bioconductor: ArrayExpress | Projects

10.1186/bcr3116

Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker
Cited by: 102
Author(s): Ida Johansson, Cecilia Nilsson, Pontus Berglund, Martin Lauss, Markus Ringnér, Håkan Olsson, Lena Luts, Edith Sim, Sten Thorstensson, Marie-Louise Fjällskog, Ingrid Hedenfalk
Software Mentions: 5
Published: over 12 years ago

10.1038/s41598-019-47343-w

A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line
Cited by: 9
Author(s): Nikolaï Genov, Alireza Basti, Marconi Abreu, Rosario Astaburuaga, Angela Relógio
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0184795

F-MAP: A Bayesian approach to infer the gene regulatory network using external hints
Cited by: 4
Author(s): Maryam Shahdoust, Hamid Pezeshk, Hossein Mahjub, Mehdi Sadeghi
Software Mentions: 5
Published: over 6 years ago

10.1186/s13068-021-01915-z

Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species
Cited by: 10
Author(s): Jose J De Vega, Abel Teshome, Manfred Klaas, Jim Grant, John Finnan, Susanne Barth
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.ppat.1002567

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy
Cited by: 197
Author(s): Adam J. Reid, Sarah J. Vermont, James A. Cotton, David J. Harris, Grant A. Hill-Cawthorne, Stephanie Könen‐Waisman, Sophia M. Latham, Tobias Mourier, Rebecca Norton, Michael A. Quail, Mandy Sanders, Dhanasekaran Shanmugam, Amandeep Sohal, James D. Wasmuth, Brian P. Brunk, Michael E. Grigg, Jonathan C. Howard, John Parkinson, David S. Roos, A. J. Trees, Matthew Berriman, Arnab Pain, Jonathan M. Wastling
Software Mentions: 5
Published: about 12 years ago

10.1371/journal.pone.0236889

Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia
Cited by: 13
Author(s): Rhiannon L. Wallace, Dieter Bulach, Amy V. Jennison, Mary Valcanis, Angus McLure, James J. Smith, Trudy Graham, Themy Saputra, Simon M. Firestone, Sally Symes, Natasha Waters, Anastasia Stylianopoulos, Martyn Kirk, Kathryn Glass
Software Mentions: 5
Published: almost 4 years ago

10.1038/sdata.2018.136

A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0118731

Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis
Cited by: 77
Author(s): Katherine C. H. Amrine, Bárbara Blanco-Ulate, Dario Cantu
Software Mentions: 5
Published: about 9 years ago

10.1155/2020/6034670

Bioinformatics Analysis to Screen the Key Prognostic Genes in Tumor Microenvironment of Bladder Cancer
Cited by: 6
Author(s): Zhao Zhang, Dongshan Chen, Zeyan Li, Zhao Liu, Lei Yan, Zhonghua Xu
Software Mentions: 5
Published: over 4 years ago

10.3389/fnut.2021.675935

Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue
Cited by: 1
Author(s): Marianthi Kalafati, Michael Lenz, Gökhan Ertaylan, Ilja C. W. Arts, Chris T. Evelo, Marleen M.J. van Greevenbroek, Ellen E. Blaak, Michiel E. Adriaens, Martina Kutmon
Software Mentions: 5
Published: almost 3 years ago

10.3389/fonc.2014.00251

Hidden Treasures in â€œAncientâ€ Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue
Cited by: 14
Author(s): Konstantinos Kerkentzes, Vincenzo Lagani, Ioannis Tsamardinos, Mogens Vyberg, Oluf Dimitri Røe
Software Mentions: 5
Published: over 9 years ago

10.1186/s13062-015-0051-z

Test on existence of histology subtype-specific prognostic signatures among early stage lung adenocarcinoma and squamous cell carcinoma patients using a Cox-model based filter
Cited by: 25
Author(s): Suyan Tian, Chi Wang, Ming-Wen An
Software Mentions: 5
Published: about 9 years ago

10.18632/oncotarget.23748

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of <i>COX7A1</i> in embryonic and cancer cells
Cited by: 27
Author(s): Michael West, Ivan Labat, Hal Sternberg, Dana Larocca, Igor O. Nasonkin, Karen Chapman, Ratnesh Singh, Eugene Makarev, Alex Aliper, Andrey Kazennov, Andrey Alekseenko, Nikolai Shuvalov, Evgenia Cheskidova, Aleksandr Alekseev, Artemov Av, Evgeny Putin, Polina Mamoshina, Nikita Pryanichnikov, Jacob Larocca, Karen A. F. Copeland, Evgeny Izumchenko, Mikhail Korzinkin, Alex Zhavoronkov
Software Mentions: 5
Published: over 6 years ago

10.1007/s11306-015-0879-3

Data standards can boost metabolomics research, and if there is a will, there is a way
Cited by: 89
Author(s): Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Elon Correa, Saravanan Dayalan, Alejandra González-Beltrán, Timothy M. D. Ebbels, Royston Goodacre, Janna Hastings, Kenneth Haug, Albert Koulman, Macha Nikolski, Matej Orešič, Susanna-Assunta Sansone, Daniel Schober, James M. Smith, Christoph Steinbeck, Mark R. Viant, Steffen Neumann
Software Mentions: 5
Published: over 8 years ago

10.1186/1471-2105-14-174

PMTED: a plant microRNA target expression database
Cited by: 46
Author(s): Xiaofan Sun, Boquan Dong, Lingjie Yin, Rongzhi Zhang, Wei Du, Dongfeng Liu, Nan Shi, Aili Li, Yanchun Liang, Long Mao
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0232963

Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury
Cited by: 11
Author(s): Eric Zhang, Thanh Nguyen, Meng Zhao, Son Do Hai Dang, Jake Y. Chen, Weihua Bian, Gregory P. Walcott
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pntd.0002905

Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions
Cited by: 59
Author(s): Young Jun Choi, Matthew T. Aliota, George F. Mayhew, Sara M. Erickson, Bruce M. Christensen
Software Mentions: 5
Published: almost 10 years ago

10.1093/bioinformatics/btt016

Grape RNA-Seq analysis pipeline environment
Cited by: 28
Author(s): David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó
Software Mentions: 5
Published: over 11 years ago

10.1186/s12864-018-4746-2

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Cited by: 19
Author(s): Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann‐Kristin Östlund Farrants, Neus Visa
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pgen.1000302

The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex
Cited by: 171
Author(s): Tobias Straub, Charlotte Grimaud, Gregor D. Gilfillan, Angelika Mitterweger, Peter B. Becker
Software Mentions: 5
Published: over 15 years ago

10.1371/journal.pgen.1007559

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
Cited by: 141
Author(s): Rachel Kaletsky, Victoria Yao, April Williams, Alexi Runnels, Alicja Tadych, Shaoqiang Zhou, Olga G. Troyanskaya, Coleen T. Murphy
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-77777-6

Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas
Cited by: 6
Author(s): Paul Tran, Lynn Tran, John Nechtman, Bruno dos Santos, Sharad Purohit, Khaled Bin Satter, Boying Dun, Ravindra Kolhe, Suash Sharma, Roni J. Bollag, Jin Xiong She
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1007793

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise
Cited by: 26
Author(s): Stefanie Schöne, Melissa Bothe, Edda Einfeldt, Marina Borschiwer, Philipp Benner, Martin Vingron, Morgane Thomas‐Chollier, Sebastiaan H. Meijsing
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0238557

eDNA metabarcoding as a biomonitoring tool for marine protected areas
Cited by: 67
Author(s): Zachary Gold, Joshua Sprague, David J. Kushner, Erick Zerecero Marin, Paul H. Barber
Software Mentions: 5
Published: about 3 years ago

10.3389/fimmu.2019.02999

Opioids Impair Intestinal Epithelial Repair in HIV-Infected Humanized Mice
Cited by: 37
Author(s): Jingjing Meng, Santanu Banerjee, Li Zhang, Gregory M. Sindberg, Shamsudheen Moidunny, Bin Li, David J. Robbins, Mohit Girotra, Bradley J. Segura, Sundaram Ramakrishnan, Sabita Roy
Software Mentions: 5
Published: over 4 years ago

10.1186/s12918-015-0174-y

SEEK: a systems biology data and model management platform
Cited by: 79
Author(s): Katy Wolstencroft, Stuart Owen, Olga Krebs, Quyen Le Hoang Thuy To Nguyen, Natalie J. Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lin An, David Shockley, Jacky L. Snoep, Wolfgang Mueller, Carole Goble
Software Mentions: 5
Published: almost 9 years ago

10.3389/fimmu.2018.01661

Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia
Cited by: 128
Author(s): Nándor Gábor Than, Roberto Romero, Adi L. Tarca, Katalin A. Kékesi, Yi Xu, Zhonghui Xu, Kata Juhász, Gaurav Bhatti, Ron Leavitt, Zsolt Gelencser, János Pálhalmi, Tzu Hung Chung, Balázs Győrffy, László Orosz, Attila Demeter, Anett Szecsi, Éva Hunyadi‐Gulyás, Zsuzsanna Darula, Attila Simor, Katalin Éder, S. Szabó, Vanessa Topping, Haidy Elazzamy, Christopher LaJeunesse, Andrea Balogh, Gábor Szalai, Susan Land, Olga Török, Zhong Dong, Ilona Kovalszky, András Falus, Hamutal Meiri, Sorin Drăghici, Sonia S. Hassan, Tinnakorn Chaiworapongsa, M Krispin, Martin Knöfler, Offer Erez, Graham J. Burton, Chong Jai Kim, Gábor Juhász, Zoltán Papp
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12885-017-3103-1

Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia
Cited by: 21
Author(s): Yock-Ping Chow, Hamidah Alias, Rahman Jamal
Software Mentions: 5
Published: over 7 years ago

10.3389/fgene.2019.00855

Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments
Cited by: 0
Author(s): Adele Ribeiro, Júlia Maria Pavan Soler, Roberto Hirata
Software Mentions: 5
Published: over 4 years ago

10.3389/fimmu.2021.657162

Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness
Cited by: 3
Author(s): Eléna Gonçalves, Yolanda Guillén, Javier R. Lama, Jorge Sánchez, Christian Berthou, Roger Paredes, Béhazine Combadière
Software Mentions: 5
Published: about 3 years ago

10.1186/1752-0509-7-12

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework
Cited by: 12
Author(s): Gaurav Kumar, Edmond J. Breen, Shoba Ranganathan
Software Mentions: 5
Published: over 11 years ago

10.1186/s12859-020-03633-z

PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients
Cited by: 10
Author(s): Young‐Chul Kim, Daewon Kim, Biwei Cao, Rodrigo Carvajal, Minjung Kim
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0226253

DNA metabarcoding-based diet survey for the Eurasian otter (Lutra lutra): Development of a Eurasian otter-specific blocking oligonucleotide for 12S rRNA gene sequencing for vertebrates
Cited by: 16
Author(s): Priyanka Kumari, Ke Dong, Kyung-Yeon Eo, Woo-Shin Lee, Junko Kimura, Naomichi Yamamoto
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2229-8-99

Regulon organization of Arabidopsis
Cited by: 95
Author(s): Wieslawa I. Mentzen, Eve Syrkin Wurtele
Software Mentions: 5
Published: over 16 years ago

10.1186/1471-2105-14-75

virtualArray: a R/bioconductor package to merge raw data from different microarray platforms
Cited by: 51
Author(s): Andreas Heider, Rüdiger Alt
Software Mentions: 5
Published: about 11 years ago

10.12688/f1000research.18276.2

Using equivalence class counts for fast and accurate testing of differential transcript usage
Cited by: 9
Author(s): Marek Cmero, N. Davidson, Alicia Oshlack
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pbio.1001229

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Cited by: 91
Author(s): Robert K. Bradley, Jason J. Merkin, Nicole Lambert, Christopher B. Burge
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pbio.3001166

Neural stem cells traffic functional mitochondria via extracellular vesicles
Cited by: 79
Author(s): Luca Peruzzotti-Jametti, Joshua D. Bernstock, Cory M. Willis, Giulia Manferrari, Rebecca Rogall, Erika Fernández-Vizarra, James C Williamson, Alice Braga, Aletta van den Bosch, Tommaso Leonardi, Grzegorz Krzak, Ágnes Kittel, Cristiane Benincá, Nunzio Vicario, Sisareuth Tan, Carlos Bastos, Iacopo Bicci, Nunzio Iraci, JA Smith, Ben Peacock, Karin H. Müller, Paul J. Lehner, Edit I. Buzás, Nuno Faria, Massimo Zeviani, Christian Frezza, Alain Brisson, Nicholas J Matheson, Carlo Viscomi, Stefano Pluchino
Software Mentions: 5
Published: about 3 years ago

10.1186/1471-2229-10-150

Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms
Cited by: 129
Author(s): Dennis Janz, Katja Behnke, Jörg‐Peter Schnitzler, Basem Kanawati, Philippe Schmitt‐Kopplin, Andrea Polle
Software Mentions: 5
Published: almost 14 years ago

10.1016/j.dib.2019.103909

RNA-sequencing data highlighting the time-of-day-dependent transcriptome of the central circadian pacemaker in Sox2-deficient mice
Cited by: 4
Author(s): Arthur H. Cheng, Pascale Bouchard-Cannon, Rob W. Ness, Hai-Ying Mary Cheng
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2105-9-558

SPRINT: A new parallel framework for R
Cited by: 33
Author(s): Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence Sloan, Florian Scharinger, Arthur Trew, Peter Ghazal
Software Mentions: 5
Published: over 15 years ago

10.1038/s42003-020-0989-y

IDO1+ Paneth cells promote immune escape of colorectal cancer
Cited by: 22
Author(s): Sandra Pflügler, Jasmin Svinka, Irene Scharf, Ilija Crnčec, Martin Filipits, Pornpimol Charoentong, Markus Tschurtschenthaler, Lukas Kenner, Monira Awad, Judith Stift, Marina Schernthanner, Romana Bischl, Dietmar Herndler‐Brandstetter, Elisabeth Glitzner, Herwig P. Moll, Emilio Casanova, Gerald Timelthaler, Maria Sibilia, Michael Gnant, Sigurd Lax, Josef Thaler, Mathias Müller, Birgit Strobl, Thomas Mohr, Arthur Kaser, Zlatko Trajanoski, Gerwin Heller, Robert Eferl
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13148-019-0608-2

Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes
Cited by: 34
Author(s): Louise F. Porter, Neil Saptarshi, Yongxiang Fang, Sonika Rathi, Anneke I. den Hollander, Eiko K. de Jong, Simon J. Clark, Paul Bishop, Timothy W. Olsen, Triantafillos Liloglou, Venkata R M Chavali, Luminita Paraoan
Software Mentions: 5
Published: over 5 years ago

10.1093/database/bau027

The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences
Cited by: 11
Author(s): Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, Pål Sætrom
Software Mentions: 5
Published: over 10 years ago

10.1186/1471-2164-10-63

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes
Cited by: 16
Author(s): Steven P. Wilder, Pamela J. Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 5
Published: over 15 years ago

10.1186/s13148-021-01083-9

Estimands in epigenome-wide association studies
Cited by: 9
Author(s): Jochen Kruppa, Miriam Sieg, Gregor Richter, Anne Pohrt
Software Mentions: 5
Published: about 3 years ago

10.1093/database/bau068

yStreX: yeast stress expression database
Cited by: 11
Author(s): Kwanjeera Wanichthanarak, Intawat Nookaew, Dina Petranović
Software Mentions: 5
Published: over 10 years ago

10.1016/j.molcel.2018.09.033

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: over 5 years ago

10.1016/j.joca.2018.12.015

Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage
Cited by: 30
Author(s): Bola Ajekigbe, Kathleen Cheung, Yaobo Xu, Andrew Skelton, Andreas Panagiotopoulos, Jamie Soul, Timothy E. Hardingham, David J. Deehan, M.J. Barter, David A. Young
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0106524

Discovering Study-Specific Gene Regulatory Networks
Cited by: 8
Author(s): V. Dal Bò, Tanya Y. Curtis, Artem Lysenko, Mansoor Saqi, Stephen Swift, Allan Tucker
Software Mentions: 5
Published: over 9 years ago

10.3390/microarrays3040212

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Cited by: 1
Author(s): Andrew R. Dalby, Ian Bailey
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0050253

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Cited by: 2
Author(s): Andrew R. Dalby, Ibrahim Emam, Raimo Franke
Software Mentions: 5
Published: over 11 years ago

10.1016/j.cels.2018.06.011

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 63
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0227303

Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection
Cited by: 8
Author(s): Yuanxiu Wang, Guihong Xiong, Zhe He, Mingfeng Yan, M. Q. Zou, Junxi Jiang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-016-3288-8

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
Cited by: 24
Author(s): Giovanna Ambrosini, René Dreos, Sunil Kumar, Philipp Bücher
Software Mentions: 5
Published: over 7 years ago

10.26508/lsa.201800283

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
Cited by: 13
Author(s): Verena Thormann, Laura V. Glaser, Maika C. Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H. Meijsing
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-9-548

GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Cited by: 34
Author(s): Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J. Butte
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0183679

Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization
Cited by: 31
Author(s): Ewa Surdziel, Ieuan Clay, Florian Nigsch, Anke Thiemeyer, Cyril Allard, Gregory R. Hoffman, John S. Reece‐Hoyes, Tanushree Phadke, Romain Gambert, Caroline Gubser Keller, Marie-Gabrielle Ludwig, Birgit Baumgarten, Mathias Frederiksen, Dirk Schübeler, Klaus Seuwen, Tewis Bouwmeester, Barna D. Fodor
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0086699

Meta-Analysis and Gene Set Analysis of Archived Microarrays Suggest Implication of the Spliceosome in Metastatic and Hypoxic Phenotypes
Cited by: 2
Author(s): Bertrand De Meulder, Fabrice Berger, Eric Bareke, Sophie Depiereux, Carine Michiels, Eric Depiereux
Software Mentions: 4
Published: over 10 years ago

10.1038/leu.2016.251

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts
Cited by: 99
Author(s): Annalisa Mupo, Monika Seiler, Vijitha Sathiaseelan, Alena Pance, Yi Yang, Anant A. Agrawal, Francesco Iorio, Rubén Bautista, Suruchi Pacharne, Konstantinos Tzelepis, Nicla Manes, Penny Wright, Elli Papaemmanuil, David G. Kent, Peter Campbell, Silvia Buonamici, Niccolò Bolli, George S. Vassiliou
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0236348

Unraveling the molecular pathobiology of vocal fold systemic dehydration using an in vivo rabbit model
Cited by: 8
Author(s): Naíla Cannes do Nascimento, Andrea Pires dos Santos, M. Preeti Sivasankar, Abigail Cox
Software Mentions: 4
Published: almost 4 years ago

10.18632/oncotarget.22423

Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome
Cited by: 2
Author(s): Shana Claeys, Geertrui Denecker, Robrecht Cannoodt, Candy Kumps, Kaat Durinck, Franki Speleman, Katleen De Preter
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0206665

Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer
Cited by: 11
Author(s): Kanthida Kusonmano, Mari K. Halle, Elisabeth Wik, Erling A. Høivik, Camilla Krakstad, Karen Klepsland Mauland, Ingvild L. Tangen, Ansgar Berg, Henrica M.J. Werner, Jone Trovik, Anne Margrete Øyan, Karl‐Henning Kalland, Inge Jonassen, Helga B. Salvesen, Kjell Petersen
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21114115

Minor Splicing Factors Zrsr1 and Zrsr2 Are Essential for Early Embryo Development and 2-Cell-Like Conversion
Cited by: 16
Author(s): Isabel Gómez-Redondo, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Ricardo Laguna‐Barraza, Alfonso Gutiérrez‐Adán
Software Mentions: 4
Published: almost 4 years ago

10.1002/cam4.3367

Identification of small molecule drugs and development of a novel autophagy‐related prognostic signature for kidney renal clear cell carcinoma
Cited by: 9
Author(s): Qianwei Xing, Chengjian Ji, Bingye Zhu, Rong Cong
Software Mentions: 4
Published: almost 4 years ago

10.1186/1748-7188-7-19

Getting DNA copy numbers without control samples
Cited by: 1
Author(s): María Ortiz-Estévez, Ander Aramburu, Ángel Rubio
Software Mentions: 4
Published: almost 12 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Cited by: 25
Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.22689

Systematic assessment of cervical cancer initiation and progression uncovers genetic panels for deep learning-based early diagnosis and proposes novel diagnostic and prognostic biomarkers
Cited by: 32
Author(s): Nguyen Phuoc Long, Kyung Hee Jung, Sang Jun Yoon, Nguyễn Hoàng Anh, Tran Diem Nghi, Yun Pyo Kang, Pengcheng Zhang, Jung Eun Min, Sung Kyung Hong, Sung Won Kwon
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-017-4086-7

The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae
Cited by: 59
Author(s): Victoria A. Ingham, Patricia Pignatelli, Jonathan D. Moore, Simon C. Wagstaff, Hilary Ranson
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-16747-x

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
Cited by: 193
Author(s): Peter W. Eide, Jarle Bruun, Ragnhild Lothe, Anita Sveen
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-29077-3

Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks
Cited by: 58
Author(s): Franziska Liesecke, Dimitri Daudu, Rodolphe Dugé de Bernonville, Sébastien Besseau, Marc Clastre, Vincent Courdavault, Johan-Owen De Craene, Joël Crèche, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0227882

Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq
Cited by: 5
Author(s): Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp
Software Mentions: 4
Published: over 4 years ago

10.1093/bib/bbv049

Empirical comparison of structure-based pathway methods
Cited by: 24
Author(s): Maria K. Jaakkola, Laura L. Elo
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-018-32972-4

Cytoplasmic location of NR4A1 in aggressive lymphomas is associated with a favourable cancer specific survival
Cited by: 4
Author(s): Karoline Fechter, Julia Feichtinger, Katharina Prochazka, Julia Judith Unterluggauer, Katrin Pansy, Elisabeth Steinbauer, Martin Pichler, Johannes Haybaeck, Andreas Prokesch, Hildegard Greinix, Christine Beham–Schmid, Peter Neumeister, Gerhard G. Thallinger, Alexander Deutsch
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0227076

All of gene expression (AOE): An integrated index for public gene expression databases
Cited by: 29
Author(s): Hidemasa Bono
Software Mentions: 4
Published: over 4 years ago

10.1038/srep29832

Identification of host transcriptional networks showing concentration-dependent regulation by HPV16 E6 and E7 proteins in basal cervical squamous epithelial cells
Cited by: 7
Author(s): Stephen Smith, Cinzia G. Scarpini, Ian J. Groves, Richard Odle, Nicholas Coleman
Software Mentions: 4
Published: almost 8 years ago

10.1128/AEM.00853-19

Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens
Cited by: 25
Author(s): Eugen Pfeifer, Slawomir Michniewski, Cornelia Gätgens, Eugenia Münch, Felix L. Müller, Tino Polen, Andrew Millard, Bastian Blombach, Julia Frunzke
Software Mentions: 4
Published: over 4 years ago

10.1016/j.ccell.2019.08.003

Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis
Cited by: 230
Author(s): René Jackstadt, Sander R. van Hooff, Joshua D.G. Leach, Xabier Cortés-Lavaud, Jeroen Lohuis, Rachel A. Ridgway, Valérie M. Wouters, Jatin Roper, Timothy J. Kendall, Campbell S.D. Roxburgh, Paul G. Horgan, Colin Nixon, Craig Nourse, Matthias Gunzer, William Clark, Ann Hedley, Ömer H. Yılmaz, Mamunur Rashid, Peter J. Bailey, Andrew V. Biankin, Andrew D. Campbell, David J. Adams, Simon T. Barry, Colin W. Steele, Jan Paul Medema, Owen J. Sansom
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.23280

Validation of a hypoxia related gene signature in multiple soft tissue sarcoma cohorts
Cited by: 32
Author(s): Lingjian Yang, Laura Forker, Joely J. Irlam, Nischalan Pillay, Ananya Choudhury, Catharine M L West
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1009768

Trichuris muris infection drives cell-intrinsic IL4R alpha independent colonic RELMα+ macrophages
Cited by: 6
Author(s): Ruth Forman, Larisa Logunova, Hannah Smith, Kelly Wemyss, Iris Mair, Louis Boon, Judith E. Allen, Werner Müller, Joanne L. Pennock, Kathryn J. Else
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0001061

Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor
Cited by: 52
Author(s): Caitlin B. Conboy, Christiana Spyrou, Natalie Thorne, Elizabeth J. Wade, Nuno L. Barbosa‐Morais, Michael D. Wilson, Arindam Bhattacharjee, Richard A. Young, Simon Tavaré, Jacqueline A. Lees, Duncan T. Odom
Software Mentions: 4
Published: over 16 years ago

10.1530/REP-19-0293

Blastocyst transfer in mice alters the placental transcriptome and growth
Cited by: 4
Author(s): Katerina Menelaou, Malwina Prater, Simon James Tunster, Georgina E T Blake, Colleen Geary Joo, James C. Cross, Russell S. Hamilton, Erica D. Watson
Software Mentions: 4
Published: over 4 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0225658

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses
Cited by: 15
Author(s): Dominika Borowska, Richard Kuo, Richard Bailey, Kellie Watson, Pete Kaiser, Lonneke Vervelde, Mark P. Stevens
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0232120

Corticosterone and testosterone treatment influence expression of gene pathways linked to meiotic segregation in preovulatory follicles of the domestic hen
Cited by: 2
Author(s): E. Wróbel, Alexandra B. Bentz, W. Walter Lorenz, Steven T. Gardner, Mary T. Mendonça, Kristen J. Navara
Software Mentions: 4
Published: about 4 years ago

10.1093/jxb/eru094

Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley
Cited by: 63
Author(s): Julien Hollmann, Per L. Gregersen, Karin Krupinska
Software Mentions: 4
Published: about 10 years ago

10.3390/genes6010001

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1
Cited by: 53
Author(s): Kristina B. V. Døssing, Tina Binderup, Bogumił Kaczkowski, Anders Jacobsen, Maria Rossing, Ole Winther, Birgitte Federspiel, Ulrich Knigge, Andreas Kjær, Lennart Friis‐Hansen
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0238202

Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii
Cited by: 2
Author(s): Cindy Xu, Greer A. Dolby, K. Kristina Drake, Todd C. Esque, Kenro Kusumi
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-015-1689-8

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
Cited by: 15
Author(s): Lars Eijssen, Varshna Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo, Marijana Radonjić
Software Mentions: 4
Published: almost 9 years ago

10.3389/fpls.2015.00718

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones
Cited by: 20
Author(s): Itziar Frades, Kibrom B. Abreha, Estelle Proux‐Wéra, Åsa Lankinen, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: over 8 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: over 10 years ago

10.1155/2013/983805

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases
Cited by: 10
Author(s): Alberto Anguita, Miguel García-Remesal, Diana de la Iglesia, Víctor Maojo
Software Mentions: 4
Published: over 11 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-015-0485-4

NMF-mGPU: non-negative matrix factorization on multi-GPU systems
Cited by: 44
Author(s): Edgardo Mejía-Roa, Daniel Tabas-Madrid, Javier Setoaín, Carlos Garcı́a, Francisco Tirado, Alberto Pascual-Montano
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0090322

Poly(ADP-Ribose)Polymerase Activity Controls Plant Growth by Promoting Leaf Cell Number
Cited by: 29
Author(s): Philipp Schulz, Karel Jansseune, Thomas Degenkolbe, Michaël Méret, Hannes Claeys, Aleksandra Skirycz, Markus Teige, Lothar Willmitzer, Matthew A. Hannah
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0021681

An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction
Cited by: 8
Author(s): Herman M. J. Sontrop, Wim Verhaegh, Marcel J. T. Reinders, Perry D. Moerland
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0238076

Deletion of Mediator 1 suppresses TGFβ signaling leading to changes in epidermal lineages and regeneration
Cited by: 3
Author(s): Yuko Oda, Thai Nguyen, Akiko Hata, Mark B. Meyer, J. Wesley Pike, Daniel Bikle
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-016-2695-1

Improving microRNA target prediction with gene expression profiles
Cited by: 22
Author(s): Cesaré Ovando-Vázquez, Daniel Lepe-Soltero, Cei Abreu‐Goodger
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0256657

Microbiota composition and mucosal immunity in patients with asymptomatic diverticulosis and controls
Cited by: 10
Author(s): Tessel Meike van Rossen, Rogier E. Ooijevaar, J. Kuyvenhoven, Anat Eck, Herman Bril, René Buijsman, Marja A. Boermeester, H. B. A. C. Stockmann, Niels de Korte, Andries E. Budding
Software Mentions: 4
Published: over 2 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962