bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0122339

The Active Tamoxifen Metabolite Endoxifen (4OHNDtam) Strongly Down-Regulates Cytokeratin 6 (CK6) in MCF-7 Breast Cancer Cells
Cited by: 4
Author(s): Thomas Helland, Jennifer Gjerde, Simon N. Dankel, Ingvild S. Fenne, Linn Skartveit, Andreas Drangevåg, Olivera Bozickovic, Marianne Hauglid Flågeng, Håvard Søiland, Gunnar Mellgren, Ernst A. Lien
Software Mentions: 4
Published: over 9 years ago

10.7150/thno.46142

A panel of eight microRNAs is a good predictive parameter for triple-negative breast cancer relapse
Cited by: 42
Author(s): Hsiao-Chin Hong, Ching-Te Chuang, Wei‐Chih Huang, Shun-Long Weng, Chia-Hung Chen, Kuang-Hsin Chang, Kuang‐Wen Liao, Hsien-Da Huang
Software Mentions: 4
Published: almost 5 years ago

10.3390/cancers11050698

NECTIN4 (PVRL4) as Putative Therapeutic Target for a Specific Subtype of High Grade Serous Ovarian Cancer—An Integrative Multi-Omics Approach
Cited by: 25
Author(s): Christine Bekos, Besnik Muqaku, Sabine Dekan, Reinhard Horvat, Stephan Polterauer, Christopher Gerner, Stefanie Aust, Dietmar Pils
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers12123789

Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk
Cited by: 16
Author(s): Stella Logotheti, Stephan Marquardt, Christin Richter, Renée Sophie Hain, Nico Murr, Işıl Takan, Athanasia Pavlopoulou, Brigitte M. Pützer
Software Mentions: 4
Published: almost 4 years ago

10.7150/thno.36378

Exosome-dependent immune surveillance at the metastatic niche requires BAG6 and CBP/p300-dependent acetylation of p53
Cited by: 41
Author(s): Maximiliane Schuldner, Bastian Dörsam, Olga Shatnyeva, Katrin S. Reiners, Andriy V. Kubarenko, Hinrich P. Hansen, Florian Finkernagel, Katrin Roth, Sebastian Theurich, Andrea Nist, Thorsten Stiewe, Annette Paschen, Gero Knittel, Hans Christian Reinhardt, Rolf Müller, Michael Hallek, Elke Pogge von Strandmann
Software Mentions: 4
Published: almost 6 years ago

10.4056/sigs.1423520

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10
Cited by: 8
Author(s): Elizabeth M. Glass, Patrick Meyer, Jack A. Gilbert, Dawn Field, Sarah Hunter, Renzo Kottmann, Nikos C. Kyrpides, Susanna Assunta Sansone, Lynn M. Schriml, Peter J. Sterk, Owen White, John Wooley
Software Mentions: 4
Published: almost 15 years ago

10.1186/s13395-019-0196-z

Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field
Cited by: 8
Author(s): Apostolos Malatras, Stéphanie Duguez, William Duddy
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms19113687

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities
Cited by: 5
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 4
Published: about 6 years ago

10.1016/j.cell.2016.09.037

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Cited by: 818
Author(s): Biola M. Javierre, Oliver S. Burren, Steven P. Wilder, Roman Kreuzhuber, Steven M. Hill, Sven Sewitz, Jonathan Cairns, Steven W. Wingett, Csilla Várnai, Michiel J. Thiecke, Frances Burden, Samantha Farrow, Antony J. Cutler, Karola Rehnström, Kate Downes, Luigi Grassi, Myrto Kostadima, Paula Freire-Pritchett, Fan Wang, Hendrik G. Stunnenberg, John A. Todd, Daniel R. Zerbino, Oliver Stegle, Willem H. Ouwehand, Mattia Frontini, Chris Wallace, Mikhail Spivakov, Peter Fraser
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-021-92932-3

Dietary phosphorus and calcium in feed affects miRNA profiles and their mRNA targets in jejunum of two strains of laying hens
Cited by: 6
Author(s): Muhammad Arsalan Iqbal, Asghar Ali, Frieder Hadlich, Michael Oster, Henry Reyer, Nares Trakooljul, Vera Sommerfeld, M. Rodehutscord, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-91864-2

Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML
Cited by: 2
Author(s): Parastoo Modarres, Farzaneh Mohamadi Farsani, Amir Abas Nekouie, Sadeq Vallian
Software Mentions: 4
Published: over 3 years ago

10.1016/j.celrep.2019.07.091

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes
Cited by: 204
Author(s): Myles Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A. Hackney, Nandhini Ramamoorthi, Christopher R. John, David S. Watson, Sarah Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michèle Bombardieri, Nora Ng, Maria DiCicco, Désirée van der Heijde, Robert Landewé, Annette H M van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis
Software Mentions: 4
Published: over 5 years ago

10.1016/j.celrep.2020.107857

GM-CSF Calibrates Macrophage Defense and Wound Healing Programs during Intestinal Infection and Inflammation
Cited by: 65
Author(s): Tomas Castro‐Dopico, Aaron Fleming, Thomas W. Dennison, John R. Ferdinand, Katherine Harcourt, Benjamin J Stewart, M Zaeem Cader, Zewen Kelvin Tuong, Chenzhi Jing, Laurence S.C. Lok, Rebeccah J. Mathews, Anaïs Portet, Arthur Kaser, Simon Clare, Menna R. Clatworthy
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0228933

Transcriptomic analysis to elucidate the response of honeybees (Hymenoptera: Apidae) to amitraz treatment
Cited by: 5
Author(s): Ye Liang, Peng Liu, Tengfei Shi, Wang AnRan, Yujie Zhu, Lai Li, Linsheng Yu
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0244643

Characterization of cerebrospinal fluid (CSF) microbiota from patients with CSF shunt infection and reinfection using high throughput sequencing of 16S ribosomal RNAgenes
Cited by: 5
Author(s): Kathryn B. Whitlock, Charles E. Pope, Paul Hodor, Lucas R. Hoffman, David L. Limbrick, Patrick J. McDonald, Jason S. Hauptman, Jeffrey G. Ojemann, Tamara D. Simon
Software Mentions: 4
Published: almost 4 years ago

10.3390/genes11091106

Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies
Cited by: 15
Author(s): Franc Casanova Ferrer, Marı́a Pascual, Marta R. Hidalgo, Pablo Malmierca-Merlo, Consuelo Guerri, Francisco García‐García
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0032080

Knockdown of SF-1 and RNF31 Affects Components of Steroidogenesis, TGFβ, and Wnt/β-catenin Signaling in Adrenocortical Carcinoma Cells
Cited by: 20
Author(s): Anna Ehrlund, Philip Jonsson, Lise Lotte Vedin, Cecilia Williams, Jan Åke Gustafsson, Eckardt Treuter
Software Mentions: 3
Published: over 12 years ago

10.1016/j.jhepr.2021.100237

Aramchol downregulates stearoyl CoA-desaturase 1 in hepatic stellate cells to attenuate cellular fibrogenesis
Cited by: 26
Author(s): Dipankar Bhattacharya, Brittany Basta, José M. Mato, Amanda Craig, David Fernández–Ramos, Fernando Lopitz‐Otsoa, Darya Tsvirkun, Liat Hayardeny, Vasuretha Chandar, Robert E. Schwartz, Augusto Villanueva, Scott L. Friedman
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0004001

TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database
Cited by: 29
Author(s): Fabrice Lopez, Julien Textoris, Aurélie Bergon, Gilles Didier, Élisabeth Rémy, Samuel Granjeaud, Jean Imbert, Catherine Nguyen, Denis Puthier
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0006646

Genome-Wide mRNA Expression Analysis of Hepatic Adaptation to High-Fat Diets Reveals Switch from an Inflammatory to Steatotic Transcriptional Program
Cited by: 55
Author(s): Marijana Radonjić, Jorn R. de Haan, Marjan J. van Erk, Ko Willems van Dijk, Sjoerd A.A. van den Berg, Philip J. de Groot, Michael Müller, Ben van Ommen
Software Mentions: 3
Published: over 15 years ago

10.1155/2015/140819

MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation
Cited by: 13
Author(s): Luman Wang, Qiaochu Mo, Jianxin Wang
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0128845

Comparison of High-Level Microarray Analysis Methods in the Context of Result Consistency
Cited by: 37
Author(s): Kornel Chromiński, Magdalena Tkacz
Software Mentions: 3
Published: over 9 years ago

10.1172/jci.insight.148652

CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking
Cited by: 1
Author(s): Tábata Takahashi França, Ashraf Al-Sbiei, Ghada Bashir, Yassir A. Mohamed, Ranieri Coelho Salgado, Lucila Akune Barreiros, Sarah Maria da Silva Napoleão, Cristiane Seganfredo Weber, Janáira Fernandes Severo Ferreira, Carolina Sánchez Aranda, Carolina Prando, Mayra B. de Barros Dorna, Igor Jurišica, Maria J. Fernández-Cabezudo, Hans D. Ochs, Antônio Condino‐Neto, Basel K. al-Ramadi, Otávio Cabral-Marques
Software Mentions: 3
Published: about 3 years ago

10.1172/jci.insight.97011

Peripheral tissues reprogram CD8+ T cells for pathogenicity during graft-versus-host disease
Cited by: 19
Author(s): Pedro M. Sousa, Séverine Cire, Thomas Conlan, Laura Jardine, Claire Tkacz, Ivana R. Ferrer, C Lomas, Sophie Ward, Heather C. West, Simone Dertschnig, Sven Blobner, Terry K. Means, Stephen Henderson, Daniel H. Kaplan, Matthew Collin, Vincent Plagnol, Clare Bennett, Ronjon Chakraverty
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0224900

UM171 induces a homeostatic inflammatory-detoxification response supporting human HSC self-renewal
Cited by: 28
Author(s): Jalila Chagraoui, Bernhard Lehnertz, Simon Girard, Jean François Spinella, Iman Fares, Elisa Tomellini, Nadine Mayotte, Sophie Corneau, Tara MacRae, Laura Simon, Guy Sauvageau
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.38309

High N-glycan multiplicity is critical for neuronal adhesion and sensitizes the developing cerebellum to N-glycosylation defect
Cited by: 41
Author(s): Daniel Medina-Cano, Ekin Ucuncu, Lam Son Nguyen, Michaël Nicouleau, Joanna Lipecka, Jean-Charles Bizot, Christian Thiel, François Foulquier, Nathalie Lefort, Catherine Faivre‐Sarrailh, Laurence Colleaux, Ida Chiara Guerrera, Vincent Cantagrel
Software Mentions: 3
Published: about 6 years ago

10.1093/gbe/evw059

Genetic Evidence of Human Adaptation to a Cooked Diet
Cited by: 26
Author(s): Rachel N. Carmody, Michael Dannemann, Adrian W. Briggs, Birgit Nickel, Emily Groopman, Richard W. Wrangham, Janet Kelso
Software Mentions: 3
Published: over 8 years ago

10.1038/onc.2015.399

The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma
Cited by: 32
Author(s): Jill E. Hunter, Jacqueline Butterworth, Bo Zhao, Hélène Sellier, Kirsteen J. Campbell, Huw D. Thomas, Chris M. Bacon, Simon Cockell, Benjamin E. Gewurz, Neil D. Perkins
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0029917

Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe
Cited by: 29
Author(s): Huei-Mei Chen, Adam P. Rosebrock, Sohail Khan, Bruce Futcher, Janet Leatherwood
Software Mentions: 3
Published: almost 13 years ago

10.1186/s13027-021-00357-4

Identification of key genes in hepatitis B associated hepatocellular carcinoma based on WGCNA
Cited by: 6
Author(s): Chang Liu, Qinghai Dai, Qian Ding, Min Wei, Xiaohong Kong
Software Mentions: 3
Published: over 3 years ago

10.1186/s13395-015-0059-1

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging
Cited by: 72
Author(s): Jing Su, Carl Johan Ekman, Nikolay Oskolkov, Leo Lahti, Kristoffer Ström, Alvis Brāzma, Leif Groop, Johan Rung, Ola Hansson
Software Mentions: 3
Published: about 9 years ago

10.1515/jib-2018-0080

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer
Cited by: 0
Author(s): Nimisha Asati, Abhinav Mishra, Ayush Shukla, Tiratha Raj Singh
Software Mentions: 3
Published: over 5 years ago

10.1111/jipb.13026

Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores
Cited by: 14
Author(s): M. Estrella Santamaría, Alejandro Dorado García, Ana Arnáiz, Irene Rosa‐Diaz, Gara Romero‐Hernandez, Isabel Dı́az, Manuel Martínez
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0228964

Genetic characteristics of Jiaji Duck by whole genome re-sequencing
Cited by: 7
Author(s): Lihong Gu, Wang Feng, Zhemin Lin, Tieshan Xu, Dajie Lin, Manping Xing, Shuo Yang, Zhe Chao, Baoguo Ye, Licong Peng, Chunhui Hui, Lizhi Liu, Shuisheng Hou
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-021-02323-0

Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
Cited by: 46
Author(s): Gareth Benjamin Gillard, Lars Grønvold, Line Lieblein Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, J. Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen Rød Sandve, Torgeir R. Hvidsten
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2013-14-10-r110

Modeling precision treatment of breast cancer
Cited by: 263
Author(s): Anneleen Daemen, Obi L. Griffith, Laura M. Heiser, Nicholas J. Wang, Oana Enache, Zachary Sanborn, François Pépin, Steffen Durinck, James E. Korkola, Malachi Griffith, Joe S. Hur, Nam Huh, Jongsuk Chung, Leslie Cope, Mary Jo Fackler, Christopher B. Umbricht, Saraswati Sukumar, Pankaj Seth, Vikas P. Sukhatme, Lakshmi R. Jakkula, Yiling Lu, Gordon B. Mills, Raymond J. Cho, Eric A. Collisson, Laura J. van’t Veer, Paul T. Spellman, Joe W. Gray
Software Mentions: 3
Published: almost 12 years ago

10.1186/gb-2012-13-4-r31

Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel
Cited by: 33
Author(s): Marieke Simonis, Santosh S. Atanur, Sam E.V. Linsen, Victor Guryev, Frans-Paul Ruzius, Laurence Gamé, Nico Lansu, Ewart de Bruijn, Sebastiaan van Heesch, Steven J.M. Jones, Michal Pravenec, Tim Aitman, Edwin Cuppen
Software Mentions: 3
Published: almost 13 years ago

10.3390/ijms18091900

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data
Cited by: 3
Author(s): Wolfgang Kaisers, Holger Schwender, Heiner Schaal
Software Mentions: 3
Published: about 7 years ago

10.1038/s41419-019-1397-4

EMT is associated with an epigenetic signature of ECM remodeling genes
Cited by: 83
Author(s): Paul Peixoto, Amandine Etcheverry, Marc Aubry, Anaïs Missey, Camille Lachat, Jérôme Perrard, Elodie Hendrick, Régis Delage-Mourroux, Jean Mosser, Christophe Borg, Jean-Paul Feugeas, Michaël Herfs, Michaël Boyer-Guittaut, Éric Hervouet
Software Mentions: 3
Published: over 5 years ago

10.1186/gb-2012-13-4-r30

Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium
Cited by: 49
Author(s): Simen M. Kristoffersen, Chad P. Haase, M. Ryan Weil, Karla D. Passalacqua, Faheem Niazi, Stephen Hutchison, Brian Desany, Anne Brit Kolstø, Nicolas J. Tourasse, Timothy D. Read, Ole Andreas Økstad
Software Mentions: 3
Published: almost 13 years ago

10.1186/gb-2010-11-8-r80

Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development
Cited by: 29
Author(s): Noëlle Billon, Raivo Kolde, Jüri Reimand, Miguel Caetano Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani
Software Mentions: 3
Published: almost 15 years ago

10.1186/s13326-016-0079-8

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease
Cited by: 16
Author(s): Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 3
Published: over 8 years ago

10.1186/2041-1480-2-S1-S1

Biomedical semantics in the Semantic Web
Cited by: 12
Author(s): Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M. Scott Marshall
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-016-0971-7

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies
Cited by: 156
Author(s): Björn Bakker, Aaron Taudt, Mirjam E. Belderbos, David Porubský, Diana C.J. Spierings, Tristan de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S.J.M. de Bont, Anke van den Berg, Victor Guryev, Peter M Lansdorp, Maria Colomé-Tatché, Floris Foijer
Software Mentions: 3
Published: over 8 years ago

10.1074/jbc.RA119.010302

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription
Cited by: 51
Author(s): Leonie Kollenstart, Anton J.L. de Groot, George M.C. Janssen, Xue Cheng, Kees Vreeken, Fabrizio Martino, Jacques Côté, Peter A. van Veelen, Haico van Attikum
Software Mentions: 3
Published: almost 5 years ago

10.1074/jbc.M117.784629

The transcription factor Pax6 is required for pancreatic β cell identity, glucose-regulated ATP synthesis, and Ca2+ dynamics in adult mice
Cited by: 48
Author(s): Ryan K. Mitchell, Marie‐Sophie Nguyen‐Tu, Pauline Chabosseau, Rebecca Callingham, Timothy J. Pullen, Rebecca Cheung, Isabelle Leclerc, David J. Hodson, Guy A. Rutter
Software Mentions: 3
Published: over 7 years ago

10.1074/jbc.M114.634816

Early Growth Response Genes 2 and 3 Regulate the Expression of Bcl6 and Differentiation of T Follicular Helper Cells
Cited by: 26
Author(s): Ane Ogbe, Tizong Miao, Alistair L. J. Symonds, Becky Omodho, Randeep Singh, Punamdip Bhullar, Suling Li, Ping Wang
Software Mentions: 3
Published: over 9 years ago

10.1186/s13073-016-0335-7

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq
Cited by: 104
Author(s): David Redmond, Asaf Poran, Olivier Elemento
Software Mentions: 3
Published: over 8 years ago

10.1186/jbiol53

Dosage compensation is less effective in birds than in mammals
Cited by: 300
Author(s): Yuichiro Itoh, Esther Melamed, Xia Yang, Kathy Kampf, Susanna Wang, Nadir Yehya, Atila van Nas, Kirstin Replogle, Mark Band, David F. Clayton, Eric E. Schadt, Aldons J. Lusis, Arthur P. Arnold
Software Mentions: 3
Published: almost 18 years ago

10.1007/s00109-012-0925-9

Early steps of microglial activation are directly affected by neuroprotectant FK506 in both in vitro inflammation and in rat model of stroke
Cited by: 33
Author(s): Małgorzata Zawadzka, Michal Dabrowski, Agata Gozdz, Barbara Szadujkis, Marcin Sliwa, Maciej Lipko, Bożena Kamińska
Software Mentions: 3
Published: over 12 years ago

10.1007/s12263-014-0439-x

White adipose tissue reference network: a knowledge resource for exploring health-relevant relations
Cited by: 10
Author(s): Thomas Kelder, Georg Summer, Martien P. M. Caspers, Evert M. van Schothorst, Jaap Keijer, Loes P. M. Duivenvoorde, К. Schimrigk, Anja Voigt, Laura Bohnert, Catalina Picó, M. Luisa Bonet, A. Dembińska-Kieć, Małgorzata Malczewska-Malec, Beata Kieć‐Wilk, Josep Maria del Bas, Antoni Caimari, Lluı́s Arola, Marjan van Erk, Ben van Ommen, Marijana Radonjić
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0031623

Genome Wide Adaptations of Plasmodium falciparum in Response to Lumefantrine Selective Drug Pressure
Cited by: 26
Author(s): Leah Mwai, Abdi Diriye, Victor Masseno, Steven Muriithi, Theresa Feltwell, Jennifer Musyoki, Jacob E. Lemieux, Avi Feller, Gunnar R. Mair, Kevin Marsh, Chris Newbold, Alexis Nzila, Céline Carret
Software Mentions: 3
Published: over 12 years ago

10.1128/mSphere.00305-16

Coordinate Regulation of Antimycin and Candicidin Biosynthesis
Cited by: 34
Author(s): Thomas C McLean, Paul A. Hoskisson, Ryan F. Seipke
Software Mentions: 3
Published: almost 8 years ago

10.1128/mSystems.00025-15

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions
Cited by: 111
Author(s): Jie Tan, John H. Hammond, Deborah A. Hogan, Casey S. Greene
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0241754

Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak
Cited by: 9
Author(s): Fredrick Eyase, Solomon Langat, Irina Maljkovic Berry, Francis Mulwa, Albert Nyunja, James Mu, Samuel Owaka, Samson Limbaso, Victor Ofula, Hellen Koka, Edith Koskei, Joel Lutomiah, Richard G. Jarman, Rosemary Sang
Software Mentions: 3
Published: about 4 years ago

10.1128/mBio.02684-19

Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources
Cited by: 49
Author(s): Stephen K. Dolan, Michael Kohlstedt, Stephen Trigg, Pedro P. Vallejo Ramirez, Clemens F. Kaminski, Christoph Wittmann, Martin Welch
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0246983

Who infects whom?—Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data
Cited by: 9
Author(s): Annette Nigsch, Suelee Robbe‐Austerman, Tod Stuber, Paulina D. Pavinski Bitar, Yrjö T. Gröhn, Y.H. Schukken
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.31362

A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree
Cited by: 11
Author(s): Marta Losa, Víctor Latorre, Munazah Andrabi, Franck Ladam, Charles G. Sagerström, Ana Nóvoa, Peyman Zarrineh, Laure Bridoux, Neil A. Hanley, Bernard Malissen, Nicoletta Bobola
Software Mentions: 3
Published: about 7 years ago

10.1155/2014/345106

Comparison of Merging and Meta-Analysis as Alternative Approaches for Integrative Gene Expression Analysis
Cited by: 45
Author(s): Jonatan Taminau, Cosmin Lazar, Stijn Meganck, Ann Nowé
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0130262

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq
Cited by: 31
Author(s): Luis Fernando García-Ortega, Octavio Martínez
Software Mentions: 3
Published: over 9 years ago

10.3390/jof4030081

Identification of Antifungal Targets Based on Computer Modeling
Cited by: 10
Author(s): Elena Bencúrová, Shishir Gupta, Edita Sarukhanyan, Thomas Dandekar
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0227154

Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers
Cited by: 8
Author(s): A. K. Lindholm‐Perry, H. C. Freetly, W. T. Oliver, Lea A. Rempel, Brittney N Keel
Software Mentions: 3
Published: almost 5 years ago

10.1155/2017/2568706

Genomewide Expression and Functional Interactions of Genes under Drought Stress in Maize
Cited by: 34
Author(s): Nepolean Thirunavukkarasu, R.C. Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Mittal Shikha, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta K. Dash, Firoz Hossain, H. S. Gupta
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.53944

Loss of centromere function drives karyotype evolution in closely related Malassezia species
Cited by: 37
Author(s): Sundar Ram Sankaranarayanan, Giuseppe Ianiri, Marco A. Coelho, Hashim Reza, Bhagya C. Thimmappa, Promit Ganguly, Rakesh Netha Vadnala, Sheng Sun, Rahul Siddharthan, Christian Tellgren-Roth, Thomas L. Dawson, Joseph Heitman, Kaustuv Sanyal
Software Mentions: 3
Published: almost 5 years ago

10.1128/mBio.01871-18

Structural and Nonstructural Genes Contribute to the Genetic Diversity of RNA Viruses
Cited by: 27
Author(s): Natalie D. Collins, Andrew S. Beck, Steven G. Widen, Thomas G. Wood, Stephen Higgs, Alan D.T. Barrett
Software Mentions: 3
Published: about 6 years ago

10.1186/gb-2008-9-10-r146

A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection
Cited by: 19
Author(s): Amanda Greenall, Guiyuan Lei, Daniel Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J. Wilkinson, David Lydall
Software Mentions: 3
Published: almost 17 years ago

10.1186/s13059-016-0992-2

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cited by: 330
Author(s): Jonathan Cairns, Paula Freire-Pritchett, Steven W. Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel R. Zerbino, Stefan Schoenfelder, Biola M. Javierre, Cameron S. Osborne, Peter Fraser, Mikhail Spivakov
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0243684

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)
Cited by: 19
Author(s): Roger Brown, Lindsey Moore, Amir Mani, Sonal Patel, Irene Salinas
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0222921

Computational identification of key genes that may regulate gene expression reprogramming in Alzheimer’s patients
Cited by: 20
Author(s): Judith A. Potashkin, Virginie Bottero, José A. Santiago, James P. Quinn
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-017-09490-w

The epigenetic modifier Fam208a is required to maintain epiblast cell fitness
Cited by: 6
Author(s): Shohag Bhargava, Brian Cox, Christiana Polydorou, Veronika Gresakova, Vladimír Kořínek, Hynek Strnad, Radislav Sedláček, Trevor Epp, Kallayanee Chawengsaksophak
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-6-268

MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data
Cited by: 20
Author(s): Mahendra Navarange, Laurence Gamé, Derek Fowler, Vihar Wadekar, H. Stanley Banks, Nicola Cooley, Fatimah Rahman, Justin Hinshelwood, Peter Broderick, Helen C. Causton
Software Mentions: 3
Published: about 19 years ago

10.1371/journal.pone.0253859

Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome
Cited by: 8
Author(s): Sujata Srikanth, Lavanya Jain, Cinthya J. Zepeda-Mendoza, Lauren Cascio, Kelly A. Jones, Rini Pauly, Barb DuPont, Curtis Rogers, Sara M. Sarasua, Katy Phelan, Cynthia C. Morton, Luigi Boccuto
Software Mentions: 3
Published: over 3 years ago

10.1186/bcr3150

Relevance of PTEN loss in brain metastasis formation in breast cancer patients
Cited by: 87
Author(s): Harriet Wikman, Katrin Lamszus, Niclas Detels, Liubov Uslar, Michaela Wrage, Christian Benner, Ina Hohensee, Bauke Ylstra, Kathrin Eylmann, Marc Zapatka, Guido Sauter, Dirk Kemming, Markus Glatzel, Volkmar Müller, Manfred Westphal, Klaus Pantel
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0226905

Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells
Cited by: 9
Author(s): Xiangqin Ji, Penglei Jiang, Juntao Luo, Mengjia Li, Yajing Bai, Junfang Zhang, Bingshe Han
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0154556

The Ontology for Biomedical Investigations
Cited by: 228
Author(s): Anita Bandrowski, Ryan R. Brinkman, Mathias Brochhausen, Matthew Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, F. Gibson, Alejandra González-Beltrán, Melissa Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez‐Boussard, Mark A. Jensen, Yuling Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa Soldatova, Christian J. Stoeckert, Chris Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng
Software Mentions: 3
Published: over 8 years ago

10.1038/srep32417

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 20
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 3
Published: about 8 years ago

10.1038/s41597-019-0011-z

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley
Cited by: 21
Author(s): Camilla Beate Hill, Debbie Wong, Josquin Tibbits, Kerrie Forrest, Matthew Hayden, Xiaoqi Zhang, Sharon Westcott, Tefera Tolera Angessa, Chengdao Li
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0251565

The protein and volatile components of trail mucus in the Common Garden Snail, Cornu aspersum
Cited by: 7
Author(s): Kaylene R. Ballard, Anne Klein, R. Andrew Hayes, Tianfang Wang, Scott F. Cummins
Software Mentions: 3
Published: over 3 years ago

10.1038/s41597-019-0046-1

Navigating in vitro bioactivity data by investigating available resources using model compounds
Cited by: 1
Author(s): Sten Ilmjärv, Fiona Augsburger, Jerven Bolleman, Robin Liechti, Alan Bridge, Jenny Sandström, Vincent Jaquet, Ioannis Xenarios, Karl-Heinz Krause
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-462

Effects of functional feeds on the lipid composition, transcriptomic responses and pathology in heart of Atlantic salmon (Salmo salar L.) before and after experimental challenge with Piscine Myocarditis Virus (PMCV)
Cited by: 34
Author(s): Laura Martínez-Rubio, Øystein Evensen, Aleksei Krasnov, Sven Martin Jørgensen, Simón Wadsworth, Kari Ruohonen, Jose L. González Vecino, Douglas R. Tocher
Software Mentions: 3
Published: almost 11 years ago

10.1007/s12551-018-0490-8

Mining data and metadata from the gene expression omnibus
Cited by: 64
Author(s): Zichen Wang, Alexander Lachmann, Avi Ma’ayan
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0179065

Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis
Cited by: 64
Author(s): Thomas Mohr, Verena Haudek-Prinz, Astrid Slany, Johannes Grillari, M. Micksche, Christopher Gerner
Software Mentions: 3
Published: over 7 years ago

10.3390/biom2010001

Exploring the Optimal Strategy to Predict Essential Genes in Microbes
Cited by: 4
Author(s): Jingyuan Deng, Lirong Tan, Xiaodong Lin, Yao Lu, Long Lu
Software Mentions: 3
Published: almost 13 years ago

10.1155/2020/5156304

Comprehensive Analyses of miRNA-mRNA Network and Potential Drugs in Idiopathic Pulmonary Arterial Hypertension
Cited by: 8
Author(s): Chan Li, Zeyu Zhang, Qian Xu, Ruizheng Shi
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-11-455

Next generation tools for genomic data generation, distribution, and visualization
Cited by: 46
Author(s): David A. Nix, Tonya L Di Sera, Brian Dalley, Brett Milash, Robert M Cundick, Kevin S Quinn, Samir Courdy
Software Mentions: 3
Published: about 14 years ago

10.1038/s41598-017-12989-x

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells
Cited by: 62
Author(s): Simone Rizzetto, Auda A. Eltahla, Peijie Lin, Rowena A. Bull, Andrew R. Lloyd, Joshua W. K. Ho, Vanessa Venturi, Fabio Luciani
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2105-11-421

Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
Cited by: 35
Author(s): Wei‐Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun‐Yi Shu, Yun‐Shien Lee, Tzu‐Hao Wang, Ji-Hong Hong, Chia-Yang Li, Ian C. Hsu
Software Mentions: 3
Published: over 14 years ago

10.1155/2015/146250

An Association Rule Mining Approach to Discover lncRNAs Expression Patterns in Cancer Datasets
Cited by: 7
Author(s): Paolo Cremaschi, Roberta Carriero, Stefania Astrologo, Caterina Colì, Antonella Lisa, Silvia Parolo, Silvia Bione
Software Mentions: 3
Published: almost 10 years ago

10.7150/jca.60647

FOXD3-induced miR-133a blocks progression and metastasis of colorectal cancer through regulating UBA2
Cited by: 4
Author(s): Yuanfang Cheng, Yajuan Wang, Yuanzun Cheng, Qingmei Yang, Lejing Zhang, Zhaoxi Li, Jiancheng Cheng
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-10-50

EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data
Cited by: 66
Author(s): Michael Dondrup, Stefan P. Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane Katja Kleindt, H. Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J. Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann
Software Mentions: 3
Published: almost 16 years ago

10.1186/s13062-016-0152-3

Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
Cited by: 14
Author(s): Suyan Tian, Howard H. Chang, Chi Wang
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2164-12-373

Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis
Cited by: 64
Author(s): Andrea Saß, Angela Marchbank, Elizabeth Tullis, John J. LiPuma, Eshwar Mahenthiralingam
Software Mentions: 3
Published: over 13 years ago

10.7150/jca.38741

Construction and validation of an eight-gene signature with great prognostic value in bladder cancer
Cited by: 13
Author(s): Xin Yan, Xun Fu, Zixin Guo, Xiaoping Li, Tong-Zu Liu, Sheng Li
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2164-8-9

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists
Cited by: 48
Author(s): Alexandre Gattiker, Riccarda Rischatsch, Philippe Demougin, Sylvia Voegeli, Fred S. Dietrich, Peter Philippsen, Michael Primig
Software Mentions: 3
Published: almost 18 years ago

10.1371/journal.pone.0240269

Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases
Cited by: 6
Author(s): Rosana Veroneze, Sâmia Cruz Tfaile Corbi, Bárbara Roque da Silva, Cristiane S. Rocha, Cláudia Vianna Maurer-Morelli, Silvana Regina Perez Orrico, Joni Augusto Cirelli, Fernando J. Von Zuben, Raquel Mantuaneli Scarel‐Caminaga
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0238809

MicroRNA expression profiles in molecular subtypes of clear-cell renal cell carcinoma are associated with clinical outcome and repression of specific mRNA targets
Cited by: 3
Author(s): Annelies Verbiest, Vincent van Hoef, Cristina Rodríguez‐Antona, Jesús García-Donás, Osvaldo Graña‐Castro, Maarten Albersen, Marcella Baldewijns, Annouschka Laenen, Eduard Roussel, Patrick Schöffski, Agnieszka Woźniak, Stefano Caruso, Gabrielle Couchy, Jessica Zucman–Rossi, Benoît Beuselinck
Software Mentions: 3
Published: about 4 years ago

10.1534/g3.119.401031

Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines
Cited by: 13
Author(s): William F. Mueller, Petra Jakob, Han Sun, Sandra Clauder‐Münster, Sonja Ghidelli-Disse, Diana Paola Serralde Ordóñez, Markus Böesche, Marcus Bantscheff, Paul Collier, Bettina Haase, Vladimı́r Beneš, Malte Paulsen, Peter Sehr, Joe Lewis, Gerard Drewes, Lars M. Steinmetz
Software Mentions: 3
Published: over 4 years ago

10.1186/2043-9113-2-22

mCOPA: analysis of heterogeneous features in cancer expression data
Cited by: 18
Author(s): Chenwei Wang, Alperen Taciroglu, Stefan Maetschke, Colleen C. Nelson, Mark A. Ragan, Melissa J. Davis
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12859-016-1210-7

Tilting the lasso by knowledge-based post-processing
Cited by: 9
Author(s): Kukatharmini Tharmaratnam, Matthew Sperrin, Thomas Jaki, Sjur Reppe, Arnoldo Frigessi
Software Mentions: 3
Published: about 8 years ago

10.3389/fphar.2019.00198

A Meta-Analysis of the Performance of a Blood-Based Exposure Response Gene Signature Across Clinical Studies on the Tobacco Heating System 2.2 (THS 2.2)
Cited by: 2
Author(s): Florian Martin, Marja Talikka, Nikolai V. Ivanov, Christelle Haziza, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962