bioconductor: maSigPro | Projects

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

10.7554/eLife.58993

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns
Cited by: 23
Author(s): Kathleen Greenham, Ryan C. Sartor, Stevan Zorich, Ping Lou, Todd C. Mockler, C. Robertson McClung
Software Mentions: 12
Published: about 4 years ago

10.7554/eLife.66738

Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave
Cited by: 15
Author(s): Lindsay A. Hohsfield, Allison R. Najafi, Yasamine Ghorbanian, Neelakshi Soni, Joshua Crapser, Dario X. Figueroa Velez, Shan Jiang, Sarah E Royer, Sung Jin Kim, Caden M Henningfield, Aileen J. Anderson, Sunil Gandhi, A Mortazavi, Matthew A. Inlay, Kim N. Green
Software Mentions: 12
Published: about 3 years ago

10.3390/genes12030352

Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data
Cited by: 10
Author(s): Vera-Khlara S. Oh, Robert W. Li
Software Mentions: 12
Published: over 3 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

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 12 years ago

10.1038/s41598-017-06110-5

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
Cited by: 10
Author(s): Brian Gloss, Bethany Signal, Seth W. Cheetham, Franziska Gruhl, Dominik C. Kaczorowski, Andrew C. Perkins, Marcel E. Dinger
Software Mentions: 10
Published: over 7 years ago

10.1186/s12915-018-0518-3

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Cited by: 21
Author(s): Angelika Schmidt, Francesco Marabita, Narsis A. Kiani, Catharina C. Groß, Henrik J. Johansson, Szabolcs Éliás, Sini Rautio, Matilda Eriksson, Sunjay Jude Fernandes, Gilad Silberberg, Ubaid Ullah, Urvashi Bhatia, Harri Lähdesmäki, Janne Lehtiö, David Gomez-Cabrero, Heinz Wiendl, Riitta Lahesmaa, Jesper Tegnér
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pgen.1008754

Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei
Cited by: 24
Author(s): Shan Jiang, Katherine Williams, Xiangduo Kong, Weihua Zeng, Nam Viet Nguyen, Xinyi Ma, Rabi Tawil, Kyoko Yokomori, A Mortazavi
Software Mentions: 8
Published: over 4 years ago

10.1186/s12859-018-2370-4

GPrank: an R package for detecting dynamic elements from genome-wide time series
Cited by: 7
Author(s): Hande Topa, Antti Honkela
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-016-1180-9

Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
Cited by: 21
Author(s): Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, Ping Ma
Software Mentions: 7
Published: about 8 years ago

10.1186/s40246-015-0050-2

A survey of computational tools for downstream analysis of proteomic and other omic datasets
Cited by: 17
Author(s): Anis Karimpour-Fard, L. Elaine Epperson, Lawrence Hunter
Software Mentions: 7
Published: about 9 years ago

10.1186/s12864-021-07593-3

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Cited by: 23
Author(s): Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-017-4304-3

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

10.7554/eLife.30860

A high-resolution mRNA expression time course of embryonic development in zebrafish
Cited by: 218
Author(s): Richard White, John Collins, Ian Sealy, Neha Wali, Christopher M. Dooley, Zsofia Digby, Derek L. Stemple, Daniel N. Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J. Enright, Elisabeth M Busch-Nentwich
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41598-018-37397-7

Temporal dynamics in meta longitudinal RNA-Seq data
Cited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
Software Mentions: 6
Published: almost 6 years ago

10.1128/mBio.01007-20

The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea
Cited by: 15
Author(s): Cynthia L. Darnell, Jenny Z. Zheng, Sean Wilson, R Bertoli, Alexandre W. Bisson‐Filho, Edward B. Garner, Amy K. Schmid
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0132798

Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration
Cited by: 20
Author(s): Lulu Huang, Sagar S. Damle, Sheri Booten, Priyam Singh, Mahyar Sabripour, Jeff Hsu, Minji Jo, Melanie Katz, Andy Watt, Christopher E. Hart, Susan M. Freier, Brett P. Monia, Shuling Guo
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0210467

Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets
Cited by: 0
Author(s): Katerina Taškova, Jean-Fred Fontaine, Ralf Mrowka, Miguel A. Andrade‐Navarro
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12864-020-6502-7

Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies
Cited by: 23
Author(s): Xiaohong Li, Nigel G. F. Cooper, Timothy E. O’Toole, Eric C. Rouchka
Software Mentions: 6
Published: almost 5 years ago

10.1534/g3.119.400180

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome
Cited by: 12
Author(s): Lorrayne Serra, Marissa Macchietto, Aide Macias-Muñoz, Cassandra McGill, Isaryhia Rodriguez, Bryan Rodriguez, Rabi Murad, A Mortazavi
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2019.00974

Identifying the Growth Modulon of Corynebacterium glutamicum
Cited by: 8
Author(s): Thorsten Haas, Michaela Graf, Alexander Nieß, Tobias Busche, Jörn Kalinowski, Bastian Blombach, Ralf Takors
Software Mentions: 6
Published: over 5 years ago

10.1016/j.devcel.2021.02.007

Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization
Cited by: 15
Author(s): Fabio M D'Orazio, Piotr J. Balwierz, Ada Jimenez González, Yixuan Guo, Benjamín Hernández-Rodríguez, Lucy Wheatley, Aleksandra Jasiulewicz, Yavor Hadzhiev, Juan M. Vaquerizas, Bradley R. Cairns, Boris Lenhard, Ferenc Müller
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-74748-9

Dynamic changes in the brain protein interaction network correlates with progression of Aβ42 pathology in Drosophila
Cited by: 6
Author(s): Harry M. Scholes, Adam Cryar, Fiona Kerr, David Sutherland, Lee A. Gethings, Johannes P.C. Vissers, Jonathan G. Lees, Christine A. Orengo, Linda Partridge, Konstantinos Thalassinos
Software Mentions: 5
Published: about 4 years ago

10.1038/s41438-019-0146-2

Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard
Cited by: 31
Author(s): Zoë Migicovsky, Zachary N. Harris, Laura L. Klein, Mao Li, Adam McDermaid, Daniel H. Chitwood, Anne Fennell, László Kovács, Misha T. Kwasniewski, Jason P. Londo, Qin Ma, Allison J. Miller
Software Mentions: 5
Published: over 5 years ago

10.3389/fpls.2020.00132

Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes
Cited by: 9
Author(s): Miguel A. Flores‐Vergara, Elen Oneal, Mário Costa, Gonzalo H. Villarino, Caitlyn Roberts, María Angels de Luis Balaguer, Sı́lvia Coimbra, John H. Willis, Robert G. Franks
Software Mentions: 5
Published: over 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

10.1098/rsob.160224

Interplay between RNA interference and heat shock response systems in Drosophila melanogaster
Cited by: 9
Author(s): S. Yu. Funikov, Sergei Ryazansky, Alexander Kanapin, Maria D. Logacheva, Aleksey A. Penin, А. В. Снежкина, Victoria Shilova, Д. Г. Гарбуз, Michael B. Evgen’ev, Olga G. Zatsepina
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-019-3072-2

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
Cited by: 3
Author(s): Hongryul Ahn, Il Bong Jung, Han–Jung Chae, Dong‐Won Kang, Wi Hoon Jung, Sun Kim
Software Mentions: 4
Published: almost 5 years ago

10.1093/bioinformatics/btu274

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Cited by: 64
Author(s): Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki
Software Mentions: 4
Published: over 10 years ago

10.3389/fgene.2021.650874

Investigating Transcriptional Dynamics Changes and Time-Dependent Marker Gene Expression in the Early Period After Skeletal Muscle Injury in Rats
Cited by: 6
Author(s): Kangning Ren, Liangliang Wang, Liang Wang, Qiu-xiang Du, Jie Cao, Qianqian Jin, Guo-shuai An, Na Li, Li-hong Dang, Yingjie Tian, Ying-Yuan Wang, Jun-hong Sun
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.668045

Multi-Omics Approaches in Immunological Research
Cited by: 16
Author(s): Xiaojing Chu, Bowen Zhang, Valerie A. C. M. Koeken, Manoj Kumar Gupta, Yang Li
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1006302

Activated entomopathogenic nematode infective juveniles release lethal venom proteins
Cited by: 87
Author(s): Dihong Lu, Marissa Macchietto, Dennis Chang, Mirayana M. Barros, J. G. Baldwin, A Mortazavi, Adler R. Dillman
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-90540-9

Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)
Cited by: 3
Author(s): Candace J. Grimes, Lene H. Petersen, Anja Schulze
Software Mentions: 4
Published: over 3 years ago

10.1007/s00109-014-1212-8

Transcriptomic profiling facilitates classification of response to influenza challenge
Cited by: 34
Author(s): Emma E Davenport, Richard Antrobus, Patrick Lillie, Sarah C. Gilbert, Julian C. Knight
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0205968

MetaboClust: Using interactive time-series cluster analysis to relate metabolomic data with perturbed pathways
Cited by: 12
Author(s): Martin Rusilowicz, Mike Dickinson, Adrian J. Charlton, Simon O’Keefe, Julie Wilson
Software Mentions: 3
Published: about 6 years ago

10.1128/mBio.02347-19

Remasking of Candida albicans β-Glucan in Response to Environmental pH Is Regulated by Quorum Sensing
Cited by: 34
Author(s): Fabien Cottier, Sarah Sherrington, Sarah Cockerill, Valentina del Olmo Toledo, Stephen Kissane, Hélène Tournu, Luisa Orsini, Glen E. Palmer, J. Christian Pérez, Rebecca Hall
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-12-13

A Platform for Processing Expression of Short Time Series (PESTS)
Cited by: 16
Author(s): Ayan Sinha, Marianthi Markatou
Software Mentions: 3
Published: almost 14 years ago

10.1038/srep44605

MicroRNA roles in signalling during lactation: an insight from differential expression, time course and pathway analyses of deep sequence data
Cited by: 65
Author(s): Duy Ngoc, Ran Li, Pier-Luc Dudemaine, Eveline M. Ibeagha‐Awemu
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-S3-S1

Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers
Cited by: 19
Author(s): Federica Riccardo, Maddalena Arigoni, Genny Buson, Elisa Zago, Manuela Iezzi, Dario Livio Longo, Matteo Carrara, Alessandra Fiore, Simona Nuzzo, Silvio Bicciato, Patrizia Nanni, Lorena Landuzzi, Federica Cavallo, Raffaele Calogero, Elena Quaglino
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-16-S6-S2

FunPat: function-based pattern analysis on RNA-seq time series data
Cited by: 56
Author(s): Tiziana Sanavia, Francesca Finotello, Barbara Di Camillo
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-017-4389-8

Time-course transcriptome analysis of human cellular reprogramming from multiple cell types reveals the drastic change occurs between the mid phase and the late phase
Cited by: 9
Author(s): Akihiro Kuno, Ken Nishimura, Satoru Takahashi
Software Mentions: 3
Published: almost 7 years ago

10.1530/REP-18-0270

Dynamic changes in gene expression and signalling during trophoblast development in the horse
Cited by: 10
Author(s): Jordan E. Read, Victoria Cabrera-Sharp, Victoria Offord, Samantha Mirczuk, Steve Allen, Robert C. Fowkes, Amanda M. de Mestre
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.ppat.1009395

Type I IFNs facilitate innate immune control of the opportunistic bacteria Burkholderia cenocepacia in the macrophage cytosol
Cited by: 6
Author(s): Michael G. Dorrington, Clinton Bradfield, Justin Lack, Bin Lin, Jonathan J. Liang, Tregei Starr, Orna Ernst, Julia L. Gross, Jing Sun, Alexandra H. Miller, Olivia Steele‐Mortimer, Iain D. C. Fraser
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009679

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Cited by: 16
Author(s): Enrique Audain, Anna Wilsdon, Jeroen Breckpot, Jose M. G. Izarzugaza, Tomas Fitzgerald, Anne‐Karin Kahlert, Alejandro Sifrim, Florian Wünnemann, Yasset Perez‐Riverol, Hashim Abdul‐Khaliq, Mads Bak, Anne S. Bassett, Woodrow Benson, Felix Berger, Ingo Daehnert, Koenraad Devriendt, Sven Dittrich, Piers E.F. Daubeney, Vidu Garg, Karl Hackmann, Kirstin Hoff, Philipp Hofmann, Gregor Dombrowsky, Thomas Pickardt, Ulrike Bauer, Bernard Keavney, Sabine Klaassen, Hans‐Heiner Kramer, Christian R. Marshall, Dianna M. Milewicz, Scott A. LeMaire, Joseph S. Coselli, Michael E. Mitchell, Aoy Tomita‐Mitchell, Siddharth K. Prakash, Karl Stamm, Alexandre F.R. Stewart, Candice K. Silversides, Reiner Siebert, Brigitte Stiller, Jill A. Rosenfeld, Inga Vater, Alex V. Postma, Almuth Caliebe, J. David Brook, Grégor Andelfinger, Matthew E. Hurles, Bernard Thienpont, Lars Allan Larsen, Marc‐Phillip Hitz
Software Mentions: 3
Published: over 3 years ago

10.3389/fbioe.2020.584614

Revisiting the Growth Modulon of Corynebacterium glutamicum Under Glucose Limited Chemostat Conditions
Cited by: 5
Author(s): Michaela Graf, Thorsten Haas, Attila Teleki, André Feith, Martin Cerff, Wolfgang Wiechert, Katharina Nöh, Tobias Busche, Jörn Kalinowski, Ralf Takors
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.ppat.1007626

A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema
Cited by: 52
Author(s): Dennis Chang, Lorrayne Serra, Dihong Lu, A Mortazavi, Adler R. Dillman
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-017-3743-1

Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python
Cited by: 30
Author(s): Audra L. Andrew, Blair W. Perry, Daren C. Card, Drew R. Schield, Robert P. Ruggiero, Suzanne E. McGaugh, Amit Choudhary, Stephen M. Secor, Todd A. Castoe
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0184838

A set of nutrient limitations trigger yeast cell death in a nitrogen-dependent manner during wine alcoholic fermentation
Cited by: 40
Author(s): Camille Duc, Martine Pradal, Isabelle Sanchez, Jessica Noble, Catherine Tesnière, Bruno Blondin
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.26851

Molecular architecture underlying fluid absorption by the developing inner ear
Cited by: 35
Author(s): Keiji Honda, Sung Huhn Kim, Michael C. Kelly, J. C. Burns, Laura A. Constance, Xiangming Li, Fei Zhou, Michael Hoa, Matthew W. Kelley, Philine Wangemann, Robert J. Morell, Andrew J. Griffith
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-019-3221-7

Longitudinal linear combination test for gene set analysis
Cited by: 2
Author(s): Elham Khodayari Moez, Morteza Hajihosseini, Jeffrey L. Andrews, Irina Dinu
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-9-415

BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments
Cited by: 53
Author(s): Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky
Software Mentions: 3
Published: about 16 years ago

10.1186/s12864-015-1646-6

Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines
Cited by: 91
Author(s): Dirkjan Schokker, Gosse Veninga, S.A. Vastenhouw, Alex Bossers, F.M. de Bree, L.M.T.E. Kaal-Lansbergen, Johanna M.J. Rebel, M.A. Smits
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0232146

Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel
Cited by: 3
Author(s): Sònia Segura, Alejandra Gadea, Lara Nonell, Evelyn Andrades, Sílvia Sánchez, Ramón M. Pujol, Inmaculada Hernández-Muñoz, Agustí Toll
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2229-9-67

Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set
Cited by: 39
Author(s): Laura Pascual, José Blanca, Joaquı́n Cañizares, Fernado Nuez
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0200783

Amino acid deprivation triggers a novel GCN2-independent response leading to the transcriptional reactivation of non-native DNA sequences
Cited by: 6
Author(s): Annarosaria De Vito, Massimo Lazzaro, Ilaria Palmisano, Davide Cittaro, Michela Riba, Dejan Lazarevic, Makoto Bannai, Davide Gabellini, Maria Vittoria Schiaffino
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-019-1651-z

Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness
Cited by: 21
Author(s): Javier Terol, María José Nueda, Daniel Ventimilla, Francisco R. Tadeo, Manuel Talón
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2229-11-159

Fortunella margarita Transcriptional Reprogramming Triggered by Xanthomonas citri subsp. citri
Cited by: 22
Author(s): Abeer Khalaf, Frederick G. Gmitter, Ana Conesa, Joaquı́n Dopazo, Gloria A. Moore
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-15-114

Drechslerella stenobrocha genome illustrates the mechanism of constricting rings and the origin of nematode predation in fungi
Cited by: 66
Author(s): Keke Liu, Weiwei Zhang, Yiling Lai, Meichun Xiang, Xiuna Wang, Xinyu Zhang, Xingzhong Liu
Software Mentions: 2
Published: almost 11 years ago

10.1093/bioinformatics/btu333

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
Cited by: 254
Author(s): María José Nueda, Sonia Tarazona, Ana Conesa
Software Mentions: 2
Published: over 10 years ago

10.3390/biology9120470

Inhibition of FGF and TGF-β Pathways in hESCs Identify STOX2 as a Novel SMAD2/4 Cofactor
Cited by: 2
Author(s): Peter F. Renz, Daniel Spies, Panagiota Tsikrika, Anton Wutz, Tobias A. Beyer, Constance Ciaudo
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13024-017-0210-z

Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss
Cited by: 58
Author(s): Michael Hernandez, Shan Jiang, Tracy Cole, Shu Hui Chu, María Isabel Fonseca, Melody J. Fang, Lindsay A. Hohsfield, M.D. Martínez del Valle Torres, Kim N. Green, Rick A. Wetsel, A Mortazavi, Andrea J. Tenner
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pbio.2006506

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation
Cited by: 7
Author(s): Isabel Ferreirós-Vidal, Thomas Carroll, Tianyi Zhang, Vincenzo Lagani, Ricardo N. Ramirez, Elizabeth Ing-Simmons, Alícia G. Gómez-Valadés, Lee Cooper, Ziwei Liang, Γεώργιος Παπουτσόγλου, Gopuraja Dharmalingam, Ya Guo, Sonia Tarazona, Sunjay Jude Fernandes, Peri Noori, Gilad Silberberg, Amanda G. Fisher, Ioannis Tsamardinos, A Mortazavi, Boris Lenhard, Ana Conesa, Jesper Tegnér, Matthias Merkenschlager, David Gomez-Cabrero
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-016-2772-5

Transcriptomic profiling of Melon necrotic spot virus-infected melon plants revealed virus strain and plant cultivar-specific alterations
Cited by: 10
Author(s): Cristina Gómez‐Aix, Laura Pascual, Joaquı́n Cañizares, M. Amelia Sánchez-Pina, Miguel A. Aranda
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0121522

Chronic Ethanol Exposure Produces Time- and Brain Region-Dependent Changes in Gene Coexpression Networks
Cited by: 70
Author(s): Elizabeth A. Osterndorff-Kahanek, Howard C. Becker, Marcelo F. López, Sean P. Farris, Gayatri R. Tiwari, Yury O. Nunez, R. Adron Harris, R. Dayne Mayfield
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0087680

Transcriptomic Profiling of the Development of the Inflammatory Response in Human Monocytes In Vitro
Cited by: 72
Author(s): Paola Italiani, Emilia Maria Cristina Mazza, Davide Lucchesi, Ingrid Cifola, Claudia Gemelli, Alexis Grande, Cristina Battaglia, Silvio Bicciato, Diana Boraschi
Software Mentions: 2
Published: almost 11 years ago

10.1038/s42003-021-02384-8

A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina
Cited by: 18
Author(s): Purushothaman Natarajan, Ashok Kumar Murugesan, Ganesan Govindan, Ayyaru Gopalakrishnan, Ravichandiran Kumar, Purushothaman Duraisamy, Raju Balaji, Tanuja Tanuja, P. Sushree Shyamli, Ajay Parida, Madasamy Parani
Software Mentions: 2
Published: over 3 years ago

10.12688/f1000research.9093.1

Cluster analysis of Plasmodium RNA-seq time-course data identifies stage-specific co-regulated biological processes and regulatory elements
Cited by: 1
Author(s): Efejiro Ashano, Itunuoluwa Isewon, Jelili Oyelade, Ezekiel Adebiyi
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2019.00814

Transcriptome Sequencing Unravels Potential Biomarkers at Different Stages of Cerebral Ischemic Stroke
Cited by: 17
Author(s): Yuanheng Cai, Yufen Zhang, Xiao Ke, Yu Guo, Chengye Yao, Na Tang, Pei Pang, Gangcai Xie, Fang Li, Zhe Zhang, Jincheng Li, Yixian Fan, Ximiao He, Ruojian Wen, Lei Pei, Youming Lu
Software Mentions: 2
Published: about 5 years ago

10.3390/antibiotics10080947

Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens
Cited by: 3
Author(s): Eva Pinatel, Matteo Calcagnile, Adelfia Talà, Fabrizio Damiano, Luisa Siculella, Clelia Peano, Giuseppe E. De Benedetto, Antonio Pennetta, Gianluca De Bellis, Pietro Alifano
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2017.00835

Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens
Cited by: 13
Author(s): Marco Fondi, Eva Pinatel, Adelfia Talà, Fabrizio Damiano, Clarissa Consolandi, Benedetta Mattorre, Daniela Fico, Mariangela Testini, Giuseppe E. De Benedetto, Luisa Siculella, Gianluca De Bellis, Pietro Alifano, Clelia Peano
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.00361

ArgR of Streptomyces coelicolor Is a Pleiotropic Transcriptional Regulator: Effect on the Transcriptome, Antibiotic Production, and Differentiation in Liquid Cultures
Cited by: 17
Author(s): Alma Botas, Rosario Pérez‐Redondo, Antonio Rodríguez‐García, Rubén Álvarez-Álvarez, Paula Yagüe, Ángel Manteca, Paloma Liras
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2021.666660

Comparative Transcriptome Analysis of Salt Stress-Induced Leaf Senescence in Medicago truncatula
Cited by: 15
Author(s): Shihao Dong, Lijun Sang, Hong Xie, Maofeng Chai, Zeng‐Yu Wang
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2018.02000

Altered Gene Regulatory Networks Are Associated With the Transition From C3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae)
Cited by: 27
Author(s): Karolina Heyduk, Michelle Hwang, Victor A. Albert, Katia Silvera, Tianying Lan, Kimberly M. Farr, Tien-Hao Chang, Ming‐Tsair Chan, Klaus Winter, Jim Leebens‐Mack
Software Mentions: 2
Published: almost 6 years ago

10.3389/fpls.2016.02007

Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola
Cited by: 30
Author(s): Heng Wan, Yixin Cui, Yijuan Ding, Jiaqin Mei, Hongli Dong, Wenxin Zhang, Shiqi Wu, Ying Liang, Chunyu Zhang, Jiana Li, Qing Xiong, Wei Qian
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-020-07140-6

Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection
Cited by: 4
Author(s): François O. Seneca, David Davtian, Laurent Boyer, Dorota Czerucka
Software Mentions: 2
Published: almost 4 years ago

10.1534/g3.115.021261

Developmental Transcriptome for a Facultatively Eusocial Bee,Megalopta genalis
Cited by: 17
Author(s): Beryl M. Jones, William T. Wcislo, Gene E. Robinson
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2121-10-87

Global transcriptional response after exposure of fission yeast cells to ultraviolet light
Cited by: 6
Author(s): Henriette C. Skjølberg, Øyvind Fensgård, Hilde Nilsen, Beáta Grallert, Erik Boye
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2105-9-542

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
Cited by: 66
Author(s): Mi-Youn Brusniak, Bernd Bodenmiller, D. S. Campbell, Kelly Cooke, James S. Eddes, Andrew Garbutt, Hollis Lau, Simon Letarte, Lukas Mueller, Vagisha Sharma, Olga Vitek, Ning Zhang, Ruedi Aebersold, Julian D. Watts
Software Mentions: 2
Published: almost 16 years ago

10.1093/gbe/evu241

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis
Cited by: 48
Author(s): Yiling Lai, Keke Liu, Xinyu Zhang, Xiaoling Zhang, Kuan Li, Niuniu Wang, Chi Shu, Yunpeng Wu, Chengshu Wang, Kathryn E. Bushley, Meichun Xiang, Xingzhong Liu
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-11-36

Quantitative model for inferring dynamic regulation of the tumour suppressor gene p53
Cited by: 16
Author(s): Junbai Wang, Tianhai Tian
Software Mentions: 2
Published: almost 15 years ago

10.3390/ijms20051245

Developmental Stage- and Genotype-Dependent Regulation of Specialized Metabolite Accumulation in Fruit Tissues of Different Citrus Varieties
Cited by: 8
Author(s): Roya Nadi, Behrouz Golein, Aurelio Gómez‐Cadenas, Vicent Arbona
Software Mentions: 2
Published: over 5 years ago

10.1038/srep03512

Identification of novel modifiers of Aβ toxicity by transcriptomic analysis in the fruitfly
Cited by: 21
Author(s): Giorgio Favrin, Daniel Bean, Elizabeth Bilsland, Hélène Boyer, Bettina Fischer, Steven Russell, Damian C. Crowther, H. A. Baylis, Stephen G. Oliver, Maria E. Giannakou
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep35064

Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection
Cited by: 24
Author(s): Zhenhong Jiang, Xiaobao Dong, Zhigang Li, Fei He, Ziding Zhang
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2105-15-333

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies
Cited by: 88
Author(s): Mohammad Ali Moni, Píetro Lió
Software Mentions: 2
Published: about 10 years ago

10.1038/s41598-020-61064-5

Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening
Cited by: 12
Author(s): Jianhua Zhao, Haoxia Li, Yue Yin, Wei An, Xiaoya Qin, Yajun Wang, Yanlong Li, Yunfang Fan, Yang Cao
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-021-04052-4

Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles
Cited by: 1
Author(s): Arika Fukushima, Masahiro Sugimoto, Satoru Hiwa, Tomoyuki Hiroyasu
Software Mentions: 2
Published: over 3 years ago

10.3390/jof7090758

Global Transcriptome Profile of the Oleaginous Yeast Saitozyma podzolica DSM 27192 Cultivated in Glucose and Xylose
Cited by: 8
Author(s): Habibu Aliyu, Olga Gorte, Anke Neumann, Katrin Ochsenreither
Software Mentions: 2
Published: about 3 years ago

10.1186/s12864-015-1733-8

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets
Cited by: 7
Author(s): Nirupama Benis, Dirkjan Schokker, María Suárez-Diez, Vítor A. P. Martins dos Santos, Hauke Smidt, M.A. Smits
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-14-372

Distinct transcriptome profiles identified in normal human bronchial epithelial cells after exposure to γ-rays and different elemental particles of high Z and energy
Cited by: 51
Author(s): Liang Ding, Seong‐Mi Park, Michael Peyton, Luc Girard, Yang Xie, John D. Minna, Michael D. Story
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.ppat.1009228

Interferon signaling suppresses the unfolded protein response and induces cell death in hepatocytes accumulating hepatitis B surface antigen
Cited by: 11
Author(s): Ian Baudi, Masanori Isogawa, Federica Moalli, Mai Onishi, Keigo Kawashima, Yuji Ishida, Chise Tateno, Yusuke Sato, Hideyoshi Harashima, Hiroyasu Ito, Tetsuya Ishikawa, Takaji Wakita, Matteo Iannacone, Yasuhito Tanaka
Software Mentions: 1
Published: over 3 years ago

10.1016/j.csbj.2015.07.001

Circadian systems biology: When time matters
Cited by: 61
Author(s): Luise Fuhr, Marconi Abreu, J. Patrick Pett, Angela Relógio
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0229843

Effects of day length- and temperature-regulated genes on annual transcriptome dynamics in Japanese cedar (Cryptomeria japonica D. Don), a gymnosperm indeterminate species
Cited by: 12
Author(s): Masato Nose, Masayuki Kurita, Miho Tamura, Michinari Matsushita, Yuichiro Hiraoka, Taiichi Iki, So Hanaoka, Kentaro Mishima, Miyoko Tsubomura, Atsushi Watanabe
Software Mentions: 1
Published: over 4 years ago

10.1038/srep28693

Mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M) and serine biosynthetic pathway genes are co-ordinately increased during anabolic agent-induced skeletal muscle growth
Cited by: 26
Author(s): David M. Brown, Hannah Williams, Kevin J. Ryan, Thomas L. Wilson, Zoe Daniel, Molebeledi Horatius Dambe Mareko, Richard D. Emes, Douglas W. Harris, Sarah J. Jones, Jonathan A. D. Wattis, Ian L. Dryden, T. C. Hodgman, John M. Brameld, Tim Parr
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pbio.2005354

Symptoms of systemic lupus erythematosus are diagnosed in leptin transgenic pigs
Cited by: 11
Author(s): Junchen Chen, Weiqi Zeng, Weirong Pan, Cong Peng, Jianglin Zhang, Juan Su, Weihu Long, Heng Zhao, Xiaoxia Zuo, Xiaoyun Xie, Jing Wu, Ling Nie, Hongyan Zhao, Hong‐Jiang Wei, Xiang Chen
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-13-S2-S2

CMRF: analyzing differential gene regulation in two group perturbation experiments
Cited by: 0
Author(s): Nirmalya Bandyopadhyay, Manas Somaiya, Sanjay Ranka, Tamer Kahveci
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-017-00651-5

Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation
Cited by: 24
Author(s): Marta E. Polak, Chuin Ying Ung, Joanna Masapust, Tom C. Freeman, Michael R. Ardern‐Jones
Software Mentions: 1
Published: over 7 years ago

10.3389/fgene.2020.00570

MiRNA Profiling in Pectoral Muscle Throughout Pre- to Post-Natal Stages of Chicken Development
Cited by: 12
Author(s): Min Chen, Shaolan Zhang, Zhongxian Xu, Jian Gao, Suchismita Mishra, Qing Zhu, Xiaoling Zhao, Yan Wang, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Deying Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Diyan Li
Software Mentions: 1
Published: over 4 years ago

10.5713/ajas.18.0648

Metabolomic approach to key metabolites characterizing postmortem aged loin muscle of Japanese Black (Wagyu) cattle
Cited by: 32
Author(s): Susumu Muroya, Mika Oe, Koichi Ojima, Akira Watanabe
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: maSigPro

Papers Mentioning maSigPro 119