bioconductor: ArrayExpress | Projects

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: about 16 years ago

10.1371/journal.pgen.1007961

A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene
Cited by: 17
Author(s): Michael Hecker, Nina Boxberger, Nicole Illner, Brit Fitzner, I Schröder, Alexander Winkelmann, Aleš Dudešek, Stefanie Meister, Dirk Koczan, Peter Lorenz, Hans‐Jürgen Thiesen, Uwe K. Zettl
Software Mentions: 4
Published: about 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: over 4 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: over 7 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: almost 6 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: about 7 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: over 13 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: over 4 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: over 9 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 8 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: over 5 years ago

10.1371/journal.pgen.1006879

Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma
Cited by: 40
Author(s): Edward Britton, Connor Rogerson, Shaveta Mehta, Yaoyong Li, Xiaodun Li, Rebecca C. Fitzgerald, Yeng Ang, Andrew D Sharrocks
Software Mentions: 4
Published: over 8 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: over 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: over 4 years ago

10.1371/journal.pgen.1004642

Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence
Cited by: 80
Author(s): Alessio Iannetti, Adeline Ledoux, Susan J. Tudhope, Hélène Sellier, Bo Zhao, Sophia Mowla, Adam J. Moore, Holger Hummerich, Benjamin E. Gewurz, Simon Cockell, Parmjit Jat, Elaine Willmore, Neil D. Perkins
Software Mentions: 4
Published: over 11 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: about 7 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 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: almost 7 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: about 11 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

10.1371/journal.pgen.1006959

Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish
Cited by: 12
Author(s): Catherine Scahill, Zsofia Digby, Ian Sealy, Sonia Wojciechowska, Richard White, John Collins, Derek L. Stemple, Till Bartke, Marie E. Mathers, E. Elizabeth Patton, Elisabeth M Busch-Nentwich
Software Mentions: 4
Published: over 8 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: almost 5 years ago

10.1371/journal.pcbi.1006760

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data
Cited by: 6
Author(s): Vikash Pandey, Vassily Hatzimanikatis
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pcbi.1008219

A simple, scalable approach to building a cross-platform transcriptome atlas
Cited by: 12
Author(s): Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim‐Anh Lê Cao, Jarny Choi, Christine A. Wells
Software Mentions: 4
Published: over 5 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: over 10 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: about 11 years ago

10.1016/j.celrep.2019.07.091

Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes
Cited by: 204
Author(s): Myles Lewis, Michael R. Barnes, Kevin Blighe, Katriona Goldmann, Sharmila Rana, Jason A. Hackney, Nandhini Ramamoorthi, Christopher R. John, David S. Watson, Sarah Kummerfeld, Rebecca Hands, Sudeh Riahi, Vidalba Rocher-Ros, Felice Rivellese, Frances Humby, Stephen Kelly, Michèle Bombardieri, Nora Ng, Maria DiCicco, Désirée van der Heijde, Robert Landewé, Annette H M van der Helm-van Mil, Alberto Cauli, Iain B. McInnes, Christopher D. Buckley, Ernest Choy, Peter Taylor, Michael J. Townsend, Costantino Pitzalis
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2229-14-97

ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks
Cited by: 35
Author(s): Ricardo A. Chávez Montes, Gerardo Coello, Karla L. González-Aguilera, Nayelli Marsch-Martínez, Stefan de Folter, Elena Álvarez-Buylla
Software Mentions: 4
Published: almost 12 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: about 5 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: over 9 years ago

10.1371/journal.pgen.1005474

Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
Cited by: 16
Author(s): Christian Kappel, Gerda Trost, Hjördis Czesnick, Anna Ramming, Benjamin Kolbe, Son Lang, Cláudia Bispo, Jörg Becker, Cornelia H. de Moor, Michael Lenhard
Software Mentions: 4
Published: over 10 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: almost 11 years ago

10.1016/j.celrep.2020.107857

GM-CSF Calibrates Macrophage Defense and Wound Healing Programs during Intestinal Infection and Inflammation
Cited by: 65
Author(s): Tomas Castro‐Dopico, Aaron Fleming, Thomas W. Dennison, John R. Ferdinand, Katherine Harcourt, Benjamin J Stewart, M Zaeem Cader, Zewen Kelvin Tuong, Chenzhi Jing, Laurence S.C. Lok, Rebeccah J. Mathews, Anaïs Portet, Arthur Kaser, Simon Clare, Menna R. Clatworthy
Software Mentions: 4
Published: over 5 years ago

10.3390/cancers11050698

NECTIN4 (PVRL4) as Putative Therapeutic Target for a Specific Subtype of High Grade Serous Ovarian Cancer—An Integrative Multi-Omics Approach
Cited by: 25
Author(s): Christine Bekos, Besnik Muqaku, Sabine Dekan, Reinhard Horvat, Stephan Polterauer, Christopher Gerner, Stefanie Aust, Dietmar Pils
Software Mentions: 4
Published: almost 7 years ago

10.1002/1878-0261.12073

Stromal SPOCK1 supports invasive pancreatic cancer growth
Cited by: 26
Author(s): Veronique L. Veenstra, Helene Damhofer, Cynthia Waasdorp, Anne Steins, Hemant M. Kocher, Jan Paul Medema, Hanneke W. M. van Laarhoven, Maarten F. Bijlsma
Software Mentions: 4
Published: over 8 years ago

10.1039/c8mo00042e

Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data
Cited by: 78
Author(s): Benjamin Alexander-Dann, Lavinia Lorena Pruteanu, Erin Oerton, Naomi L. Sharma, Ioana Berindan‐Neagoe, Dezső Módos
Software Mentions: 4
Published: about 8 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: about 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: almost 11 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: over 5 years ago

10.1186/1471-213X-9-30

Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation
Cited by: 17
Author(s): Daniel Hughes, Roger J. Keynes, David Tannahill
Software Mentions: 4
Published: almost 17 years ago

10.1186/1471-2105-9-S2-S12

Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
Cited by: 30
Author(s): Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì Maria Victoria Grober, Maria Ravo, Angelo Facchiano, Claudia Angelini, Alessandro Weisz
Software Mentions: 4
Published: about 18 years ago

10.1111/acel.12293

Genetic variants modify the effect of age on<i><scp>APOE</scp></i>methylation in the<scp>G</scp>enetics of<scp>L</scp>ipid<scp>L</scp>owering<scp>D</scp>rugs and<scp>D</scp>iet<scp>N</scp>etwork study
Cited by: 34
Author(s): Yiyi Ma, Caren E. Smith, Chao‐Qiang Lai, Marguerite R. Irvin, Laurence D. Parnell, Yu Chi Lee, Lucia D. Pham, Stella Aslibekyan, Steven A. Claas, Michael Y. Tsai, Ingrid B. Borecki, Edmond K. Kabagambe, Silvia Berciano, José M. Ordovás, Devin Absher, Donna K. Arnett
Software Mentions: 4
Published: about 11 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: almost 6 years ago

10.1186/s12943-015-0358-5

Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer
Cited by: 198
Author(s): Sören Müller, Susanne Raulefs, Philipp Bruns, Fabian Afonso-Grunz, Anne Plötner, Rolf Thermann, Carsten Jäger, Anna Melissa Schlitter, Bo Kong, Ivonne Regel, W. Kurt Roth, Björn Rotter, Klaus Hoffmeier, Günter Kahl, Ina Koch, Fabian J. Theis, Jörg Kleeff, Peter Winter, Christoph Michalski
Software Mentions: 4
Published: almost 11 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: about 5 years ago

10.1186/s12859-019-3072-2

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
Cited by: 3
Author(s): Hongryul Ahn, Il Bong Jung, Han–Jung Chae, Dong‐Won Kang, Wi Hoon Jung, Sun Kim
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0244556

Pathways of calcium regulation, electron transport, and mitochondrial protein translation are molecular signatures of susceptibility to recurrent exertional rhabdomyolysis in Thoroughbred racehorses
Cited by: 6
Author(s): Kennedy Aldrich, Deborah Velez‐Irizarry, Clara Fenger, Melissa Schott, Stephanie J. Valberg
Software Mentions: 4
Published: about 5 years ago

10.1186/1475-2859-8-37

Interactive visualization of clusters in microarray data: an efficient tool for improved metabolic analysis of E. coli
Cited by: 7
Author(s): Theresa Scharl, Gerald Striedner, Florentina Pötschacher, Friedrich Leisch, Karl Bayer
Software Mentions: 4
Published: over 16 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: almost 10 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

10.1186/s12885-021-08111-0

A novel 10 glycolysis-related genes signature could predict overall survival for clear cell renal cell carcinoma
Cited by: 20
Author(s): Qianwei Xing, Taidui Zeng, Shouyong Liu, Hong Cheng, Limin Ma, Yi Wang
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-15-884

A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions
Cited by: 46
Author(s): Beatrix Bicskei, James E. Bron, Kevin A. Glover, John B. Taggart
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0256353

Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
Cited by: 6
Author(s): Claus M. Zacho, Martina Abenhus Bager, Ashot Margaryan, Peter Gravlund, Anders Galatius, Arne Redsted Rasmussen, Morten E. Allentoft
Software Mentions: 4
Published: over 4 years ago

10.1186/s12870-014-0254-y

Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans
Cited by: 77
Author(s): Dharani Dhar Burra, Oliver Berkowitz, Pete E. Hedley, Jenny Morris, Svante Resjö, Fredrik Levander, Erland Liljeroth, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0114461

Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium Infection
Cited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: about 11 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 9 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: over 5 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: about 5 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: over 4 years ago

10.7717/peerj.9812

Using bioinformatics and metabolomics to identify altered granulosa cells in patients with diminished ovarian reserve
Cited by: 6
Author(s): Ruifen He, Zhongying Zhao, Yongxiu Yang, Xiaolei Liang
Software Mentions: 4
Published: over 5 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 6 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: almost 7 years ago

10.1186/s12935-021-01834-x

High expression of CDCA7 predicts poor prognosis for clear cell renal cell carcinoma and explores its associations with immunity
Cited by: 12
Author(s): Shouyong Liu, Yi Wang, Chenkui Miao, Zengjun Wang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0246508

Relationships between fox populations and rabies virus spread in northern Canada
Cited by: 17
Author(s): Susan A. Nadin-Davis, Emilie Falardeau, Alex Flynn, Hugh Whitney, H. Dawn Marshall
Software Mentions: 4
Published: about 5 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: over 11 years ago

10.1371/journal.pone.0038946

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study
Cited by: 51
Author(s): Swanhild U. Meyer, Sebastian Kaiser, Carola Wagner, Christian Thirion, Michael W. Pfaffl
Software Mentions: 4
Published: over 13 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: about 6 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: over 10 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: almost 7 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: about 7 years ago

10.1371/journal.pone.0015147

Analysis of Ultra Low Genome Conservation in Clostridium difficile
Cited by: 58
Author(s): Joy Scaria, Lalit Ponnala, Tavan Janvilisri, Weiwei Yan, Lukas A. Mueller, Yung-Fu Chang
Software Mentions: 4
Published: about 15 years ago

10.1038/s41598-021-91864-2

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

10.1093/gigascience/giab034

A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers
Cited by: 5
Author(s): Mariya Dimitrova, Rikke Louise Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0234939

Effect of bovine leukemia virus (BLV) infection on bovine mammary epithelial cells RNA-seq transcriptome profile
Cited by: 4
Author(s): Lucia Martínez Cuesta, Juan Pedro Lirón, María Victoria Nieto Farias, Guillermina Laura Dolcini, María Carolina Ceriani
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-10-389

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability
Cited by: 18
Author(s): Herman M. J. Sontrop, Perry D. Moerland, René van den Ham, Marcel J. T. Reinders, Wim Verhaegh
Software Mentions: 4
Published: over 16 years ago

10.1038/s41598-021-92932-3

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

10.1016/j.gpb.2018.08.002

PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
Cited by: 19
Author(s): Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He, Ziding Zhang
Software Mentions: 4
Published: over 7 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: about 6 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: about 13 years ago

10.1186/s13059-019-1706-3

ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C
Cited by: 25
Author(s): Yousra Ben Zouari, Anne Molitor, Natalia Sikorska, Véra Pancaldi, Tom Sexton
Software Mentions: 4
Published: almost 7 years ago

10.1093/bib/bbx080

‘Multi-omic’ data analysis using O-miner
Cited by: 13
Author(s): Ajanthah Sangaralingam, Abu Z. Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, A. Nagano, Helen Ross-Adams, Jun Wang, Nick R. Lemoine, Claude Chelala
Software Mentions: 4
Published: over 8 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 12 years ago

10.1186/s13059-016-1053-6

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms
Cited by: 114
Author(s): Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs Moed, Hailiang Mei, M.A. van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla Kallen, Albert Hofman, Diana van Heemst, Eco J. C. de Geus, Jenny van Dongen, Joris Deelen, Leonard H van den Berg, Joyce B. J. van Meurs, Ritsert C. Jansen, Peter A.C. ’t Hoen, Lude Franke, Cisca Wijmenga, Jan H. Veldink, Morris A. Swertz, Marleen M.J. van Greevenbroek, Cornelia M. van Duijn, Dorret I. Boomsma, P. Eline Slagboom, Bastiaan T. Heijmans
Software Mentions: 4
Published: over 9 years ago

10.1007/s00401-017-1743-5

Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing
Cited by: 120
Author(s): Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P. Kloosterman, Shai Rosenberg, Maïlys Daniau, Charlotte Schmitt, Julien Masliah‐Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean‐Yves Delattre, Ahmed Idbaïh
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2105-15-S1-S6

CorrelaGenes: a new tool for the interpretation of the human transcriptome
Cited by: 1
Author(s): Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione, Gianni Sacchi
Software Mentions: 4
Published: about 12 years ago

10.1093/bioinformatics/bty125

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
Cited by: 28
Author(s): Wanseon Lee, Katharine Plant, Peter Humburg, Julian C. Knight
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13059-014-0555-3

Determining the quality and complexity of next-generation sequencing data without a reference genome
Cited by: 27
Author(s): Seyed Yahya Anvar, Lusine Khachatryan, Martijn Vermaat, M.A. van Galen, Irina Pulyakhina, Yavuz Ariyürek, Ken Kraaijeveld, Johan T. den Dunnen, Peter de Knijff, Peter A C ‘t Hoen, Jeroen F. J. Laros
Software Mentions: 4
Published: over 11 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 5 years ago

10.1186/s12859-021-04070-2

Large-scale labeling and assessment of sex bias in publicly available expression data
Cited by: 10
Author(s): Emily Flynn, Annie C. Y. Chang, Russ B. Altman
Software Mentions: 4
Published: almost 5 years ago

10.1186/gb-2013-14-12-r147

Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties
Cited by: 77
Author(s): Aurélien A. Sérandour, Gordon D. Brown, Joshua D. Cohen, Jason S. Carroll
Software Mentions: 4
Published: about 13 years ago

10.1093/bioinformatics/btx143

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
Cited by: 26
Author(s): Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brāzma
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-021-07646-7

Transcriptomic analysis reveals pronounced changes in gene expression due to sub-lethal pyrethroid exposure and ageing in insecticide resistance Anopheles coluzzii
Cited by: 18
Author(s): Victoria A. Ingham, Faye Brown, Hilary Ranson
Software Mentions: 4
Published: almost 5 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: over 14 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 4 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 12 years ago

10.1186/s13040-015-0052-6

DNA microarray integromics analysis platform
Cited by: 11
Author(s): Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar, Wiktor Jurkowski
Software Mentions: 4
Published: almost 11 years ago

10.1186/s13223-021-00584-9

Expression profiling of ileal mucosa in asthma reveals upregulation of innate immunity and genes characteristic of Paneth and goblet cells
Cited by: 1
Author(s): Jan Krzysztof Nowak, Marzena Dworacka, Nazgul Gubaj, Arystan Dossimov, Zhumabek Dossimov, Jarosław Walkowiak
Software Mentions: 4
Published: over 4 years ago

10.1186/1752-0509-6-54

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks
Cited by: 96
Author(s): Florian Martin, Timothy M. Thomson, Alain Sewer, David A. Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 4
Published: almost 14 years ago

10.1186/s13059-015-0735-9

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population
Cited by: 39
Author(s): Joke Baute, Dorota Herman, Frederik Coppens, Jolien De Block, Bram Slabbinck, Matteo Dell’Acqua, Mario Enrico Pè, Steven Maere, Hilde Nelissen, Dirk Inzé
Software Mentions: 4
Published: over 10 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962