Lei, Yuhua Fu, Jiaju Zhao, Meng-Fei Ao, Li Xu
Software Mentions: 5
Published: almost 7 years ago

10.1093/bioinformatics/btaa1063

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

10.1186/s13059-020-02028-w

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Cited by: 34
Author(s): Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue‐Agudo, Pablo Bonilla, Jeremy R.B. Newman, Shunichi Kosugi, Lauren McIntyre, Victoria Moreno‐Manzano, Ana Conesa
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0159093

Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex
Cited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0175464

Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cell transcriptomics
Cited by: 12
Author(s): Gianluca Mazzoni, Suraya Mohamad Salleh, Kristine Freude, Helene Helboe Pedersen, Lotte Stroebech, Henrik Callesen, Poul Hyttel, Haja N. Kadarmideen
Software Mentions: 5
Published: over 7 years ago

10.1098/rspb.2020.2244

Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation
Cited by: 3
Author(s): Devika Singh, Dan Sun, Andrew King, David E. Alquezar‐Planas, Rebecca N. Johnson, David Alvarez‐Ponce, Soojin V. Yi
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2164-14-586

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions
Cited by: 46
Author(s): Brian R. Johnson, Joel Atallah, David C. Plachetzki
Software Mentions: 4
Published: almost 12 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

10.1186/s12864-021-07790-0

A scaling-free minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
Cited by: 4
Author(s): Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu, Guo‐Liang Tian
Software Mentions: 4
Published: over 3 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: over 5 years ago

10.1080/07853890.2020.1858234

Increased expression of hypoxia-induced factor 1α mRNA and its related genes in myeloid blood cells from critically ill COVID-19 patients
Cited by: 40
Author(s): Keiko Taniguchi‐Ponciano, Eduardo Vadillo, Héctor Mayani, César González-Bonilla, Javier Torres, Abraham Majluf, Guillermo Flores‐Padilla, Niels H. Wacher, Juan Carlos Galán, Eduardo Ferat‐Osorio, Francisco Blanco-Favéla, Constantino López-Macı́as, Aldo Ferreira‐Hermosillo, Claudia Ramírez‐Rentería, Eduardo Peña-Martínez, Gloria Silva-Román, Sandra Vela-Patiño, Carlos Mata-Lozano, Roberto Carvente-Garcia, Lourdes Basurto-Acevedo, Renata Saucedo, Patricia Piña‐Sánchez, Antonieta Chávez‐González, Daniel Marrero‐Rodríguez, Moisés Mercado
Software Mentions: 4
Published: almost 4 years ago

10.1534/g3.118.200560

Mushroom Body Specific Transcriptome Analysis Reveals Dynamic Regulation of Learning and Memory Genes After Acquisition of Long-Term Courtship Memory in Drosophila
Cited by: 28
Author(s): Spencer G. Jones, Kevin C.J. Nixon, Melissa C. Chubak, Jamie M. Kramer
Software Mentions: 4
Published: about 6 years ago

10.1186/s40168-018-0404-9

Commensal microbiota modulate gene expression in the skin
Cited by: 126
Author(s): Jacquelyn S. Meisel, Georgia Sfyroera, Casey Bartow‐McKenney, Ciara Gimblet, Julia Bugayev, Joseph Horwinski, Brian Kim, Jonathan R. Brestoff, Amanda S. Tyldsley, Qi Zheng, Brendan P. Hodkinson, David Artis, Elizabeth A. Grice
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41368-018-0037-7

Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses
Cited by: 74
Author(s): Susan Yost, Philip Stashenko, Yoon-Hee Choi, Maria A. Kukuruzinska, Caroline A. Genco, Andrew Salama, Ellen O. Weinberg, Carolyn D. Kramer, Jorge Frias-Lopez
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.isci.2021.102807

Identification of response signatures for tankyrase inhibitor treatment in tumor cell lines
Cited by: 6
Author(s): Line Mygland, Jo Waaler, Martin Frank Strand, Petter Olsen, Aleksandra Aizenshtadt, Kaja Lund, Nina Solberg, Max Lycke, Tor Espen Thorvaldsen, Sandra Espada, Dorna Misaghian, Christian M. Page, Oleg Agafonov, Ståle Nygård, Nai‐Wen Chi, Eva Lin, Jenille Tan, Yihong Yu, Mike Costa, Stefan Krauß, Jo Waaler
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: about 5 years ago

10.1186/s13068-015-0248-5

Genome-wide analysis of the endoplasmic reticulum stress response during lignocellulase production in Neurospora crassa
Cited by: 52
Author(s): Fan Feng, Guoli Ma, Jingen Li, Qian Liu, J. Philipp Benz, Chaoguang Tian, Yanhe Ma
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-74564-1

ScatLay: utilizing transcriptome-wide noise for identifying and visualizing differentially expressed genes
Cited by: 5
Author(s): Thuy Tien Bui, Daniel Lee, Kumar Selvarajoo
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-017-17337-7

Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes
Cited by: 2
Author(s): Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F. Tsinoremas
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12915-017-0352-z

The landscape of sex-differential transcriptome and its consequent selection in human adults
Cited by: 180
Author(s): Moran Gershoni, Shmuel Pietrokovski
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2019.00210

Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle
Cited by: 23
Author(s): Wellison J. S. Diniz, Gianluca Mazzoni, Luiz Lehmann Coutinho, Priyanka Banerjee, Ludwig Geistlinger, Francesca Bertolini, Juliana Afonso, P. S. N. Oliveira, P. C. Tizioto, Haja N. Kadarmideen, Luciana Correia de Almeida Regitano
Software Mentions: 4
Published: over 5 years ago

10.1038/srep46553

Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism
Cited by: 60
Author(s): Ling Yin, Yunhe An, Junjie Qu, Xinlong Li, Yali Zhang, Ian B. Dry, Huijuan Wu, Jiang Lu
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2016.01416

Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild-Type Using Small RNA and Degradome Sequencing
Cited by: 19
Author(s): Juxun Wu, Saisai Zheng, Guizhi Feng, Hualin Yi
Software Mentions: 4
Published: about 8 years ago

10.1186/s12870-021-02956-0

Transcriptome architecture reveals genetic networks of bolting regulation in spinach
Cited by: 10
Author(s): Reza Abolghasemi, Maryam Haghighi, Nematollah Etemadi, Shui Wang, Aboozar Soorni
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-1853-1

RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
Cited by: 23
Author(s): Henriette Irmer, Sonia Tarazona, Christoph Sasse, Patrick Olbermann, Jürgen Loeffler, Sven Krappmann, Ana Conesa, Gerhard H. Braus
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-020-6586-0

Loci associated with variation in gene expression and growth in juvenile salmon are influenced by the presence of a growth hormone transgene
Cited by: 5
Author(s): Erin K. McClelland, Michelle Chan, Xiang Lin, Dionne Sakhrani, Felicia Vincelli, Jin-Hyoung Kim, Daniel D. Heath, Robert H. Devlin
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-019-5452-4

Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds
Cited by: 16
Author(s): Per K.I. Wilhelmsson, Jake O. Chandler, Noé Fernandez-Pozo, Kai Graeber, Kristian K. Ullrich, Waheed Arshad, Safina Khan, Johannes A. Hofberger, Karl Buchta, Patrick P. Edger, J. Chris Pires, M. Eric Schranz, Gerhard Leubner‐Metzger, Stefan A. Rensing
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.cell.2016.05.029

Dynamic Axonal Translation in Developing and Mature Visual Circuits
Cited by: 345
Author(s): Toshiaki Shigeoka, Hosung Jung, Jane Jung, Benita Turner-Bridger, Jiyeon Ohk, Julie Qiaojin Lin, Paul S. Amieux, Christine E. Holt
Software Mentions: 3
Published: over 8 years ago

10.1038/srep23219

Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data
Cited by: 42
Author(s): Kai Xing, Feng Zhu, Lichao Zhai, ShaoKang Chen, Zhen Tan, Yangyang Sun, Zhuocheng Hou, ChuDuan Wang
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-744

Transcriptome differences in the hypopharyngeal gland between Western Honeybees (Apis mellifera) and Eastern Honeybees (Apis cerana)
Cited by: 26
Author(s): Hao Líu, Zilong Wang, Li Tian, Qiuhong Qin, Xiaobo Wu, Yan Wei, Zhen Zeng
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0126143

The Intraperitoneal Transcriptome of the Opportunistic Pathogen Enterococcus faecalis in Mice
Cited by: 29
Author(s): Cécile Muller, Margherita Cacaci, Nicolas Sauvageot, Maurizio Sanguinetti, Thomas Rattei, Thomas Eder, Jean‐Christophe Giard, Jörn Kalinowski, Torsten Hain, Axel Hartke
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-019-6229-5

Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae
Cited by: 14
Author(s): Marco Tulio Solano-De la Cruz, Jacel Adame-García, Josefat Gregorio-Jorge, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Lourdes Georgina Iglesias-Andreu, Esteban Elías Escobar-Hernández, Mauricio Luna-Rodríguez
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0122396

Integration of Transcriptome and Whole Genomic Resequencing Data to Identify Key Genes Affecting Swine Fat Deposition
Cited by: 19
Author(s): Kai Xing, Feng Zhu, Lichao Zhai, Huijie Liu, Yuan Wang, Zhijun Wang, Shaokang Chen, Zhuocheng Hou, Chuduan Wang
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0196913

Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens
Cited by: 36
Author(s): Emily Prendergast, Marcos Abraão de Souza Fonseca, Felipe Segato Dezem, Jenny Lester, Beth Y. Karlan, Houtan Noushmehr, Xianzhi Lin, Kate Lawrenson
Software Mentions: 3
Published: over 6 years ago

10.1186/s12983-017-0245-6

Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics
Cited by: 17
Author(s): Yalin Cheng, Bin Gao, Haitao Wang, Ning Han, Shimiao Shao, Shaoyuan Wu, Gang Song, Yong E. Zhang, Zhu Xihua, Xin Lü, Yanhua Qu, Fumin Lei
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2105-14-S9-S1

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Cited by: 84
Author(s): Xiao Xu, Yuanhao Zhang, Jennie L. Williams, Eric Antoniou, W. Richard McCombie, Song Wu, Wei Zhu, Nicholas O. Davidson, Paula Denoya, Ellen Li
Software Mentions: 3
Published: over 11 years ago

Projects: bioconductor: NOISeq

Papers Mentioning NOISeq 321