bioconductor: ArrayExpress | Projects

10.1098/rstb.2017.0073

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing
Cited by: 12
Author(s): Clare Pacini, Magdalena J. Koziol
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-10-147

Effects of sample size on robustness and prediction accuracy of a prognostic gene signature
Cited by: 79
Author(s): Seon‐Young Kim
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0089187

Miz1 Deficiency in the Mammary Gland Causes a Lactation Defect by Attenuated Stat5 Expression and Phosphorylation
Cited by: 7
Author(s): Adrián Sanz-Moreno, David Fuhrmann, Elmar Wolf, Björn von Eyß, Martin Eilers, Hans–Peter Elsässer
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1003868

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection
Cited by: 71
Author(s): Nicholas J. Croucher, Andrea M. Mitchell, Katherine A. Gould, Donald Inverarity, Lars Barquist, Theresa Feltwell, María Fookes, Simon R. Harris, Janina Dordel, Susannah J. Salter, Sarah Browall, Helena Žemličková, Julian Parkhill, Staffan Normark, Birgitta Henriques‐Normark, Jason Hinds, Tim Mitchell, Stephen D. Bentley
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pgen.1009679

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

10.7717/peerj.175

Data reuse and the open data citation advantage
Cited by: 358
Author(s): Heather Piwowar
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0242200

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
Cited by: 17
Author(s): N. A. Zinovieva, Arsen V Dotsev, A.A. Sermyagin, Tatiana Deniskova, Alexandra Abdelmanova, В. Р. Харзинова, Johann Sölkner, Henry Reyer, Klaus Wimmers, Gottfried Brem
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.0030145

Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
Cited by: 80
Author(s): Marica Grs̆ković, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
Software Mentions: 3
Published: about 17 years ago

10.1186/1471-2350-13-25

Systems analysis of inflammatory bowel disease based on comprehensive gene information
Cited by: 7
Author(s): Satoru Suzuki, Takako Toda, Yutaka Fukuoka, Dennis P. Wall, Hiroshi Tanaka, Peter J. Tonellato
Software Mentions: 3
Published: over 12 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0251245

Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus
Cited by: 6
Author(s): Amanda K. Kitten, Laurajo Ryan, Grace C. Lee, Belinda T. Flores, Kelly R. Reveles
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0224448

Understanding allergic multimorbidity within the non-eosinophilic interactome
Cited by: 10
Author(s): Daniel Aguilar, Nathanaël Lemonnier, Gerard H. Koppelman, Erik Melén, Baldo Oliva, Mariona Pinart, Stefano Guerra, Jean Bousquet, Josep M. Antó
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0223341

Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma
Cited by: 29
Author(s): David Hervás‐Marín, Faatiemah Higgins, O. Sanmartín, José Antonio Löpez‐Guerrero, M. Carmen Bañó, J. Carlos Igual, Inma Quilis, Juan Sandoval
Software Mentions: 3
Published: almost 5 years ago

10.3390/nu13082521

A Convergent Functional Genomics Analysis to Identify Biological Regulators Mediating Effects of Creatine Supplementation
Cited by: 5
Author(s): Diego A. Bonilla, Yurany Moreno, Eric S. Rawson, Diego A. Forero, Jeffrey R. Stout, Chad M. Kerksick, Michael D. Roberts, Richard B. Kreider
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0229467

Discovery of antitumor lectins from rainforest tree root transcriptomes
Cited by: 3
Author(s): Atip Lawanprasert, Caitlin A. Guinan, Erica A. Langford, Carly E. Hawkins, Janna N. Sloand, Howard W. Fescemyer, Matthew R. Aronson, Jacob A. Halle, James H. Marden, Scott H. Medina
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-7-228

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts
Cited by: 26
Author(s): Claudia Mabel Terenti Romero, David DeShazer, Tamara Feldblyum, Jacques Ravel, Donald E. Woods, Heenam Stanley Kim, Yan Yu, Catherine M. Ronning, William C. Nierman
Software Mentions: 3
Published: about 18 years ago

10.1371/journal.pone.0039766

Myoferlin Depletion in Breast Cancer Cells Promotes Mesenchymal to Epithelial Shape Change and Stalls Invasion
Cited by: 44
Author(s): Ruth Li, William E. Ackerman, Cosmin Mihai, Leonithas I. Volakis, Samir N. Ghadiali, Douglas A. Kniss
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0147475

Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women
Cited by: 11
Author(s): Hao He, Shaolong Cao, Tianhua Niu, Yu Zhou, Lan Zhang, Yong Zeng, Wei Zhu, Yu Ping Wang, Hong‐Wen Deng
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1000574

Alternative Splicing of NURF301 Generates Distinct NURF Chromatin Remodeling Complexes with Altered Modified Histone Binding Specificities
Cited by: 53
Author(s): So Yeon Kwon, Hua Xiao, Carl Wu, Paul Badenhorst
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0231376

Exploring differentially expressed genes between anagen and telogen secondary hair follicle stem cells from the Cashmere goat (Capra hircus) by RNA-Seq
Cited by: 14
Author(s): Nimantana He, Rui Su, Zhiying Wang, Yanjun Zhang, Jinquan Li
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-14-514

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data
Cited by: 15
Author(s): Leandro Hermida, Carine Poussin, Michael Stadler, Sylvain Gubian, Alain Sewer, Dimos Gaidatzis, Hans-Rudolf Hotz, Florian Martin, Vincenzo Belcastro, Stéphane Cano, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 3
Published: almost 12 years ago

10.1002/1878-0261.12522

PARP1 expression in soft tissue sarcomas is a poor‐prognosis factor and a new potential therapeutic target
Cited by: 15
Author(s): François Bertucci, Pascal Finetti, Audrey Monneur, Delphine Perrot, Christine Chevreau, Axel Le Cesne, Jean‐Yves Blay, Olivier Mir, Daniel Birnbaum
Software Mentions: 3
Published: over 5 years ago

10.4172/jpb.1000370

Mining the Breast Cancer Proteome for Predictors of Drug Sensitivity
Cited by: 7
Author(s): Leslie C Timpe Dian Li, Ten Yang Yen Judi Wong
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.isci.2021.102848

Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana
Cited by: 10
Author(s): Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Antonia Angelopoulou, C.-L. Jen, William Duddy, Γεράσιμος Δάρας, Polydefkis Hatzopoulos, David Westhead, Ioannis Michalopoulos
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-10-420

Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation
Cited by: 13
Author(s): Tamara Aid-Pavlidis, Pavlos Pavlidis, Tõnis Timmusk
Software Mentions: 3
Published: almost 16 years ago

10.18632/oncotarget.7248

MicroRNA-34a promotes genomic instability by a broad suppression of genome maintenance mechanisms downstream of the oncogene KSHV-vGPCR
Cited by: 14
Author(s): Claudia J. Krause, Oliver Popp, Nanthakumar Thirunarayanan, Gunnar Dittmar, Martin Lipp, Gerd Müller
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0253864

The KrasG12D;Trp53fl/fl murine model of undifferentiated pleomorphic sarcoma is macrophage dense, lymphocyte poor, and resistant to immune checkpoint blockade
Cited by: 3
Author(s): Karys Hildebrand, Arvind K. Singla, Reid McNeil, Kayla L. Marritt, Kurt Hildebrand, Franz J. Zemp, Jahanara Rajwani, Doha Itani, Pinaki Bose, Douglas J. Mahoney, Frank R. Jirik, Michael J. Monument
Software Mentions: 3
Published: over 3 years ago

10.1155/2020/5943014

Bioinformatic Identification of Neuroblastoma Microenvironment-Associated Biomarkers with Prognostic Value
Cited by: 4
Author(s): Yi Wang, Huan Luo, Jing Cao, Chi Ma
Software Mentions: 3
Published: about 4 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-8-428

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
Cited by: 226
Author(s): S. Pilati, Michele Perazzolli, A. Malossini, Alessandro Cestaro, L. Dematté, Paolo Fontana, A. Dal Rì, Roberto Viola, Riccardo Velasco, C. Moser
Software Mentions: 3
Published: about 17 years ago

10.1016/j.molmet.2020.101015

The type 2 diabetes gene product STARD10 is a phosphoinositide-binding protein that controls insulin secretory granule biogenesis
Cited by: 20
Author(s): Gaëlle Carrat, Elizabeth Haythorne, Alejandra Tomás, Leena Haataja, Andreas Müller, Peter Arvan, Alexandra Piunti, Kaiying Cheng, Mutian Huang, Timothy J. Pullen, Eleni Georgiadou, Theodoros Stylianides, Nur Shabrina Amirruddin, Victoria Salem, Walter Distaso, Andrew Cakebread, Kate J Heesom, Philip A. Lewis, David J. Hodson, Linford J.B. Briant, Annie Fung, Richard B. Sessions, Fabien Alpy, Alice Pik‐Shan Kong, Peter I. Benke, Federico Torta, Adrian Kee Keong Teo, Isabelle Leclerc, Michele Solimena, Dale B. Wigley, Guy A. Rutter
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-019-49410-8

Spodoptera frugiperda transcriptional response to infestation by Steinernema carpocapsae
Cited by: 13
Author(s): Louise Huot, Simon C. George, Pierre-Alain Girard, Dany Séverac, Nicolas Nègre, Bernard Duvic
Software Mentions: 3
Published: about 5 years ago

10.1016/j.mce.2020.111007

Hypoxia regulates GR function through multiple mechanisms involving microRNAs 103 and 107
Cited by: 11
Author(s): Nan Yang, Andrew Berry, Carolin M Sauer, Matthew Baxter, Ian J. Donaldson, Karen Forbes, Rachelle Donn, Laura Matthews, David Ray
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-11-73

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Cited by: 11
Author(s): Mark Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0064497

Gene Expression Profiling of Solitary Fibrous Tumors
Cited by: 21
Author(s): François Bertucci, Corinne Bouvier‐Labit, Pascal Finetti, Philippe Métellus, José Adelaı̈de, Karima Mokhtari, Dominique Figarella‐Branger, Anne‐Valérie Decouvelaere, Catherine Miquel, Jean‐Michel Coindre, Daniel Birnbaum
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-10-98

SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip® expression data
Cited by: 26
Author(s): Adriane Menßen, Götz Edinger, Joachim R. Grün, Ulrike Haase, Ria Baumgrass, Andreas Grützkau, Andreas Radbruch, G.-R. Burmester, Thomas Häupl
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12943-020-01155-z

Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme
Cited by: 57
Author(s): Mathilde Cheray, Amandine Etcheverry, Camille Jacques, Romain Pacaud, Gwenola Bougras-Cartron, Marc Aubry, Florent Denoual, Pierre Peterlongo, Arulraj Nadaradjane, Joséphine Briand, Farida Akcha, Dominique Heymann, François M. Vallette, Jean Mosser, Benjamin Ory, Pierre-François Cartron
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-14-127

Genetic analysis of the Trichuris muris-induced model of colitis reveals QTL overlap and a novel gene cluster for establishing colonic inflammation
Cited by: 20
Author(s): Scott Levison, Paul Fisher, Jenny Hankinson, Leo Zeef, Steve Eyre, William Ollier, John McLaughlin, Andy Brass, Richard K. Grencis, Joanne L. Pennock
Software Mentions: 3
Published: over 11 years ago

10.1186/s12943-016-0554-y

Systems analysis identifies miR-29b regulation of invasiveness in melanoma
Cited by: 18
Author(s): Miles C. Andrews, Joseph Cursons, Daniel Hurley, Matthew Anaka, Jonathan Cebon, Andreas Behren, Edmund J. Crampin
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0226707

High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer
Cited by: 15
Author(s): Ryotaro Ohkuma, Erica Yada, Shumpei Ishikawa, Daisuke Komura, Hidenobu Ishizaki, Koji Tamada, Yutaro Kubota, Kazuyuki Hamada, Hiroo Ishida, Yuya Hirasawa, Hirotsugu Ariizumi, Etsuko Satoh, Midori Shida, Makoto Watanabe, Rie Onoue, Kiyohiro Ando, Junji Tsurutani, Kiyoshi Yoshimura, Takehiko Yokobori, Tetsuro Sasada, Takeshi Aoki, Masahiko Murakami, Tomoko Norose, Nobuyuki Ohike, Masafumi Takimoto, Masahiko Izumizaki, Shinichi Kobayashi, Takuya Tsunoda, Satoshi Wada
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms21082818

Identification of the Key Molecular Drivers of Phosphorus Utilization Based on Host miRNA-mRNA and Gut Microbiome Interactions
Cited by: 14
Author(s): Siriluck Ponsuksili, Henry Reyer, Frieder Hadlich, Frank Weber, Nares Trakooljul, Michael Oster, Puntita Siengdee, Eduard Muráni, M. Rodehutscord, Amélia Camarinha‐Silva, Jörn Bennewitz, Klaus Wimmers
Software Mentions: 3
Published: over 4 years ago

10.1523/ENEURO.0226-19.2019

Mega-Analysis of Gene Expression in Mouse Models of Alzheimer’s Disease
Cited by: 6
Author(s): Beryl Zhuang, B. Ogan Mancarci, Lilah Toker, Paul Pavlidis
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-27258-8

A data mining paradigm for identifying key factors in biological processes using gene expression data
Cited by: 13
Author(s): Jin Li, Le Zheng, Akihiko Uchiyama, Lianghua Bin, Theodora M. Mauro, Peter M. Elias, Tadeusz Pawełczyk, Monika Sakowicz-Burkiewicz, Magdalena Trzeciak, Donald Y.M. Leung, María I. Morasso, Peng Yu
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-23514-z

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level
Cited by: 22
Author(s): Vicky L. Hunt, Akinori Hino, Akemi Yoshida, Taisei Kikuchi
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-15-S14-S4

linkedISA: semantic representation of ISA-Tab experimental metadata
Cited by: 55
Author(s): Alejandra N. González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0115911

The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues
Cited by: 14
Author(s): Sandra Andersson, Kenneth Nilsson, Linn Fagerberg, Björn M. Hallström, Christer Sundström, Anna Danielsson, Karolina Edlund, Mathias Uhlén, Anna Asplund
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-017-17730-2

Constitutively elevated levels of SOCS1 suppress innate responses in DF-1 immortalised chicken fibroblast cells
Cited by: 28
Author(s): Efstathios S. Giotis, CS Ross, RC Robey, Axel Nohturfft, Stephen Goodbourn, Michael A. Skinner
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-25085-5

RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Cited by: 67
Author(s): Anda R. Gliga, Sebastiano Di Bucchianico, Jessica M. Lindvall, Bengt Fadeel, Hanna Karlsson
Software Mentions: 3
Published: over 6 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

10.1371/journal.pone.0234299

Yellow sea mediated segregation between North East Asian Dryophytes species
Cited by: 18
Author(s): Amaël Borzée, Kevin R. Messenger, Shinhyeok Chae, Desiree Andersen, Jordy Groffen, Ye Inn Kim, Junghwa An, Siti N. Othman, Kyongsin Ri, Tu Yong Nam, Yoonhyuk Bae, Jin Ren, Jia Tang Li, Ming‐Feng Chuang, Yoonjung Yi, Yucheol Shin, Taejoon Kwon, Yikweon Jang, Mi Sook Min
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-26170-5

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions
Cited by: 6
Author(s): David Talavera, Christopher J. Kershaw, Joseph L. Costello, Lydia M. Castelli, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Graham D. Pavitt, Simon J. Hubbard
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-35868-5

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
Cited by: 11
Author(s): Suzanne Vanhauwaert, Bieke Decaesteker, Sara De Brouwer, Carina Leonelli, Kaat Durinck, Pieter Mestdagh, Jo Vandesompele, Karen Sermon, Geertrui Denecker, Christophe Van Neste, Franki Speleman, Katleen De Preter
Software Mentions: 3
Published: almost 6 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

10.3390/microarrays5030023

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories
Cited by: 9
Author(s): Sriram P. Chockalingam, Maneesha Aluru, Srinivas Aluru
Software Mentions: 3
Published: about 8 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

10.3390/metabo11040221

Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling
Cited by: 5
Author(s): Özlem Altay, Cheng Cheng Zhang, Hasan Türkez, Jens Nielsen, Mathias Uhlén, Adil Mardinoğlu
Software Mentions: 3
Published: over 3 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

10.1038/sdata.2018.198

RNA-seq of macrophages of amoeboid or mesenchymal migratory phenotype due to specific structure of environment
Cited by: 13
Author(s): Vladimı́r Čermák, Aneta Gandalovičová, Ladislav Merta, Jitka Fučíková, Radek Špíšek, Daniel Rösel, Jan Brábek
Software Mentions: 3
Published: about 6 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: over 7 years ago

10.1038/s41598-019-43862-8

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Cited by: 53
Author(s): Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0005559

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni
Cited by: 32
Author(s): Anna V. Protasio, Stijn van Dongen, Julie Collins, Leonor Quintais, Diogo M Ribeiro, Florian Sessler, Martin Hunt, Gabriel Rinaldi, James J. Collins, Anton J. Enright, Matthew Berriman
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pntd.0008059

Exposure of Anopheles mosquitoes to trypanosomes reduces reproductive fitness and enhances susceptibility to Plasmodium
Cited by: 10
Author(s): Constentin Dieme, Natalia Marta Zmarlak, Emma Brito-Fravallo, Christelle Travaillé, Adrien Pain, Floriane Cherrier, Corinne Genève, Estefanía Calvo-Álvarez, Michelle M. Riehle, Kenneth D. Vernick, Brice Rotureau, Christian Mitri
Software Mentions: 3
Published: almost 5 years ago

10.18632/aging.103073

MicroRNA-375 exacerbates knee osteoarthritis through repressing chondrocyte autophagy by targeting ATG2B
Cited by: 30
Author(s): Hongxing Li, Zhiling Li, Yigang Pi, Yang Chen, Lin Mei, Yiliao Luo, Jingping Xie, Xinzhan Mao
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-018-5176-x

funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data
Cited by: 5
Author(s): Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1003067

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function
Cited by: 102
Author(s): Jacy L. Wagnon, Michael Briese, Wenzhi Sun, Connie L. Mahaffey, Tomaž Curk, Gregor Rot, Jernej Ule, Wayne N. Frankel
Software Mentions: 3
Published: almost 12 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

10.7150/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

10.1002/cam4.1633

Molecular heterogeneity in human papillomavirus‐dependent and ‐independent vulvar carcinogenesis
Cited by: 16
Author(s): Dorian R.A. Swarts, Quirinus J.M. Voorham, Annina P. van Splunter, Saskia M. Wilting, Daoud Sie, Divera T.M. Pronk, Marc van Beurden, Daniëlle A.M. Heideman, Peter J.F. Snijders, Chris J.L.M. Meijer, Renske D.M. Steenbergen, Maaike Bleeker
Software Mentions: 3
Published: over 6 years ago

10.1007/s00262-020-02718-1

Immune checkpoint-related serum proteins and genetic variants predict outcomes of localized prostate cancer, a cohort study
Cited by: 35
Author(s): Qinchuan Wang, Yuanqing Ye, Hao Yu, Shu-Hong Lin, Huakang Tu, Dong Liang, David W. Chang, Maosheng Huang, Xifeng Wu
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2105-13-S14-S5

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: about 12 years ago

10.1186/s12935-021-01932-w

SNRPD1 confers diagnostic and therapeutic values on breast cancers through cell cycle regulation
Cited by: 7
Author(s): Xiaofeng Dai, Lihui Yu, Xiao Chen, Jianying Zhang
Software Mentions: 3
Published: over 3 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/s12859-020-3364-6

Detection of suspicious interactions of spiking covariates in methylation data
Cited by: 0
Author(s): Miriam Sieg, Gregor Richter, Arne S. Schäefer, Jochen Kruppa
Software Mentions: 3
Published: almost 5 years ago

10.3389/fphys.2018.00618

Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response
Cited by: 14
Author(s): Korbinian Bösl, Miriam S. Giambelluca, Markus Haug, Marit Bugge, Terje Espevik, Richard K. Kandasamy, Bjarte Bergstrøm
Software Mentions: 3
Published: over 6 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

10.1186/1471-2164-11-27

Genomics Portals: integrative web-platform for mining genomics data
Cited by: 13
Author(s): Kaustubh Shinde, Mukta Phatak, Johannes M. Freudenberg, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jarosław Meller, Mario Medvedovic
Software Mentions: 3
Published: almost 15 years ago

10.1093/bib/bby051

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Cited by: 103
Author(s): Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura E. Taggart, Huiru Zheng, Eileen E. Parkes, Jaine K. Blayney
Software Mentions: 3
Published: over 5 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

10.1186/s12864-019-5748-4

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Cited by: 1
Author(s): Dirkjan Schokker, Ina Hulsegge, H. Woelders, Johanna M.J. Rebel
Software Mentions: 3
Published: over 5 years ago

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: about 13 years ago

10.1186/bcr2926

Identification of germline alterations of the mad homology 2 domain of SMAD3 and SMAD4 from the Ontario site of the breast cancer family registry (CFR)
Cited by: 17
Author(s): Eric Tram, Irada Ibrahim‐Zada, Laurent Briollais, Julia A. Knight, Irene L. Andrulis, Hilmi Özçelik
Software Mentions: 3
Published: over 13 years ago

10.1186/s12859-019-2912-4

TACITuS: transcriptomic data collector, integrator, and selector on big data platform
Cited by: 2
Author(s): Salvatore Alaimo, Annalisa Di Maria, Dennis Shasha, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1005250

Genetic Regulation of Bone Metabolism in the Chicken: Similarities and Differences to Mammalian Systems
Cited by: 41
Author(s): Martin Johnsson, Kenneth B. Jonsson, Leif C. Andersson, Per Jensen, I. A. Wright
Software Mentions: 3
Published: over 9 years ago

10.3389/fphys.2019.00433

Increasing Upstream Chromatin Long–Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells
Cited by: 16
Author(s): Angus Li, Yu Sun, Charles Drummer, Yifan Lu, Daohai Yu, Yan Zhou, Xinyuan Li, Simone J. Pearson, Candice Johnson, Catherine C. Yu, William Y. Yang, Kevin Mastascusa, Xiaohua Jiang, Jianxin Sun, Thomas J. Rogers, Wenhui Hu, Hong Wang, Xiaofeng Yang
Software Mentions: 3
Published: over 5 years ago

10.1186/bcr2256

Gene expression in murine mammary epithelial stem cell-like cells shows similarities to human breast cancer gene expression
Cited by: 46
Author(s): Cecilia Williams, Luísa A. Helguero, Karin Edvardsson, Lars Arne Haldosén, Jan‐Åke Gustafsson
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2105-6-264

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination
Cited by: 33
Author(s): David G. Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, Andrew J. Wood, Karim Nashar, Douglas B. Kell, Andy Brass
Software Mentions: 2
Published: about 19 years ago

10.1186/bcr2109

PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes
Cited by: 25
Author(s): Anna Git, Inmaculada Spiteri, Cherie Blenkiron, Mark J. Dunning, Jessica C. Pole, Suet-Feung Chin, Yanzhong Wang, James Smith, Frederick J. Livesey, Carlos Caldas
Software Mentions: 2
Published: over 16 years ago

10.1186/bcr2192

A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer
Cited by: 117
Author(s): Fabien Reyal, Martin H. van Vliet, Nicola J. Armstrong, Hugo M. Horlings, Karin E. de Visser, M Kok, Andrew E. Teschendorff, Stella Mook, Laura van ’t Veer, Carlos Caldas, Rémy Salmon, Marc J. van de Vijver, Lodewyk F.A. Wessels
Software Mentions: 2
Published: about 16 years ago

10.1186/bcr2334

Genomic profiling of breast tumours in relation to BRCAabnormalities and phenotypes
Cited by: 131
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Óskar Þór Jóhannsson, Katrín Ólafsdóttir, Margrét Steinarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-9-232

Genomic analysis of post-mating changes in the honey bee queen (Apis mellifera)
Cited by: 122
Author(s): Sarah D. Kocher, Freddie-Jeanne Richard, David R. Tarpy, Christina M. Grozinger
Software Mentions: 2
Published: over 16 years ago

10.1186/bcr3403

Embryonic mammary signature subsets are activated in Brca1 -/- and basal-like breast cancers
Cited by: 47
Author(s): Marketa Zvelebil, Erik Oliemuller, Qiong Gao, Olivia Wansbury, Alan Mackay, Howard Kendrick, Matthew J. Smalley, Jorge S. Reis‐Filho, Beatrice A. Howard
Software Mentions: 2
Published: over 11 years ago

10.3389/fnana.2016.00086

HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development
Cited by: 63
Author(s): Susan Lindsay, Yaobo Xu, Steven Lisgo, Lauren F. Harkin, Andrew J. Copp, Dianne Gerrelli, Gavin J. Clowry, Aysha Talbot, Michael J. Keogh, Jonathan Coxhead, Mauro Santibanez‐Koref, Patrick F. Chinnery
Software Mentions: 2
Published: about 8 years ago

10.1186/s13058-015-0539-6

Mouse mammary stem cells express prognostic markers for triple-negative breast cancer
Cited by: 32
Author(s): Kelly Soady, Howard Kendrick, Qiong Gao, Andrew Tutt, Marketa Zvelebil, Liliana Ordonez, Jelmar Quist, David Wei-Min Tan, Clare M. Isacke, Anita Grigoriadis, Matthew J. Smalley
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-6-101

MARS: Microarray analysis, retrieval, and storage system
Cited by: 59
Author(s): Michael Maurer, Robert Molidor, Alexander Sturn, Jürgen Hartler, Hubert Hackl, Gernot Stocker, Andreas Prokesch, Marcel Scheideler, Zlatko Trajanoski
Software Mentions: 2
Published: over 19 years ago

10.1590/1414-431X2020e10388

Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification
Cited by: 0
Author(s): Lucas Delmonico, John C. Obenauer, Thomas P. Stockfisch, Marcia V. Fournier
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-020-03932-5

GEOlimma: differential expression analysis and feature selection using pre-existing microarray data
Cited by: 4
Author(s): Liangqun Lu, Kevin Townsend, Bernie J. Daigle
Software Mentions: 2
Published: almost 4 years ago

10.1002/biot.201100305

Molecular signatures from omics data: From chaos to consensus
Cited by: 103
Author(s): Jaeyun Sung, Yuliang Wang, Sriram Chandrasekaran, Daniela Witten, Nathan D. Price
Software Mentions: 2
Published: over 12 years ago

10.3389/fmicb.2018.01955

Active HHV-6 Infection of Cerebellar Purkinje Cells in Mood Disorders
Cited by: 41
Author(s): Bhupesh K. Prusty, Nitish Gulve, Sheila Govind, G. R. F. Krueger, Julia Feichtinger, Lee Larcombe, Richard Aspinall, Dharam V. Ablashi, Carla Toro
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.01314

Network-Based Analysis of OMICs Data to Understand the HIV–Host Interaction
Cited by: 13
Author(s): Sergey Ivanov, Alexey Lagunin, Dmitry Filimonov, O. Tarasova
Software Mentions: 2
Published: over 4 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962