bioconductor: topGO | Projects | Ecosyste.ms: Papers

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

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.1186/s12859-020-03819-5

ideal: an R/Bioconductor package for interactive differential expression analysis
Cited by: 18
Author(s): Fédérico Marini, Jan Linke, Harald Binder
Software Mentions: 17
Published: about 4 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

10.1038/s41597-021-00998-5

A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression
Cited by: 4
Author(s): Michael Rohr, Jordan M. Beardsley, Sai Preethi Nakkina, Xiang Zhu, Jihad Aljabban, Dexter Hadley, Deborah A. Altomare
Software Mentions: 17
Published: over 3 years ago

10.1093/gigascience/giz061

LION/web: a web-based ontology enrichment tool for lipidomic data analysis
Cited by: 110
Author(s): Martijn R. Molenaar, Aike Jeucken, Tsjerk A. Wassenaar, Chris H.A. van de Lest, Jos F. Brouwers, J. Bernd Helms
Software Mentions: 16
Published: over 5 years ago

10.12688/f1000research.8987.2

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Cited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago

10.12688/f1000research.24956.2

gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
Cited by: 274
Author(s): Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Software Mentions: 14
Published: about 4 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.1186/s12920-019-0578-4

Deconvolution of transcriptomes and miRNomes by independent component analysis provides insights into biological processes and clinical outcomes of melanoma patients
Cited by: 21
Author(s): Petr V. Nazarov, Anke Wienecke-Baldacchino, Andreï Zinovyev, Urszula Czerwińska, Arnaud Muller, Dorothée Nashan, Gunnar Dittmar, Francisco Azuaje, Stephanie Kreis
Software Mentions: 14
Published: over 5 years ago

10.3390/ijms22073681

Circulating miRNAs as Biomarkers for Mitochondrial Neuro-Gastrointestinal Encephalomyopathy
Cited by: 4
Author(s): Mark Mencias, Michelle Levene, Kevin Blighe, Bridget E. Bax
Software Mentions: 14
Published: over 3 years ago

10.1038/srep42130

Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: almost 8 years ago

10.1126/sciadv.abg6070

Enhancing the heat tolerance of reef-building corals to future warming
Cited by: 36
Author(s): Emily J. Howells, David Abrego, Yi Jin Liew, John A. Burt, Eli Meyer, Manuel Aranda
Software Mentions: 13
Published: over 3 years ago

10.1186/s12861-018-0163-7

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells
Cited by: 4
Author(s): Anna Mantsoki, Guillaume Devailly, Anagha Joshi
Software Mentions: 13
Published: almost 7 years ago

10.12688/f1000research.8967.2

An end to end workflow for differential gene expression using Affymetrix microarrays
Cited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: over 6 years ago

10.1186/s13068-019-1584-7

A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock
Cited by: 14
Author(s): Karel Sedlář, Jan Kolek, Markus Gruber, Katerina Jureckova, Barbora Branská, Gergely Csaba, Maryna Vasylkivska, Ralf Zimmer, Petra Patáková, Ivo Provazník
Software Mentions: 13
Published: about 5 years ago

10.12688/f1000research.17548.2

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
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

10.3389/fcimb.2021.687607

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

10.12688/f1000research.12544.1

Easy and efficient ensemble gene set testing with EGSEA
Cited by: 45
Author(s): Monther Alhamdoosh, Charity W. Law, Tian Li, Julie Sheridan, Milica Ng, Matthew E. Ritchie
Software Mentions: 12
Published: about 7 years ago

10.1038/s41392-021-00753-7

Single-cell immune profiling reveals distinct immune response in asymptomatic COVID-19 patients
Cited by: 18
Author(s): Xiang-Na Zhao, Yue You, Xiaoming Cui, Han Gao, Guolin Wang, Shengbo Zhang, Lilin Ye, Lei Duan, Ka-Li Zhu, Yuling Wang, Li Li, Jianhua Lu, Haibin Wang, Jingfang Fan, Huanwei Zheng, Erfu Dai, Luyi Tian, Mai‐Juan Ma
Software Mentions: 11
Published: over 3 years ago

10.1002/sim.8116

Correlation‐adjusted regression survival scores for high‐dimensional variable selection
Cited by: 10
Author(s): Thomas Welchowski, Verena Zuber, Matthias Schmid
Software Mentions: 11
Published: almost 6 years ago

10.1371/journal.pcbi.1003929

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
Cited by: 18
Author(s): Hai Fang
Software Mentions: 11
Published: about 10 years ago

10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: over 7 years ago

10.1371/journal.pcbi.1002276

BeadArray Expression Analysis Using Bioconductor
Cited by: 50
Author(s): Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch
Software Mentions: 11
Published: about 13 years ago

10.1534/g3.120.401270

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

10.3390/cells9030779

Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.)
Cited by: 12
Author(s): Yury V. Malovichko, O. Y. Shtark, Ekaterina N. Vasileva, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 10
Published: almost 5 years ago

10.1186/s41065-021-00202-z

RNA-Seq based transcriptome analysis in oral lichen planus
Cited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: about 3 years ago

10.1126/sciadv.1600760

Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia
Cited by: 85
Author(s): S. Picaud, Katharina Leonards, Jean-Philippe Lambert, Oliver M. Dovey, Christopher Wells, Oleg Fedorov, Octovia Monteiro, Takao Fujisawa, Chenyi Wang, Hannah Lingard, C. Tallant, Nikzad Nikbin, Lucie Guetzoyan, Richard J. Ingham, Steven V. Ley, P.E. Brennan, Susanne Müller, Anastasia Samsonova, Anne‐Claude Gingras, Juerg Schwaller, George S. Vassiliou, Stefan Knapp, P. Filippakopoulos
Software Mentions: 10
Published: about 8 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

10.1038/s42003-021-02009-0

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora
Cited by: 15
Author(s): Adam Healey, Mervyn Shepherd, Graham J. King, Jakob B. Butler, Jules S. Freeman, David J Lee, Brad M. Potts, Orzenil B. Silva‐Junior, Abdul Baten, Jerry Jenkins, Shengqiang Shu, John T. Lovell, Avinash Sreedasyam, Jane Grimwood, Agnelo Furtado, Dário Grattapaglia, Kerrie Barry, Hope Hundley, Blake A. Simmons, Jeremy Schmutz, René E. Vaillancourt, Robert J. Henry
Software Mentions: 10
Published: over 3 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: about 4 years ago

10.1038/s41598-020-72569-4

Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata
Cited by: 2
Author(s): Joshua Niklas Ebner, Danilo Ritz, Stefanie von Fumetti
Software Mentions: 9
Published: about 4 years ago

10.3390/insects12070577

Transcriptome Analyses Provide Insights into the Aggressive Behavior toward Conspecific and Heterospecific in Thitarodes xiaojinensis (Lepidoptera: Hepialidae)
Cited by: 1
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Richou Han
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pcbi.1008778

Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells
Cited by: 4
Author(s): Jared Brown, Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Michael P. Schwartz, Amy Van Aartsen, John Steill, Scott Swanson, Ron Stewart, James A. Thomson, Christina Kendziorski
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12864-018-5092-0

High-throughput proteomic profiling of the fish liver following bacterial infection
Cited by: 58
Author(s): Dwight R. Causey, Moritz A N Pohl, David Stead, Samuel Martín, Christopher J. Secombes, Daniel J. Macqueen
Software Mentions: 9
Published: about 6 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

10.3390/ijms151221788

Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs
Cited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: about 10 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: over 4 years ago

10.1038/s41388-018-0450-6

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
Cited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: over 6 years ago

10.1007/s00401-020-02187-x

Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier
Cited by: 44
Author(s): Judith Hauptmann, Lisa Johann, Fédérico Marini, Maja Kitic, E. Colombo, Ilgiz A. Mufazalov, Martin W. Krueger, Khalad Karram, Sonja Moos, Florian Wanke, Florian C. Kurschus, Matthias Klein, Sílvia Cardoso, Johannes Strauß, Subhashini Bolisetty, Fred Lühder, Markus Schwaninger, Harald Binder, Ingo Bechman, Tobias Bopp, Anupam Agarwal, Miguel P. Soares, Tommy Regen, Ari Waisman
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.33105

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites
Cited by: 152
Author(s): Adam J. Reid, Arthur M. Talman, Hayley M. Bennett, Ana Gomes, Mandy Sanders, Christopher J. R. Illingworth, Oliver Billker, Matthew Berriman, Mara Lawniczak
Software Mentions: 9
Published: over 6 years ago

10.1111/1755-0998.13280

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic
Cited by: 13
Author(s): Michael Nowak, Siri Birkeland, Terezie Mandáková, Rimjhim Roy Choudhury, Xi Guo, Lovisa Gustafsson, Abel Gizaw, Audun Schrøder-Nielsen, Marco Fracassetti, Anne K. Brysting, Loren H. Rieseberg, Tanja Slotte, Christian Parisod, Martin A. Lysak, Christian Brochmann
Software Mentions: 8
Published: about 4 years ago

10.1186/1471-2105-14-133

How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis
Cited by: 23
Author(s): Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka M. Axmann, Ralf Steuer
Software Mentions: 8
Published: over 11 years ago

10.3390/genes10110875

The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander Population
Cited by: 6
Author(s): Joana Sabino‐Pinto, Daniel J. Goedbloed, Eugenia Sanchez, Thomas Czypionka, Arne W. Nolte, Sebastian Steinfartz
Software Mentions: 8
Published: about 5 years ago

10.15252/msb.20199002

Endogenous fluctuations of <scp>OCT</scp> 4 and <scp>SOX</scp> 2 bias pluripotent cell fate decisions
Cited by: 35
Author(s): Daniel Strebinger, Cédric Deluz, Elias T Friman, Subashika Govindan, Andrea Brigitta Alber, David M. Suter
Software Mentions: 8
Published: over 5 years ago

10.1002/ece3.4894

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations
Cited by: 8
Author(s): Suda Parimala Ravindran, Maike Herrmann, Mathilde Cordellier
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.ppat.1009933

Trypanosoma brucei triggers a broad immune response in the adipose tissue
Cited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: over 3 years ago

10.1038/s42003-020-1097-8

CD70 expression determines the therapeutic efficacy of expanded human regulatory T cells
Cited by: 30
Author(s): Rebeca Arroyo Hornero, Christos Georgiadis, Peng Hua, Dominik Trzupek, He L-Z., Waseem Qasim, John A. Todd, Ricardo C. Ferreira, Kathryn J. Wood, Fadi Issa, Joanna Hester
Software Mentions: 8
Published: over 4 years ago

10.18632/oncotarget.13467

Effects of Abies sibirica 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

10.7717/peerj.9056

Transcriptional profiling to identify the key genes and pathways of pterygium
Cited by: 11
Author(s): Yihui Chen, Haoyu Wang, Yaping Jiang, Xiaoyan Zhang, Qingzhong Wang
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.58810

Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in mouse models of breast cancer
Cited by: 38
Author(s): Syn Kok Yeo, Xiaoting Zhu, Takaaki Okamoto, Mingang Hao, Cailian Wang, Peixin Lu, Long Lu, Jun‐Lin Guan
Software Mentions: 8
Published: over 4 years ago

10.1111/pbi.12958

The developmental dynamics of the Populus stem transcriptome
Cited by: 92
Author(s): Qing Chao, Zili Gao, Dong Zhang, Biligen-Gaowa Zhao, Fengqin Dong, Chunxiang Fu, Lijun Liu, Bai-Chen Wang
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-018-4649-2

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation
Cited by: 15
Author(s): Zhisong He, Qianhui Yu
Software Mentions: 8
Published: over 6 years ago

10.1186/s12915-017-0379-1

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
Cited by: 55
Author(s): Édouard Evangelisti, Anna Gogleva, Thomas Hainaux, Mehdi Doumane, Frej Tulin, Clément Quan, T. S. Yunusov, Kévin Floch, Sebastián Schornack
Software Mentions: 8
Published: over 7 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: over 3 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

10.1038/s41598-020-73391-8

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
Cited by: 36
Author(s): Meaghan L. Pimsler, Kennan Oyen, James D. Herndon, Jason M. Jackson, James P. Strange, Michael E. Dillon, Jeffrey D. Lozier
Software Mentions: 7
Published: about 4 years ago

10.3390/microorganisms9020315

TAL Effector Repertoires of Strains of Xanthomonas phaseoli pv. manihotis in Commercial Cassava Crops Reveal High Diversity at the Country Scale
Cited by: 6
Author(s): Carlos A Zárate-Chaves, Daniela Osorio-Rodríguez, Ruben E. Mora, Álvaro L. Pérez‐Quintero, Alexis Dereeper, Silvia Restrepo, Camilo López, Boris Szurek, Adriana Bernal
Software Mentions: 7
Published: almost 4 years ago

10.1002/cam4.3434

The clinical value and potential molecular mechanism of the downregulation of MAOA in hepatocellular carcinoma tissues
Cited by: 20
Author(s): Yu‐Yan Pang, Jian‐Di Li, Gao Li, Xia Yang, Yi‐Wu Dang, Zhiyong Lai, Li‐Min Liu, Jie Yang, Huayu Wu, Rong‐Quan He, Zhi‐Guang Huang, Dandan Xiong, Lihua Yang, Lin Shi, Wei‐Jia Mo, Deng Tang, Huiping Lu, Gang Chen
Software Mentions: 7
Published: over 4 years ago

10.1186/s12864-020-07338-8

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria
Cited by: 10
Author(s): Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulín, Petri Auvinen
Software Mentions: 7
Published: almost 4 years ago

10.1038/srep29042

Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Cited by: 35
Author(s): Frédéric Bouché, Maria D’Aloia, Pierre Tocquin, Guillaume Lobet, Nathalie Detry, Claire Périlleux
Software Mentions: 7
Published: over 8 years ago

10.3390/cells10050973

Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing
Cited by: 5
Author(s): Shaojian Gao, Zhijie Wu, Jeerthi Kannan, Liza Mathews, Xingmin Feng, Sachiko Kajigaya, Neal S. Young
Software Mentions: 7
Published: over 3 years ago

10.15252/embr.201642378

Linear ubiquitination by <scp>LUBEL</scp> has a role in Drosophila heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: about 8 years ago

10.1111/pbi.13205

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Cited by: 45
Author(s): Linkai Huang, Guangyan Feng, Haidong Yan, Zhongren Zhang, B. Shaun Bushman, Jianping Wang, Aureliano Bombarely, Mingzhou Li, Zhongfu Yang, Gang Nie, Wengang Xie, Lei Xu, Peilin Chen, Xinxin Zhao, Wenkai Jiang, Xinquan Zhang
Software Mentions: 7
Published: over 5 years ago

10.3390/plants9121700

Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots
Cited by: 8
Author(s): Evgeny A. Zorin, Alexey М. Afonin, Olga A. Kulaeva, Emma S. Gribchenko, O. Y. Shtark, Vladimir A. Zhukov
Software Mentions: 7
Published: about 4 years ago

10.1186/1471-2164-12-227

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
Cited by: 144
Author(s): Susanne U. Franssen, Ranjit Shrestha, Andrea Bräutigam, Erich Bornberg‐Bauer, Andreas Weber
Software Mentions: 7
Published: over 13 years ago

10.7554/eLife.60176

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus
Cited by: 21
Author(s): Taro Maeda, Shunichi Takahashi, Takao Yoshida, Shigeru Shimamura, Yoshihiro Takaki, Yukiko Nagai, Atsushi Toyoda, Yutaka Suzuki, Asuka Arimoto, Hisaki Ishii, Nori Satoh, Tomoaki Nishiyama, Mitsuyasu Hasebe, Tadashi Maruyama, Jun Minagawa, Junichi Obokata, Shuji Shigenobu
Software Mentions: 7
Published: over 3 years ago

10.1111/acel.12819

Gene expression-based drug repurposing to target aging
Cited by: 53
Author(s): Handan Melike Dönertaş, Matías Fuentealba, Linda Partridge, Janet M. Thornton
Software Mentions: 7
Published: over 6 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: about 7 years ago

10.1186/s10194-021-01285-9

Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: about 3 years ago

10.3389/fnins.2021.621121

Analysis of the Neuroproteome Associated With Cell Therapy After Intranigral Grafting in a Mouse Model of Parkinson Disease
Cited by: 1
Author(s): Hassan Dakik, Sarah Mantash, Ali Nehme, Firas Kobeissy, Masoud Zabet-Moghaddam, Parvin Mirzaei, Yehia Mechref, Afsaneh Gaillard, Laetitia Prestoz, Kazem Zibara
Software Mentions: 7
Published: almost 4 years ago

10.1534/g3.114.011759

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: over 10 years ago

10.3389/fpls.2021.637115

The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype
Cited by: 9
Author(s): Tatiana Arias, Chad E. Niederhuth, Paula McSteen, J. Chris Pires
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13059-017-1286-z

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy
Cited by: 68
Author(s): Matthias Heinig, Michiel E. Adriaens, Sebastian Schäfer, Hanneke W. M. van Deutekom, Elisabeth M. Lodder, James S. Ware, Valentin Schneider, Leanne E. Felkin, Esther E. Creemers, Benjamin Meder, Hugo A. Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, András Varró, Nanette H. Bishopric, Alfred L. George, Cristobal dos Remedios, Aida Moreno‐Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J.R. Barton, Stuart A. Cook, Yigal M. Pinto, Connie R. Bezzina, Norbert Hübner
Software Mentions: 7
Published: over 7 years ago

10.1111/mec.15047

Caste‐ and pesticide‐specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees
Cited by: 53
Author(s): Thomas J. Colgan, Isabel Fletcher, Andres N. Arce, Richard J. Gill, Ana Ramos Rodrigues, Eckart Stolle, Lars Chittka, Yannick Wurm
Software Mentions: 6
Published: almost 6 years ago

10.3389/fimmu.2020.628804

Transcriptomic Analysis of Long-Term Protective Immunity Induced by Vaccination With Mycoplasma gallisepticum Strain ts-304
Cited by: 5
Author(s): Sathya N Kulappu Arachchige, Neil D. Young, Anna Kanci Condello, Oluwadamilola S Omotainse, Amir H. Noormohammadi, Nadeeka K. Wawegama, Glenn F. Browning
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12920-016-0164-y

Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease
Cited by: 84
Author(s): Alexandra Dumitriu, Javad Golji, Adam Labadorf, Benbo Gao, Thomas G. Beach, Richard H. Myers, Kenneth A. Longo, Jeanne C. Latourelle
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0143563

RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression
Cited by: 135
Author(s): Adam Labadorf, Andrew G. Hoss, Valentina N. Lagomarsino, Jeanne C. Latourelle, Tiffany C. Hadzi, Joli Bregu, Marcy E. MacDonald, James F. Gusella, Jiang‐Fan Chen, Schahram Akbarian, Zhiping Weng, Richard H. Myers
Software Mentions: 6
Published: about 9 years ago

10.1186/1471-2105-14-7

GSVA: gene set variation analysis for microarray and RNA-Seq data
Cited by: 6,480
Author(s): Sonja Hänzelmann, Robert Castelo, Justin Guinney
Software Mentions: 6
Published: almost 12 years ago

10.1038/s41598-020-75998-3

Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption
Cited by: 8
Author(s): S. Lee, Stephen J. Bush, Susan Thorne, Nicola Mawson, Colin Farquharson, Guraa Bergkvist
Software Mentions: 6
Published: about 4 years ago

10.1186/s13072-020-00379-z

DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna
Cited by: 15
Author(s): Jack Hearn, Fiona A. Plenderleith, Tom J. Little
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-019-45714-x

Transcriptome Analysis of Long-lived Drosophila melanogaster E(z) Mutants Sheds Light on the Molecular Mechanisms of Longevity
Cited by: 30
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Nadezhda Zemskaya, Liubov Koval, Eugenia V. Schegoleva, Zulfiya G. Guvatova, George S. Krasnov, Ilya Solovev, Maksim A. Sheptyakov, Alex Zhavoronkov, Anna V. Kudryavtseva
Software Mentions: 6
Published: over 5 years ago

10.1186/s13068-021-01948-4

Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids
Cited by: 6
Author(s): Jose J De Vega, Ned Peel, Sarah Purdy, Sarah Hawkins, Iain S. Donnison, Sarah Dyer, Kerrie Farrar
Software Mentions: 6
Published: over 3 years ago

10.7150/jca.55570

Upregulating KTN1 promotes Hepatocellular Carcinoma progression
Cited by: 1
Author(s): Jian Pan, Naixia Chao, Yao‐Yao Zhang, Tianyi Huang, Chengxiao Chen, Qiuhong Qin, Jinhong Guo, Rongshi Huang, Guopei Luo
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1005694

PCSF: An R-package for network-based interpretation of high-throughput data
Cited by: 34
Author(s): Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
Software Mentions: 6
Published: over 7 years ago

10.1093/gigascience/giaa059

Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats
Cited by: 16
Author(s): Yocelyn T. Gutiérrez-Guerrero, Enrique Ibarra-Laclette, Carlos Martı́nez del Rio, Josué Barrera‐Redondo, Eria A. Rebollar, Jorge Ortega, Livia León‐Paniagua, Araxi O. Urrutia, Erika Aguirre‐Planter, Luis E. Eguiarte
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-020-06831-4

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure
Cited by: 13
Author(s): Shubha Suresh, Teresa J. Crease, Melania E. Cristescu, Frédéric J. J. Chain
Software Mentions: 6
Published: over 4 years ago

10.1161/CIRCULATIONAHA.119.039596

Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins
Cited by: 74
Author(s): Sonia Chothani, Sebastian Schäfer, Eleonora Adami, V. Sivakumar, Anissa A. Widjaja, Sarah R. Langley, Jessie Tan, Mao Wang, Nicholas M Quaife, Chee Jian Pua, G. D’Agostino, Shamini Guna Shekeran, Benjamin L. George, Si Ching Lim, Elaine Yiqun Cao, Sebastiaan van Heesch, Franziska Witte, Leanne E. Felkin, Eleni G. Christodoulou, Jinqiao Dong, Susanne Blachut, Giannino Patone, Paul J.R. Barton, Norbert Hübner, Stuart A. Cook, Owen J. L. Rackham
Software Mentions: 6
Published: over 5 years ago

10.1186/s13073-015-0237-0

Identification of global regulators of T-helper cell lineage specification
Cited by: 36
Author(s): Kartiek Kanduri, Subhash Tripathi, Antti Larjo, Henrik Mannerström, Ubaid Ullah, Riikka Lund, R. David Hawkins, Bing Ren, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pgen.1006279

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity
Cited by: 43
Author(s): Barbara Mair, Tomasz Konopka, Claudia Kerzendorfer, Katia Sleiman, Šejla Šalic, Violeta Serra, Markus K. Muellner, Vassiliki Théodorou, Sebastian M. Nijman
Software Mentions: 6
Published: over 8 years ago

10.18632/aging.203448

Effects of Siberian fir terpenes extract Abisil on antioxidant activity, autophagy, transcriptome and proteome of human fibroblasts
Cited by: 1
Author(s): Anastasiya V. Lipatova, George S. Krasnov, Pavel Vorobyov, Pavel Melnikov, Olga N. Alekseeva, Yulia S. Vershinina, Alexander G. Brzhozovskiy, Daria Goliusova, Faniya Maganova, Natalia F. Zakirova, Anna V. Kudryavtseva, Alexey Moskalev
Software Mentions: 6
Published: over 3 years ago

10.1002/ece3.4724

Highly flexible infection programs in a specialized wheat pathogen
Cited by: 72
Author(s): Janine Haueisen, Mareike Möller, Christoph Eschenbrenner, Jonathan Grandaubert, Heike Seybold, Holger Adamiak, Eva H. Stukenbrock
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.celrep.2020.108629

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide
Cited by: 10
Author(s): Kathrin Leppek, Gun Woo Byeon, Kotaro Fujii, Maria Barna
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-018-1419-z

Gene-level differential analysis at transcript-level resolution
Cited by: 97
Author(s): Lynn Yi, Harold Pimentel, Nicolas Bray, Lior Pachter
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0066826

A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development
Cited by: 31
Author(s): Alicia N. Schep, Boris Adryan
Software Mentions: 6
Published: over 11 years ago

10.3390/genes11040434

Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups
Cited by: 5
Author(s): Daniil S. Wiebe, N. A. Omelyanchuk, Aleksey M. Mukhin, Ivo Große, Sergey A. Lashin, Elena V. Zemlyanskaya, В. В. Миронова
Software Mentions: 6
Published: over 4 years ago

10.1186/s12915-020-00842-z

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo
Cited by: 19
Author(s): Jialin Liu, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson‐Rechavi
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0052299

Cell-Type Specific DNA Methylation Patterns Define Human Breast Cellular Identity
Cited by: 22
Author(s): Petr Novák, Martha R. Stampfer, José L. Muñoz-Rodríguez, James C. Garbe, Mathias Ehrich, Bernard W. Futscher, Taylor J. Jensen
Software Mentions: 6
Published: about 12 years ago

Projects: bioconductor: topGO

Papers Mentioning topGO 652