bioconductor: ArrayExpress | Projects

10.1186/s12263-021-00692-6

Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis
Cited by: 7
Author(s): Kaitlin Day, Aimee L. Dordevic, Helen Truby, Melissa C. Southey, Susan L. Coort, Chiara Murgia
Software Mentions: 5
Published: about 5 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 13 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: about 6 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: about 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: about 7 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: about 7 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 12 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 18 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: over 13 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 12 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 7 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: over 5 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: about 6 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: almost 8 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 9 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 14 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: over 5 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: about 16 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 6 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: almost 12 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 6 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 17 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 17 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: almost 8 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: over 7 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 5 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: almost 12 years ago

10.1371/journal.pone.0241861

Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections
Cited by: 5
Author(s): Raquel Morais de Paiva Daibert, Carlos Alberto Oliveira de Biagi, Felipe de Oliveira Vieira, Marcos Vinícius Gualberto Barbosa da Silva, Eugênio D. Hottz, Mariana Brandi Mendonça Pinheiro, Daniele Ribeiro de Lima Reis Faza, Hyago Passe Pereira, Marta Fonseca Martins, Humberto M. Brandão, M. A. Machado, Wanessa A. Carvalho
Software Mentions: 5
Published: almost 6 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 13 years ago

10.1371/journal.pone.0236796

Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management
Cited by: 9
Author(s): Antonio J. Fernández‐González, Nuria M. Wentzien, Pablo J. Villadas, Antonio Valverde-Corredor, Ana V. Lasa, Carmen Gómez-Lama Cabanás, Jesús Mercado‐Blanco, Manuel Fernández‐López
Software Mentions: 5
Published: about 6 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 8 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: about 8 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: over 5 years ago

10.1371/journal.pone.0225805

Food from faeces: Evaluating the efficacy of scat DNA metabarcoding in dietary analyses
Cited by: 25
Author(s): David Thuo, Elise M. Furlan, Femke Broekhuis, Joseph Kamau, Kyle Macdonald, Dianne Gleeson
Software Mentions: 5
Published: over 6 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 6 years ago

10.7554/eLife.58716

Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?
Cited by: 210
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Francesca Luca, Yi Xu, Adnan Alazizi, Yaozhu Leng, Chaur Dong Hsu, Nardhy Gomez-López
Software Mentions: 5
Published: about 6 years ago

10.1155/2020/2450569

Infiltration of Immunoinflammatory Cells and Related Chemokine/Interleukin Expression in Different Gastric Immune Microenvironments
Cited by: 13
Author(s): Ang Wang, Siru Nie, Zhi Lv, Jing Wen, Yuan Yuan
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.03346

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network
Cited by: 82
Author(s): Carine Gubelmann, Petra Schwalie, Sunil K. Raghav, Eva Röder, Tenagne Delessa, Elke Kiehlmann, Sebastian M. Waszak, Andrea Corsinotti, Gilles Udin, Wiebke Holcombe, Gottfried Rudofsky, Didier Trono, Christian Wolfrum, Bart Deplancke
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pone.0254556

Simple mapping-based quantification of a mock microbial community using total RNA-seq data
Cited by: 4
Author(s): Shigeharu Moriya
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0244724

Geography as non-genetic modulation factor of chicken cecal microbiota
Cited by: 8
Author(s): Natalia Daniela Pin Viso, Enzo A. Redondo, Juan María Díaz Carrasco, Leandro M. Redondo, Javier García, Mariano E. Fernández‐Miyakawa, Marisa Diana Farber
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms20143543

Sex-Dimorphic Behavioral Alterations and Altered Neurogenesis in U12 Intron Splicing-Defective Zrsr1 Mutant Mice
Cited by: 9
Author(s): Francisco Alén, Isabel Gómez-Redondo, Patricia Rivera, Juan Suárez, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Serafín Pérez‐Cerezales, Keiko Horiuchi, Laura Orío, Fernando Rodríguez de Fonseca, Alfonso Gutiérrez‐Adán
Software Mentions: 5
Published: about 7 years ago

10.7554/eLife.53948

Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling
Cited by: 14
Author(s): Y. Claire, John C. Marioni, Gillian M. Griffiths, Alison F. Richard
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0161504

Comparison of Normal and Pre-Eclamptic Placental Gene Expression: A Systematic Review with Meta-Analysis
Cited by: 58
Author(s): Obed Brew, Mark Sullivan, Anthony C. Woodman
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0075578

Role of Alternative Polyadenylation during Adipogenic Differentiation: An In Silico Approach
Cited by: 7
Author(s): Lucía Spangenberg, Alejandro Correa, Bruno Dallagiovanna, Hugo Naya
Software Mentions: 5
Published: almost 13 years ago

10.1371/journal.pone.0226616

Insights into fungal diversity of a shallow-water hydrothermal vent field at Kueishan Island, Taiwan by culture-based and metabarcoding analyses
Cited by: 25
Author(s): Ka−Lai Pang, Sheng−Yu Guo, I-An Chen, Gaëtan Burgaud, Zengwei Luo, Hans-Uwe Dahms, Jiang‐Shiou Hwang, Yi-Li Lin, Jian-Shun Huang, Tsz-Wai Ho, Ling Ming Tsang, Michael Chiang, Hyojung Cha
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0081167

Cytokeratin 15 Marks Basal Epithelia in Developing Ureters and Is Upregulated in a Subset of Urothelial Cell Carcinomas
Cited by: 21
Author(s): Guihua Tai, Parisa Ranjzad, Fiona Marriage, Samrina Rehman, Helen Denley, Jill Dixon, Karen S. Mitchell, Philip J. Day, Adrian S. Woolf
Software Mentions: 5
Published: over 12 years ago

10.7554/eLife.35788

A promoter interaction map for cardiovascular disease genetics
Cited by: 111
Author(s): Lindsey Montefiori, Débora R. Sobreira, Noboru Jo Sakabe, Ivy Aneas, Amelia C Joslin, Grace Hansen, Grazyna Bozek, Ivan P. Moskowitz, Elizabeth M. McNally, Marcelo A. Nóbrega
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0102579

Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action
Cited by: 60
Author(s): Daniel Gusenleitner, Scott S. Auerbach, Tisha Melia, Harold F. Gómez, David H. Sherr, Stefano Monti
Software Mentions: 5
Published: about 12 years ago

10.7554/eLife.58659

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation
Cited by: 22
Author(s): Bjoern Gaertner, Sebastiaan van Heesch, Valentin Schneider-Lunitz, Jana Felicitas Schulz, Franziska Witte, Susanne Blachut, Steven Nguyen, Richard L. Wong, Ileana Matta, Norbert Hübner
Software Mentions: 5
Published: about 6 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: almost 7 years ago

10.1038/s41598-021-84270-1

Serial transplantation unmasks galectin-9 contribution to tumor immune escape in the MB49 murine model
Cited by: 4
Author(s): Valentin Baloche, Julie Rivière, Thi Bao Tram Tran, Aurore Gelin, Olivia Bawa, Nicolas Signolle, Mouhamadou Diop, Philippe Dessen, Stéphanie Beq, Muriel D. David, P. Busson
Software Mentions: 5
Published: over 5 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: almost 12 years ago

10.1038/s41422-018-0128-1

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis
Cited by: 46
Author(s): Marcos Morgan, Yuka Kabayama, Christian Much, Ivayla Ivanova, Monica Di Giacomo, Tatsiana Auchynnikava, Jack Monahan, Dimitrios Vitsios, Lina Vasiliauskaitė, Stefano Comazzetto, Juri Rappsilber, Robin C. Allshire, Bo T. Porse, Anton J. Enright, Dónal O’Carroll
Software Mentions: 5
Published: over 7 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: about 8 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: about 5 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: about 7 years ago

10.1371/journal.pone.0243911

The pharmacodynamic and differential gene expression analysis of PPAR α/δ agonist GFT505 in CDAHFD-induced NASH model
Cited by: 12
Author(s): Linfu Liu, Chuang Liu, Menglong Zhao, Qianru Zhang, Ying Lu, Ping Liu, Hua Yang, Jinliang Yang, Xiaoxin Chen, Yuqin Yao
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0122143

Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer
Cited by: 27
Author(s): Pushpinder Bawa, Sajna Zackaria, Mohit Verma, Saurabh Gupta, Srivatsan Raghunathan, Bibha Chaudhary, Subhashini Srinivasan
Software Mentions: 4
Published: over 11 years ago

10.1038/s41396-017-0043-3

Energy limitation of cyanophage development: implications for marine carbon cycling
Cited by: 54
Author(s): Richard John Puxty, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 4
Published: over 8 years ago

10.1128/mSystems.00187-19

Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
Cited by: 10
Author(s): Joseph P. Webb, V S Springthorpe, Luca Rossoni, David-Paul Minde, Swen Langer, Heather Walker, Amias Alstrom-Moore, Tony R. Larson, Kathryn S. Lilley, Graham R. Eastham, Gill Stephens, Gavin H. Thomas, David J. Kelly, Jeffrey Green
Software Mentions: 4
Published: almost 7 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: over 5 years ago

10.3389/fcvm.2021.627873

Essential Genes and MiRNA–mRNA Network Contributing to the Pathogenesis of Idiopathic Pulmonary Arterial Hypertension
Cited by: 7
Author(s): Shengyu Hao, Pan Jiang, Liang Xie, Guiling Xiang, Zilong Liu, Weiping Hu, Qiao Wu, Liyan Jiang, Yi Xiao, Shanqun Li
Software Mentions: 4
Published: over 5 years ago

10.3389/fnmol.2018.00363

Assessing Transcriptome Quality in Patch-Seq Datasets
Cited by: 33
Author(s): Shreejoy J. Tripathy, Lilah Toker, Claire Bomkamp, B. Ogan Mancarci, Manuel Belmadani, Paul Pavlidis
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2021.635794

Multi-Transcript Level Profiling Revealed Distinct mRNA, miRNA, and tRNA-Derived Fragment Bio-Signatures for Coping Behavior Linked Haplotypes in HPA Axis and Limbic System
Cited by: 3
Author(s): Kevin Gley, Frieder Hadlich, Nares Trakooljul, Fiete Haack, Eduard Muráni, Ulrike Gimsa, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: almost 5 years ago

10.3389/fimmu.2017.01199

Plasmodium berghei NK65 in Combination with IFN-γ Induces Endothelial Glucocorticoid Resistance via Sustained Activation of p38 and JNK
Cited by: 9
Author(s): Karolina Zielińska, Lode De Cauwer, Sofie Knoops, Kristof Van der Molen, Alexander Sneyers, Jonathan Thommis, J. Brian de Souza, Ghislain Opdenakker, Karolien De Bosscher, Philippe E. Van den Steen
Software Mentions: 4
Published: almost 9 years ago

10.3389/fnmol.2021.699562

Spatial RNA Sequencing Identifies Robust Markers of Vulnerable and Resistant Human Midbrain Dopamine Neurons and Their Expression in Parkinson’s Disease
Cited by: 20
Author(s): Julio Águila, Shu Cheng, Nigel Kee, Mengshu Cao, Menghan Wang, Qiaolin Deng, Eva Hedlund
Software Mentions: 4
Published: about 5 years ago

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 11 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: over 6 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: about 7 years ago

10.3389/fimmu.2021.636108

Impact of Tenascin-C on Radiotherapy in a Novel Syngeneic Oral Squamous Cell Carcinoma Model With Spontaneous Dissemination to the Lymph Nodes
Cited by: 5
Author(s): Caroline Spenlé, Thomas Loustau, Hélène Burckel, Gilles Riegel, Chérine Abou Faycal, Chengbei Li, Alev Yılmaz, Luciana Petti, Fanny Steinbach, Constance Ahowesso, Camille Jost, Nicodème Paul, Raphaël Carapito, Georges Noël, Fabienne Anjuère, Nathalie Salomé, Gertraud Orend
Software Mentions: 4
Published: about 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: over 5 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: over 7 years ago

10.3389/fimmu.2018.03075

Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis
Cited by: 22
Author(s): Andrea Iannello, Simona Rolla, Alessandro Maglione, Giulio Ferrero, Valentina Bardina, Ilenia Inaudi, Stefania De Mercanti, Francesco Novelli, Lucrezia D'Antuono, Simona Cardaropoli, Tullia Todros, Maria Vittoria Turrini, Cinzia Cordioli, Giorgia Puorro, Angela Marsili, Roberta Lanzillo, Vincenzo Brescia Morra, Francesca Cordero, Michele De Bortoli, Luca Durelli, Andrea Visconti, Santina Cutrupi, Marinella Clerico
Software Mentions: 4
Published: over 7 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: over 16 years ago

10.3389/fphar.2019.00747

Bioinformatic Study of Transcriptome Changes in the Mice Lumbar Spinal Cord After the 30-Day Spaceflight and Subsequent 7-Day Readaptation on Earth: New Insights Into Molecular Mechanisms of the Hypogravity Motor Syndrome
Cited by: 8
Author(s): M. S. Kuznetsov, Artur Nicolaevich Lisukov, Albert A. Rizvanov, O. V. Tyapkina, Oleg Gusev, P. N. Rezvyakov, I. B. Kozlovskaya, E. E. Nikolskiy, Р. Р. Исламов
Software Mentions: 4
Published: about 7 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 7 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: over 7 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 6 years ago

10.3389/fcell.2019.00299

Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data
Cited by: 23
Author(s): Geng Chen, Jiwei Chen, Huanlong Liu, Shuangguan Chen, Yang Zhang, Peng Li, Danielle Thierry-Mieg, Jean Thierry‐Mieg, William B. Mattes, Baitang Ning, Tieliu Shi
Software Mentions: 4
Published: over 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: almost 10 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: about 5 years ago

10.3389/fimmu.2018.02902

Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens
Cited by: 35
Author(s): Joannah R. Fergusson, Michael D. Morgan, Mélanie Bruchard, Leonie F. A. Huitema, Balthasar A. Heesters, Vincent van Unen, Jan Piet van Hamburg, Nicole N. van der Wel, Daisy I. Picavet, Frits Koning, Sander W. Tas, Mark S. Anderson, John C. Marioni, Georg A. Holländer, Hergen Spits
Software Mentions: 4
Published: over 7 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: about 5 years ago

10.1371/journal.pone.0240183

Transcriptome analysis revealed misregulated gene expression in blastoderms of interspecific chicken and Japanese quail F1 hybrids
Cited by: 0
Author(s): Satoshi Ishishita, Shoji Tatsumoto, Keiji Kinoshita, Mitsuo Nunome, Takayuki Suzuki, Yasuhiro Go, Yoichi Matsuda
Software Mentions: 4
Published: almost 6 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 11 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: almost 11 years ago

10.7554/eLife.02626

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Cited by: 80
Author(s): Benoît Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Marc E. Rothenberg, Kyle Chessman, Aline Faure, Alister P. W. Funnell, Ângela Gonçalves, Claudia Kutter, Margus Lukk, Suraj Menon, William McLaren, Klara Stefflova, Stephen Watt, Matthew T. Weirauch, Merlin Crossley, John C. Marioni, Duncan T. Odom, Paul Flicek, Michael D. Wilson
Software Mentions: 4
Published: almost 12 years ago

10.3389/fmicb.2016.01688

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways
Cited by: 19
Author(s): Sadegh Azimzadeh Jamalkandi, Sayed‐Hamidreza Mozhgani, Hamid Gholami Pourbadie, Mehdi Mirzaie, Farshid Noorbakhsh, Behrouz Vaziri, Alireza Gholami, Naser Ansari-Pour, Mohieddin Jafari
Software Mentions: 4
Published: almost 10 years ago

10.3389/fmicb.2020.00495

Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator
Cited by: 7
Author(s): Natalia M. Vior, Eva Cea-Torrescassana, Tom H. Eyles, Govind Chandra, Andrew W. Truman
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.566734

Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging
Cited by: 4
Author(s): Yujuan Gui, Mélanie Thomas, Pierre Garcia, Mona Karout, Rashi Halder, Alessandro Michelucci, Heike Kollmus, Cuiqi Zhou, Shlomo Melmed, Klaus Schughart, Rudi Balling, Michel Mittelbronn, Joseph H. Nadeau, Robert W. Williams, Thomas Sauter, Manuel Buttini, Lasse Sinkkonen
Software Mentions: 4
Published: almost 6 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: about 6 years ago

10.3389/fgene.2019.00159

A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures
Cited by: 22
Author(s): Adib Shafi, Tin Nguyen, Azam Peyvandipour, Hung Son Nguyen, Sorin Drăghici
Software Mentions: 4
Published: over 7 years ago

10.3389/fmolb.2021.719982

Identification of Mast Cell-Based Molecular Subtypes and a Predictive Signature in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Hanxiang Liu, Yi Yang
Software Mentions: 4
Published: almost 5 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: over 7 years ago

10.26508/lsa.202000809

Reduced RNA turnover as a driver of cellular senescence
Cited by: 9
Author(s): Nowsheen Mullani, Yevheniia Porozhan, Adèle Mangelinck, Christophe Rachez, Mickaël Costallat, Éric Batsché, Michèle Goodhardt, Giovanni Cenci, Carl Mann, Christian Muchardt
Software Mentions: 4
Published: over 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 17 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: about 8 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: almost 10 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: almost 8 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 8 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962