bioconductor: biomaRt | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: about 16 years ago

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.7554/eLife.43966

Unified single-cell analysis of testis gene regulation and pathology in five mouse strains
Cited by: 91
Author(s): Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon Myers, Donald F. Conrad
Software Mentions: 22
Published: over 5 years ago

10.3389/fimmu.2021.632333

Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic Mice
Cited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: almost 4 years ago

10.3390/cancers13092163

Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Ariane L. Moore, Aashil A. Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Software Mentions: 20
Published: over 3 years ago

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: about 14 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.3389/fimmu.2020.01691

Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human Malignancies
Cited by: 22
Author(s): Tony Yao, Parisa Shooshtari, S. M. Mansour Haeryfar
Software Mentions: 18
Published: over 4 years ago

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: almost 8 years ago

10.1038/s41597-019-0171-x

A multi-omics digital research object for the genetics of sleep regulation
Cited by: 8
Author(s): Jan M, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xénarios
Software Mentions: 17
Published: about 5 years ago

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: over 3 years ago

10.1186/s13059-021-02335-w

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: over 3 years ago

10.1371/journal.pgen.1008927

On the cross-population generalizability of gene expression prediction models
Cited by: 34
Author(s): Kevin L. Keys, Angel C. Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. LeNoir, Jimmie C. Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard, Christopher R. Gignoux
Software Mentions: 16
Published: over 4 years ago

10.1038/s41598-020-69683-8

Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiation
Cited by: 5
Author(s): Nicholas Holzscheck, Jörn Söhle, T. Schläger, Cassandra Falckenhayn, Elke Grönniger, Ludger Kolbe, Horst Wenck, Lara Terstegen, Lars Kaderali, Marc Winnefeld, Katharina Gorges
Software Mentions: 16
Published: over 4 years ago

10.1186/s12859-016-0971-3

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
Cited by: 20
Author(s): Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew Parnell, Stephen V. Gordon, David E. MacHugh
Software Mentions: 14
Published: almost 9 years ago

10.1371/journal.pcbi.1009317

Meta-analysis of transcriptomic data reveals clusters of consistently deregulated gene and disease ontologies in Down syndrome
Cited by: 11
Author(s): Ilario De Toma, Cesar Sierra, Mara Dierssen
Software Mentions: 14
Published: about 3 years ago

10.1186/s13072-020-00342-y

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Cited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: over 4 years ago

10.12688/f1000research.10742.2

haploR: an R package for querying web-based annotation tools
Cited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: over 7 years ago

10.7554/eLife.07836

Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence
Cited by: 158
Author(s): Michael J. Steinbaugh, Sri Devi Narasimhan, Stacey Robida-Stubbs, Lorenza E Moronetti Mazzeo, Jonathan M. Dreyfuss, John M. Hourihan, Prashant Raghavan, Theresa N. Operaña, Reza Esmaillie, T. Keith Blackwell
Software Mentions: 13
Published: over 9 years ago

10.3934/mbe.2020007

Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis
Cited by: 1
Author(s): Yonghua Zhuang, Kristen J. Wade, Laura Saba, Katerina Kechris
Software Mentions: 13
Published: almost 5 years ago

10.7554/eLife.50087

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle
Cited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: about 5 years ago

10.3389/fimmu.2019.02887

Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo
Cited by: 29
Author(s): Hung Jen Chen, Andrew Y. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
Software Mentions: 13
Published: about 5 years ago

10.1371/journal.pcbi.1007113

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Cited by: 28
Author(s): Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
Software Mentions: 13
Published: over 5 years ago

10.1186/s12859-015-0453-z

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: almost 10 years ago

10.3390/cancers13174311

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
Cited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: over 11 years ago

10.3389/fcell.2020.618552

A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation
Cited by: 12
Author(s): Jenny Ostrop, Rosalie T. Zwiggelaar, Marianne Terndrup Pedersen, François Gerbe, Korbinian Bösl, Håvard T. Lindholm, Alberto Díez-Sánchez, Naveen Parmar, Silke Radetzki, Jens Peter von Kries, Philippe Jay, Kim B. Jensen, C.H. Arrowsmith, Menno J. Oudhoff
Software Mentions: 12
Published: almost 4 years ago

10.1186/s12967-017-1285-6

In silico prediction of novel therapeutic targets using gene–disease association data
Cited by: 79
Author(s): Enrico Ferrero, Ian Dunham, Philippe Sanséau
Software Mentions: 12
Published: over 7 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: about 4 years ago

10.1371/journal.pntd.0009321

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature
Cited by: 15
Author(s): Camila Farias Amorim, Fernanda O. Novais, Ba Tiep Nguyen, Maurício T. Nascimento, Jamile Lago, Alexsandro S. Lago, Lucas P. Carvalho, Daniel P. Beiting, Phillip Scott
Software Mentions: 11
Published: over 3 years ago

10.1534/g3.120.401270

Application of Transcriptional Gene Modules to Analysis of <i>Caenorhabditis elegans</i>’ Gene Expression Data
Cited by: 7
Author(s): Michael Cary, Katie Podshivalova, Cynthia Kenyon
Software Mentions: 11
Published: about 4 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: almost 10 years ago

10.18632/oncotarget.22928

Comparing the genomes of cutaneous melanoma tumors to commercially available cell lines
Cited by: 10
Author(s): Stephen A. Luebker, Weiwei Zhang, Scott A. Koepsell
Software Mentions: 11
Published: about 7 years ago

10.3390/ijms20225621

APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival
Cited by: 45
Author(s): Mariko Asaoka, Takashi Ishikawa, Kazuaki Takabe, Santosh K. Patnaik
Software Mentions: 11
Published: about 5 years ago

10.7554/eLife.62210

Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells
Cited by: 18
Author(s): Balyn W. Zaro, Joseph J. Noh, Victoria L. Mascetti, János Demeter, Benson M. George, Monika Żukowska, Gunsagar S. Gulati, Rahul Sinha, Ryan A. Flynn, Allison Banuelos, Allison Zhang, Adam C. Wilkinson, Peter K. Jackson, Irving L. Weissman
Software Mentions: 10
Published: about 4 years ago

10.1186/s12859-017-1847-x

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Cited by: 42
Author(s): Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes‐Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Software Mentions: 10
Published: about 7 years ago

10.1242/dev.169474

An integrated transcriptional analysis of the developing human retina
Cited by: 67
Author(s): Carla Mellough, R. Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David Dolan, Carl M. Jones, Osagie Izuogu, Min Yu, Dean Hallam, Jannetta S. Steyn, Kathryn White, David Steel, Mauro Santibanez‐Koref, David Elliott, Michael S. Jackson, Susan Lindsay, Sushma Nagaraja Grellscheid, Majlinda Lako
Software Mentions: 10
Published: almost 6 years ago

10.1371/journal.pcbi.1007803

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Cited by: 9
Author(s): Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pgen.1003209

Centromere-Like Regions in the Budding Yeast Genome
Cited by: 36
Author(s): Philippe Lefrançois, Raymond K. Auerbach, Christopher M. Yellman, G. Shirleen Roeder, M Snyder
Software Mentions: 10
Published: almost 12 years ago

10.3389/fimmu.2021.722860

Transcriptional Changes in Regulatory T Cells From Patients With Autoimmune Polyendocrine Syndrome Type 1 Suggest Functional Impairment of Lipid Metabolism and Gut Homing
Cited by: 1
Author(s): A Berger, Eirik Bratland, Thea Sjøgren, Marte Heimli, Torgeir Tyssedal, Øyvind Bruserud, Stefan Johansson, Eystein S. Husebye, Bergithe E. Oftedal, Anette Susanne Bøe Wolff
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2020.569572

Aberrantly Methylated-Differentially Expressed Genes Identify Novel Atherosclerosis Risk Subtypes
Cited by: 6
Author(s): Yuzhou Xue, Yongzheng Guo, Suxin Luo, Wei Zhou, Jun Xiang, Yuansong Zhu, Zhenxian Xiang, Ju Shen
Software Mentions: 10
Published: about 4 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: almost 4 years ago

10.1038/tp.2016.119

Transcriptomic signatures of neuronal differentiation and their association with risk genes for autism spectrum and related neuropsychiatric disorders
Cited by: 23
Author(s): Andreas G. Chiocchetti, Denise Haslinger, Jason L. Stein, Luis de la Torre-Ubieta, Enrico Cocchi, Thomas Rothämel, Silvia Lindlar, Regina Waltes, Simone Fulda, Daniel H. Geschwind, Christine M. Freitag
Software Mentions: 10
Published: over 8 years ago

10.1371/journal.pone.0131656

iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data
Cited by: 1
Author(s): Ashis Saha, Minji Jeon, Aik Choon Tan, Jaewoo Kang
Software Mentions: 10
Published: over 9 years ago

10.1001/jamanetworkopen.2021.14162

Association of Copy Number Variation Signature and Survival in Patients With Serous Ovarian Cancer
Cited by: 14
Author(s): Ryon P. Graf, Ramez N. Eskander, Leo Brueggeman, Dwayne G. Stupack
Software Mentions: 10
Published: over 3 years ago

10.12688/f1000research.13925.3

BED: a Biological Entity Dictionary based on a graph data model
Cited by: 1
Author(s): Patrice Godard, Jonathan van Eyll
Software Mentions: 10
Published: over 6 years ago

10.7554/eLife.42675

The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila
Cited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: over 5 years ago

10.1186/1471-2105-14-254

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Cited by: 49
Author(s): Mikel Esnaola, Pedro Puig, David Herrera González, Robert Castelo, Juan R. González
Software Mentions: 9
Published: over 11 years ago

10.3389/fonc.2021.695006

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers
Cited by: 7
Author(s): Zhenyu Yang, Yulan Deng, Jinghui Cheng, Shiyou Wei, Hao Luo, Lunxu Liu
Software Mentions: 9
Published: over 3 years ago

10.26508/lsa.202000757

multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
Cited by: 16
Author(s): Aditya Bhagwat, Johannes Graumann, René Wiegandt, Mette Bentsen, Jordan M. Welker, Carsten Kuenne, Jens Preussner, Thomas Braun, Mario Looso
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-021-96095-z

Cell survival and DNA damage repair are promoted in the human blood thanatotranscriptome shortly after death
Cited by: 1
Author(s): Laura G. Antiga, Lode Sibbens, Yasmina Abakkouy, Ronny Decorte, Wouter Van Den Bogaert, Wim Van de Voorde
Software Mentions: 9
Published: over 3 years ago

10.1038/s42003-021-01945-1

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression
Cited by: 5
Author(s): Andrea Cerase, Alexander N. Young, Nerea Ruiz, Andreas Buneß, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, Giuseppe Trigiante, Sarah Marzi, Philip Avner
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2020.564301

Identification of Specific Circular RNA Expression Patterns and MicroRNA Interaction Networks in Mesial Temporal Lobe Epilepsy
Cited by: 10
Author(s): Lachlan G. Gray, James D. Mills, Ashton Curry‐Hyde, Sasha Devore, Daniel Friedman, Maria Thom, Catherine Scott, Roland D. Thijs, Eleonora Aronica, Orrin Devinsky, Michael Janitz
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pgen.1009773

Transcriptional progression during meiotic prophase I reveals sex-specific features and X chromosome dynamics in human fetal female germline
Cited by: 7
Author(s): Xueying Fan, Ioannis Moustakas, Vanessa Torrens-Juaneda, Qijing Lei, Geert Hamer, Leoni A. Louwé, Gonneke S. K. Pilgram, Károly Szuhai, Roberto Matorras, Cristina Eguizábal, Lucette van der Westerlaken, Hailiang Mei, Susana M. Chuva de Sousa Lopes
Software Mentions: 9
Published: over 3 years ago

10.1186/s13040-021-00267-6

eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals
Cited by: 11
Author(s): Theodore G. Drivas, Anastasia Lucas, Marylyn D. Ritchie
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2015.00339

Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome
Cited by: 23
Author(s): Emanuele Libertini, Alice Lebreton, Goran Lakisic, Marie‐Agnès Dillies, Stephan Beck, Jean‐Yves Coppée, Pascale Cossart, Hélène Bierne
Software Mentions: 9
Published: about 9 years ago

10.3390/ijms21145044

Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth
Cited by: 10
Author(s): Elena Spada, Luciano Calzari, Luigi Corsaro, Teresa Fazia, Monica Mencarelli, Anna Maria Di Blasio, Luisa Bernardinelli, G. Zangheri, Michele Vignali, Davide Gentilini
Software Mentions: 9
Published: over 4 years ago

10.1093/bioinformatics/bts477

easyRNASeq: a bioconductor package for processing RNA-Seq data
Cited by: 96
Author(s): Nicolas Delhomme, Ismaël Padioleau, Eileen E. M. Furlong, Lars M. Steinmetz
Software Mentions: 9
Published: over 12 years ago

10.1186/s40246-019-0242-2

Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis
Cited by: 4
Author(s): Carlos Ruiz‐Arenas, Alejandro Cáceres, Vı́ctor Moreno, Juan R. González
Software Mentions: 9
Published: about 5 years ago

10.3389/fcell.2020.00268

Comparative Transcriptome Landscape of Mouse and Human Hearts
Cited by: 14
Author(s): Tatsuya Anzai, Takanori Yamagata, Hideki Uosaki
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.64919

Tissue-autonomous immune response regulates stress signaling during hypertrophy
Cited by: 11
Author(s): Robert Krautz, Dilan Khalili, Ulrich Theopold
Software Mentions: 8
Published: almost 4 years ago

10.3389/fimmu.2020.596173

The Peripheral Blood Transcriptome Is Correlated With PET Measures of Lung Inflammation During Successful Tuberculosis Treatment
Cited by: 4
Author(s): Trust Odia, Stephanus T. Malherbe, Stuart Meier, Elizna Maasdorp, Léanie Kleynhans, Nelita du Plessis, André G. Loxton, Daniel E. Zak, Ethan Thompson, Fergal J. Duffy, Helena Kuivaniemi, Katharina Ronacher, Jill Winter, Gerhard Walzl, Gerard Tromp
Software Mentions: 8
Published: almost 4 years ago

10.1016/j.devcel.2018.07.005

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development
Cited by: 184
Author(s): Sueli Marques, David van Bruggen, Darya Vanichkina, Elisa M. Floriddia, Hermany Munguba, Leif Väremo, Stefania Giacomello, Ana Mendanha Falcão, Mandy Meijer, Åsa K. Björklund, Jens Hjerling-Leffler, Ryan J. Taft, Gonçalo Castelo‐Branco
Software Mentions: 8
Published: over 6 years ago

10.1242/dmm.040444

Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma
Cited by: 19
Author(s): Parisa Amini, Sina Nassiri, Julia Ettlin, Alexandra Malbon, Enni Markkanen
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-021-93570-5

Three dimensional modeling of biologically relevant fluid shear stress in human renal tubule cells mimics in vivo transcriptional profiles
Cited by: 18
Author(s): Emily J. Ross, Emily R. Gordon, Hanna Sothers, Roshan Darji, Oakley Baron, Dustin W. Haithcock, Balabhaskar Prabhakarpandian, Kapil Pant, R Myers, Sara J. Cooper, Nancy J. Cox
Software Mentions: 8
Published: over 3 years ago

10.3390/cells8101161

An Efficient and Flexible Method for Deconvoluting Bulk RNA-Seq Data with Single-Cell RNA-Seq Data
Cited by: 15
Author(s): Xifang Sun, Shuang Sun, Sheng Yang
Software Mentions: 8
Published: about 5 years ago

10.1016/j.csbj.2020.06.023

Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
Cited by: 10
Author(s): Susan Idicula‐Thomas, Ulka Gawde, Sameeksha Bhaye, Khushal Pokar, Gary D. Bader
Software Mentions: 8
Published: almost 5 years ago

10.1038/srep38411

Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians
Cited by: 34
Author(s): Ming Zhao, Jian Qin, Hang Yin, Yixin Tan, Wei Liao, Qian Liu, Shuangyan Luo, Min He, Gongping Liang, Yajing Shi, Qing Zhang, Wenjun Cai, Guangliang Yin, Yin Zhou, Jing Wang, Mengying Li, Yi Huang, Aiyun Liu, Haijian Wu, Zhiyong Zhang, Qianjin Lu
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pone.0051609

Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) Genotypes
Cited by: 129
Author(s): Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Simona Urso, Laura Crispino, Pamela Abbruscato, Pietro Piffanelli, Elisabetta Lupotto, Luigi Cattivelli, Giampiero Valè
Software Mentions: 8
Published: about 12 years ago

10.3390/jpm11020154

Comprehensive Profiling of Genomic and Transcriptomic Differences between Risk Groups of Lung Adenocarcinoma and Lung Squamous Cell Carcinoma
Cited by: 19
Author(s): Talip Zengin, Tuğba Önal-Süzek
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41598-018-29378-7

Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer
Cited by: 7
Author(s): Beatríz González, Ferran Fece de la Cruz, Johanna Samuelsson, Andreu Alibés, Sergio Alonso
Software Mentions: 8
Published: over 6 years ago

10.18632/oncotarget.13467

Effects of <i>Abies sibirica</i> terpenes on cancer- and aging-associated pathways in human cells
Cited by: 9
Author(s): Anna V. Kudryavtseva, George S. Krasnov, Anastasiya V. Lipatova, B. Ya. Alekseev, Faniya Maganova, Mikhail Shaposhnikov, Maria S. Fedorova, Anastasiya V. Snezhkina, Alexey Moskalev
Software Mentions: 8
Published: about 8 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

10.1186/s13073-019-0615-0

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney
Cited by: 144
Author(s): Alexander N. Combes, Luke Zappia, Pei X. Er, Alicia Oshlack, Melissa H. Little
Software Mentions: 8
Published: almost 6 years ago

10.3390/cells9030786

Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration
Cited by: 13
Author(s): Jingxin Tao, Youjin Hao, Xudong Li, Huachun Yin, Xiner Nie, Jie Zhang, Bo-Ying Xu, Chen Qiao, Bo Li
Software Mentions: 8
Published: over 4 years ago

10.1186/s13059-018-1567-1

Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders
Cited by: 119
Author(s): Heath O’Brien, Eilís Hannon, Matthew Hill, Carolina Toste, Matthew J. Robertson, Joanne Morgan, Gemma M. McLaughlin, Cathryn M. Lewis, Leonard C Schalkwyk, Lynsey S. Hall, Antonio F. Pardiñas, Michael John Owen, Michael O’Donovan, Jonathan Mill, Nicholas John Bray
Software Mentions: 8
Published: about 6 years ago

10.1038/s41598-020-60998-0

Temporal changes in the gene expression heterogeneity during brain development and aging
Cited by: 28
Author(s): Ulas Işıldak, Mehmet Somel, Janet M. Thornton, Handan Melike Dönertaş
Software Mentions: 8
Published: almost 5 years ago

10.1038/s41431-020-0675-z

Evaluation of CNV detection tools for NGS panel data in genetic diagnostics
Cited by: 63
Author(s): José Marcos Moreno-Cabrera, Jesús Del Valle, Elisabeth Castellanos, Lídia Feliubadaló, Marta Pineda, Joan Brunet, Eduard Serra, Gabriel Capellá, Conxi Lázaro, Bernat Gel
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2021.568729

Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid
Cited by: 7
Author(s): Thomas J. Colgan, Peter Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Software Mentions: 7
Published: almost 4 years ago

10.1242/dmm.049068

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

10.7554/eLife.65394

The whale shark genome reveals patterns of vertebrate gene family evolution
Cited by: 18
Author(s): Milton Tan, Anthony K. Redmond, Helen Dooley, Ryo Nozu, Keiichi Sato, Shigehiro Kuraku, Sergey Koren, Adam M. Phillippy, Alistair D. M. Dove, Timothy D. Read
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2021.694680

Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients
Cited by: 5
Author(s): Teresa Domaszewska, Joanna Żyła, Raik Otto, Stefan H. E. Kaufmann, January Weiner
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2164-15-480

Detection of copy number variations and their effects in Chinese bulls
Cited by: 50
Author(s): Liangzhi Zhang, Shangang Jia, Mingjuan Yang, Yao Xu, Congjun Li, Jiajie Sun, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Yang Zhou, Chunlei Zhang, Xin Zhao, Hong Chen
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.pone.0187735

Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection
Cited by: 16
Author(s): Maren Pröll, Christiane Neuhoff, K. Schellander, Muhammad Jasim Uddin, Mehmet Ulaş Çınar, Sudeep Sahadevan, Xuecheng Qu, M. S. Islam, Mikhaël Poirier, Marcel A. Müller, Christian Drosten, Dawit Tesfaye, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 7
Published: about 7 years ago

10.18632/aging.101912

The widespread increase in inter-individual variability of gene expression in the human brain with age
Cited by: 19
Author(s): Veronika R. Kedlian, Handan Melike Dönertaş, Janet M. Thornton
Software Mentions: 7
Published: over 5 years ago

10.1002/jev2.12127

Inflammasome‐induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses
Cited by: 26
Author(s): Christina F. Budden, Linden J. Gearing, Romina Kaiser, Lena Standke, Paul J. Hertzog, Eicke Latz
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.51413

Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation
Cited by: 190
Author(s): Ankit Jambusaria, Zhigang Hong, Lianghui Zhang, Shubhi Srivastava, Arundhati Jana, Péter T. Tóth, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 7
Published: almost 5 years ago

10.1186/s13148-018-0510-3

Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception
Cited by: 25
Author(s): Davide Gentilini, Edgardo Somigliana, Luca Pagliardini, Elisa Rabellotti, Paolo Garagnani, Luisa Bernardinelli, Enrico Papaleo, Massimo Candiani, Anna Maria Di Blasio, Paola Viganò
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-021-81451-w

Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19
Cited by: 33
Author(s): Ilario De Toma, Mara Dierssen
Software Mentions: 7
Published: almost 4 years ago

10.1186/1471-2164-15-452

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
Cited by: 52
Author(s): Arun Kommadath, Hua Bao, Adriano S. Arantes, Graham Plastow, Christopher K. Tuggle, Shawn M. D. Bearson, Le Luo Guan, Paul Stothard
Software Mentions: 7
Published: over 10 years ago

10.1186/s12859-019-2852-z

Differential analysis of combinatorial protein complexes with CompleXChange
Cited by: 4
Author(s): Thorsten Will, Volkhard Helms
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1009763

Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
Cited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: over 3 years ago

10.1186/s12859-021-04012-y

CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network
Cited by: 4
Author(s): Wen Xiao, Lin Gao, Tuo Song, Chaoqun Jiang
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-020-69082-z

Immune expression signatures as candidate prognostic biomarkers of age and gender survival differences in cutaneous melanoma
Cited by: 6
Author(s): Yi Jun Kim, Kyubo Kim, Kye Hwa Lee, Jiyoung Kim, Wonguen Jung
Software Mentions: 7
Published: over 4 years ago

10.1016/j.cell.2019.09.035

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity
Cited by: 322
Author(s): Chrysothemis C. Brown, Herman Gudjonson, Yuri Pritykin, Deeksha Deep, Vincent Philippe Lavallée, Alejandra Mendoza, Rachel M. Fromme, Linas Mažutis, Charlotte E. Ariyan, Christina Leslie, Dana Pe’er, Alexander Y. Rudensky
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-017-05927-4

Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity
Cited by: 35
Author(s): Handan Melike Dönertaş, Hamit İzgi, Altuğ Kamacıoğlu, Zhisong He, Philipp Khaitovich, Mehmet Somel
Software Mentions: 7
Published: over 7 years ago

10.12688/f1000research.9005.3

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Cited by: 297
Author(s): Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Tian Li, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 7
Published: almost 6 years ago

Projects: bioconductor: biomaRt

Papers Mentioning biomaRt 446