bioconductor: ArrayExpress | Projects

10.12688/f1000research.17916.1

Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
Cited by: 19
Author(s): Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch
Software Mentions: 7
Published: about 5 years ago

10.12688/f1000research.11290.1

Gene length and detection bias in single cell RNA sequencing protocols
Cited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: about 7 years ago

10.1093/gigascience/giz087

ascend: R package for analysis of single-cell RNA-seq data
Cited by: 35
Author(s): Anne Senabouth, Samuel W. Lukowski, Jose Alquicira Hernandez, Stacey Andersen, Xin Mei, Quan Nguyen, Joseph E. Powell
Software Mentions: 7
Published: almost 5 years ago

10.3390/jpm11060496

Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models
Cited by: 10
Author(s): Mahdi Jalili, Martin Scharm, Olaf Wolkenhauer, Mehdi Damaghi, Ali Salehzadeh‐Yazdi
Software Mentions: 7
Published: almost 3 years ago

10.1016/j.ebiom.2021.103390

AI-guided discovery of the invariant host response to viral pandemics
Cited by: 31
Author(s): Debashis Sahoo, Gajanan D. Katkar, Soni Khandelwal, Mahdi Behroozikhah, Amanraj Claire, Vanessa Castillo, Courtney Tindle, MacKenzie Fuller, Sahar Taheri, Thomas F. Rogers, Nathan Beutler, Sydney I. Ramirez, Stephen A. Rawlings, Victor Pretorius, Davey M Smith, Dennis R. Burton, Laura E. Crotty Alexander, Jason Duran, Shane Crotty, Jennifer M. Dan, Soumita Das, Pradipta Ghosh
Software Mentions: 7
Published: almost 3 years ago

10.1371/journal.pone.0012657

A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses
Cited by: 13
Author(s): Mikhail G. Dozmorov, Joel M. Guthridge, Robert E. Hurst, Igor Dozmorov
Software Mentions: 6
Published: over 13 years ago

10.1186/gb-2013-14-11-r124

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation
Cited by: 27
Author(s): Sarah Aldridge, Stephen Watt, Michael A. Quail, Tim Rayner, Margus Lukk, Michael F Bimson, Daniel J. Gaffney, Duncan T. Odom
Software Mentions: 6
Published: over 11 years ago

10.3390/ijms22094598

Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways
Cited by: 6
Author(s): Rebeka Popovic, Ivana Celardo, Yao Yu, Ana Carolina Oliveira Costa, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0241848

Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle)
Cited by: 3
Author(s): Hyo Jun Lee, Young Jin Chung, Sungbong Jang, Dongil Seo, Hak Kyo Lee, Duhak Yoon, Dajeong Lim, Seung Hwan Lee
Software Mentions: 6
Published: over 3 years ago

10.1186/gb-2005-6-9-r76

Cited by: 122
Author(s): Stephen Henderson, David B. Guiliano, Nadège Presneau, Sean R. McLean, Richard Frow, Sonja Vujovic, John Anderson, Neil J. Sebire, Jeremy Whelan, Nick Athanasou, Adrienne M. Flanagan, Chris Boshoff
Software Mentions: 6
Published: over 19 years ago

10.1016/j.dib.2018.05.107

Integration of genome-wide mRNA and miRNA expression, and DNA methylation data of three cell lines exposed to ten carbon nanomaterials
Cited by: 8
Author(s): Giovanni Scala, Veer Singh Marwah, Pia Anneli Sofia Kinaret, Jukka Sund, Vittorio Fortino, Dario Greco
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-020-02147-4

CSS: cluster similarity spectrum integration of single-cell genomics data
Cited by: 29
Author(s): Zhisong He, Agnieska Brazovskaja, Sebastian Ebert, J. Gray Camp, Barbara Treutlein
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giaa064

Integrative computational epigenomics to build data-driven gene regulation hypotheses
Cited by: 10
Author(s): Tyrone Chen, Sonika Tyagi
Software Mentions: 6
Published: almost 4 years ago

10.1242/dmm.047225

Hearing impairment due to <i>Mir183/96/182</i> mutations suggests both loss-of-function and gain-of-function effects
Cited by: 10
Author(s): Morag A. Lewis, Francesca Di Domenico, Neil J. Ingham, Haydn M. Prosser, Karen P. Steel
Software Mentions: 6
Published: over 3 years ago

10.1016/j.ebiom.2021.103383

Clinically relevant aberrant Filip1l DNA methylation detected in a murine model of cutaneous squamous cell carcinoma
Cited by: 4
Author(s): Kevin A. Roth, Louis Coussement, Elena V. Knatko, Maureen Higgins, Sandra Steyaert, Charlotte M. Proby, Tim De Meyer, Albena T. Dinkova‐Kostova
Software Mentions: 6
Published: about 3 years ago

10.3390/genes11070802

Convergence of Prognostic Gene Signatures Suggests Underlying Mechanisms of Human Prostate Cancer Progression
Cited by: 6
Author(s): Bogdan A. Luca, Vincent Moulton, Christopher Ellis, Shea P. Connell, Daniel Brewer, Christopher S. Cooper
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-017-1374-0

Epigenetic supersimilarity of monozygotic twin pairs
Cited by: 76
Author(s): Timothy E. Van Baak, Cristian Coarfa, Pierre Antoine Dugué, Giovanni Fiorito, Eleonora Laritsky, Maria S. Baker, Noah J. Kessler, Jianrong Dong, Jack D. Duryea, Matt J. Silver, Ayden Saffari, Andrew M. Prentice, Sophie E. Moore, Akram Ghantous, Michael N. Routledge, Yun Gong, Zdenko Herceg, Paolo Víneis, Gianluca Severi, John L. Hopper, Melissa C. Southey, Graham G. Giles, Roger L. Milne, Robert A. Waterland
Software Mentions: 6
Published: over 6 years ago

10.1242/dev.167833

Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development
Cited by: 145
Author(s): Thorsten Boroviak, Giuliano Giuseppe Stirparo, Sabine Dietmann, Irene Hernando-Herraez, Hisham Mohammed, Wolf Reik, Austin Smith, Erika Sasaki, Jennifer Nichols, Paul Bertone
Software Mentions: 6
Published: over 5 years ago

10.1016/j.immuni.2019.01.001

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation
Cited by: 322
Author(s): Ricardo J. Miragaia, Tomás Gomes, Agnieszka Chomka, Laura Jardine, Angela Riedel, Ahmed N. Hegazy, Natasha Whibley, A. Tucci, Xi Chen, Ida Lindeman, Guy Emerton, Thomas Krausgruber, Jacqueline D. Shields, Muzlifah Haniffa, Fiona Powrie, Sarah A. Teichmann
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0246695

Analysis of lung transcriptome in calves infected with Bovine Respiratory Syncytial Virus and treated with antiviral and/or cyclooxygenase inhibitor
Cited by: 5
Author(s): Maxim Lebedev, Heather McEligot, Victoria Mutua, Paul Walsh, Francisco R. Carvallo Chaigneau, Laurel J. Gershwin
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giaa117

Correcting for experiment-specific variability in expression compendia can remove underlying signals
Cited by: 16
Author(s): Alexandra Lee, YoSon Park, Georgia Doing, Deborah A. Hogan, Casey S. Greene
Software Mentions: 6
Published: over 3 years ago

10.1186/gm549

A genome scale overexpression screen to reveal drug activity in human cells
Cited by: 30
Author(s): Anthony Arnoldo, Saranya Kittanakom, Lawrence E. Heisler, Anthony B. Mak, Andrey I. Shukalyuk, Dax Torti, Jason Moffat, Guri Giaever, Corey Nislow
Software Mentions: 6
Published: over 10 years ago

10.1074/mcp.RA120.002036

Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC
Cited by: 9
Author(s): Yan Zhou Tran, Rezan Minozada, Xiaofang Cao, Henrik J. Johansson, Rui M. Branca, Brinton Seashore‐Ludlow, Lukas M. Orre
Software Mentions: 6
Published: almost 4 years ago

10.1186/1471-2105-10-201

A-MADMAN: Annotation-based microarray data meta-analysis tool
Cited by: 35
Author(s): Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi
Software Mentions: 6
Published: almost 15 years ago

10.1371/journal.pone.0096376

Large Sex Differences in Chicken Behavior and Brain Gene Expression Coincide with Few Differences in Promoter DNA-Methylation
Cited by: 38
Author(s): Daniel Nätt, Beatrix Agnvall, Per Jensen
Software Mentions: 6
Published: about 10 years ago

10.1186/s12859-015-0610-4

Factors affecting the accuracy of a class prediction model in gene expression data
Cited by: 17
Author(s): Putri W. Novianti, Victor L. Jong, Kit C. B. Roes, Marinus J.C. Eijkemans
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0252207

Genomic diversity of 39 samples of Pyropia species grown in Japan
Cited by: 4
Author(s): Yukio Nagano, Kei Kimura, Genta Kobayashi, Yoshio Kawamura
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pone.0235294

Comparative RNA-Seq analyses of Drosophila plasmatocytes reveal gene specific signatures in response to clean injury and septic injury
Cited by: 22
Author(s): Elodie Ramond, Jan Paul Dudzic, Bruno Lemaître
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0068414

NanoMiner — Integrative Human Transcriptomics Data Resource for Nanoparticle Research
Cited by: 20
Author(s): Lingjia Kong, Soile Tuomela, Lauri Hahne, Helena Ahlfors, Olli Yli‐Harja, Bengt Fadeel, Riitta Lahesmaa, Reija Autio
Software Mentions: 6
Published: almost 11 years ago

10.7554/eLife.20235

Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis
Cited by: 4
Author(s): Christina Ernst, Jeremy Pike, Sarah J. Aitken, Hannah K. Long, Nils Eling, Lovorka Stojic, Michelle C. Ward, Frances Connor, Timothy F. Rayner, Margus Lukk, Robert J. Klose, Claudia Kutter, Duncan T. Odom
Software Mentions: 6
Published: over 7 years ago

10.1128/AAC.00504-21

Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance
Cited by: 4
Author(s): Andrej Trauner, Amir Banaei‐Esfahani, Sebastian M. Gygli, Philipp Warmer, Julia Feldmann, Mattia Zampieri, Sònia Borrell, Ben C. Collins, Christian Beisel, Ruedi Aebersold, Sébastien Gagneux
Software Mentions: 6
Published: almost 3 years ago

10.7150/ijbs.32899

A robust 6-mRNA signature for prognosis prediction of pancreatic ductal adenocarcinoma
Cited by: 14
Author(s): Chixing Zhou, Yue Zhao, Yuehui Yin, Zhiqiu Hu, Manar Atyah, Wanyong Chen, Zhi Qiang Meng, Huarong Mao, Qiang Zhou, Wei‐Guo Tang, Pengcheng Wang, Zhanming Li, Juyang Weng, Christiane Bruns, Marie Popp, Felix Popp, Qiongzhu Dong, Ning Ren
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-019-2643-6

First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_
Cited by: 8
Author(s): Marco Moretto, Paolo Sonego, Ana B. Villasenõr-Altamirano, Kristof Engelen
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0155802

Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis
Cited by: 6
Author(s): Bernard Fongang, Andrzej Kudlicki
Software Mentions: 6
Published: about 8 years ago

10.1128/mSphere.00167-17

Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans
Cited by: 25
Author(s): Tobias Weil, Rodrigo Santamaría, Wanseon Lee, Johan Rung, Noemi Tocci, Darren Abbey, Ana R. Bezerra, Laura Carreto, Gabriela Moura, Mònica Bayés, Marta Gut, Attila Csikász‐Nagy, Duccio Cavalieri, Judith Berman, Manuel A. S. Santos
Software Mentions: 6
Published: over 6 years ago

10.26508/lsa.201800175

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Cited by: 16
Author(s): Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.57189

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to oesophageal adenocarcinoma
Cited by: 11
Author(s): Connor Rogerson, Samuel Ogden, Edward Britton, Yeng Ang, Andrew D. Sharrocks
Software Mentions: 6
Published: over 3 years ago

10.1016/j.stemcr.2017.09.018

Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos
Cited by: 33
Author(s): Rachel Jennings, Andrew Berry, Dave T. Gerrard, Stephen J. Wearne, James Strutt, Sarah Withey, Mariya Chhatriwala, Karen Piper Hanley, Ludovic Vallier, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 6
Published: over 6 years ago

10.3390/cancers13010143

Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies
Cited by: 17
Author(s): Irene Pérez-Díez, Marta R. Hidalgo, Pablo Malmierca-Merlo, Zoraida Andreu, Sergio Romera-Giner, Rosa Farràs, María de la Iglesia-Vayá, Mariano Provencio, Atocha Romero, Francisco García‐García
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-018-23494-0

Methylation-to-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, and Pathologic Complete Response in Multiple Cohorts
Cited by: 6
Author(s): Jeffrey Thompson, Brock C. Christensen, Carmen J. Marsit
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0243807

Optimised generation of iPSC-derived macrophages and dendritic cells that are functionally and transcriptionally similar to their primary counterparts
Cited by: 17
Author(s): Susan J. Monkley, Jayendra Kumar Krishnaswamy, Melker Göransson, Maryam Clausen, Johan Meuller, Kristofer Thörn, Ryan Hicks, Stephen Delaney, Louise Stjernborg
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2020.544610

Identification of Four Immune Subtypes in Bladder Cancer Based on Immune Gene Sets
Cited by: 25
Author(s): Chaozhi Tang, Jiakang Ma, Xiuli Liu, Zhengchun Liu
Software Mentions: 6
Published: over 3 years ago

10.3389/fpls.2019.00698

PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation
Cited by: 5
Author(s): Hongryul Ahn, Kyuri Jo, Dabin Jeong, Minwoo Pak, Jihye Hur, Wi Hoon Jung, Sun Kim
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-020-66224-1

Genomic deregulation of PRMT5 supports growth and stress tolerance in chronic lymphocytic leukemia
Cited by: 5
Author(s): Ann-Kathrin Schnormeier, Claudia Pommerenke, Maren Kaufmann, Hans Drexler, Max Koeppel
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0150705

Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications
Cited by: 26
Author(s): Simon Schafferer, Rimpi Khurana, Violetta Refolo, Serena Venezia, Edith Sturm, Paolo Piatti, Clara Hechenberger, Hubert Hackl, Roman Kessler, Michaela Willi, Ronald Gstir, Anne Krogsdam, Alexandra Lusser, Werner Poewe, Gregor K. Wenning, Alexander Hüttenhofer, Nadia Stefanova
Software Mentions: 6
Published: about 8 years ago

10.1534/g3.112.004283

Transcriptional Networks Controlling the Cell Cycle
Cited by: 24
Author(s): Martin Bonke, Mikko Turunen, Maria Sokolova, Anna Vähärautio, Teemu Kivioja, Minna Taipale, Mikael Björklund, Jussi Taipale
Software Mentions: 6
Published: over 11 years ago

10.1186/1471-2164-14-14

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity
Cited by: 26
Author(s): Katie S Viljoen, Jonathan M. Blackburn
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pgen.1005908

Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease
Cited by: 83
Author(s): James E. Peters, Paul Lyons, James C. Lee, Alison F. Richard, Mary D Fortune, Paul Newcombe, Sylvia Richardson, Kenneth G. C. Smith
Software Mentions: 6
Published: about 8 years ago

10.1186/1752-0509-8-17

Identification of core T cell network based on immunome interactome
Cited by: 4
Author(s): Gabriel Teku, Csaba Ortutay, Mauno Vihinen
Software Mentions: 6
Published: over 10 years ago

10.3389/fgene.2016.00183

Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans
Cited by: 78
Author(s): Benjamin Mayne, Tina Bianco‐Miotto, Sam Buckberry, James Breen, Vicki L. Clifton, Cheryl Shoubridge, Claire T. Roberts
Software Mentions: 6
Published: over 7 years ago

10.1038/sdata.2017.185

An RNA-Seq atlas of gene expression in mouse and rat normal tissues
Cited by: 95
Author(s): Julia F. Söllner, Germán Leparc, Tobias Hildebrandt, H. Klein, Leo Thomas, Elia Stupka, Eric J. Simon
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2105-9-493

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management
Cited by: 13
Author(s): Geraint Barton, James Abbott, Norie Chiba, Daniel Huang, Yanyan Huang, Marko Krznarić, J. Mack-Smith, Ammar Saleem, Brad T. Sherman, Brijesh K. Tiwari, Christopher Tomlinson, Timothy J. Aitman, John Darlington, Laurence Gamé, Michael J.E. Sternberg, Sarah Butcher
Software Mentions: 6
Published: over 15 years ago

10.3389/fcell.2021.638374

Single-Cell Analysis Reveals Spatial Heterogeneity of Immune Cells in Lung Adenocarcinoma
Cited by: 9
Author(s): Youyu Wang, Xiaohua Li, Peng Shu, Honglin Hu, Yuntao Wang, Mengqi Shao, Gang Feng, Yu Liu, Yifeng Bai
Software Mentions: 6
Published: over 2 years ago

10.1186/s12859-018-2338-4

Data-driven human transcriptomic modules determined by independent component analysis
Cited by: 23
Author(s): Weizhuang Zhou, Russ B. Altman
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1009162

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation
Cited by: 18
Author(s): Laure Bridoux, Peyman Zarrineh, Joshua Mallen, Mike Phuycharoen, Víctor Latorre, Frank Ladam, Marta Losa, Syed Murtuza Baker, Charles G. Sagerström, Kimberly A. Mace, Magnus Rattray, Nicoletta Bobola
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0134011

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.
Cited by: 7
Author(s): Gabriela D. A. Guardia, Luís Ferreira Pires, Ricardo Zorzetto Nicoliello Vêncio, Kelen Cristina Ribeiro Malmegrim, Cléver Ricardo Guareis de Farias
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pgen.1008531

ELF5 modulates the estrogen receptor cistrome in breast cancer
Cited by: 16
Author(s): Catherine Piggin, Daniel Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha Oakes, David Gallego‐Ortega, Susan J. Clark, Jason S. Carroll, Nenad Bartoniček, Christopher J. Ormandy
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0236186

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat
Cited by: 16
Author(s): Liangjie Lv, Wenying Zhang, Lijing Sun, Aiju Zhao, Yingjun Zhang, Limei Wang, Yuping Liu, Ziqian Li, Xiyong Chen
Software Mentions: 6
Published: over 3 years ago

10.1016/j.cell.2013.11.043

The Architecture of Parent-of-Origin Effects in Mice
Cited by: 79
Author(s): Richard Mott, Yuan Wei, Pamela J. Kaisaki, Xiangchao Gan, James Cleak, Andrew Edwards, Amelie Baud, Jonathan Flint
Software Mentions: 6
Published: over 10 years ago

10.3390/life11020115

A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression
Cited by: 6
Author(s): Theodora-Dafni Michalettou, Ioannis Michalopoulos, Sylvain V. Costes, Christine E. Hellweg, Megumi Hada, Alexandros G. Georgakilas
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pbio.3001077

Cell-level metadata are indispensable for documenting single-cell sequencing datasets
Cited by: 5
Author(s): Sidhant Puntambekar, Jay R. Hesselberth, Kent Riemondy, Rui Fu
Software Mentions: 6
Published: about 3 years ago

10.1186/s13578-019-0334-7

The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency
Cited by: 6
Author(s): Meisam Yousefi, Sayed-Amir Marashi, Ali Sharifi‐Zarchi, Sara Taleahmad
Software Mentions: 6
Published: over 4 years ago

10.7717/peerj.791

A reproducible approach to high-throughput biological data acquisition and integration
Cited by: 12
Author(s): Daniela Börnigen, Yo Sup Moon, Ali Rahnavard, Levi Waldron, Lauren J. McIver, Afrah Shafquat, Eric A. Franzosa, Larissa Miropolsky, Christopher J. Sweeney, Xochitl C. Morgan, Wendy S. Garrett, Curtis Huttenhower
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0249944

Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity
Cited by: 16
Author(s): Yu-Chi Chiu, Shih‐Wei Lee, Chen‐Wuing Liu, Rebecca Chou-Jui Lin, Yung‐Chia Huang, Tsuo-Hung Lan, Lawrence Shih Hsin Wu
Software Mentions: 6
Published: about 3 years ago

10.12688/wellcomeopenres.16791.1

Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer
Cited by: 9
Author(s): Oscar G. Wilkins, Charlotte Capitanchik, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pone.0227639

Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing
Cited by: 15
Author(s): Federica Antonelli, Alfonso Esposito, Ludovica Calvo, Valerio Licursi, Philippe Tisseyre, Sandra Ricci, Manuela Romagnoli, Silvano Piazza, Francesca Guerrieri
Software Mentions: 6
Published: over 4 years ago

10.1186/s12920-018-0358-6

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability
Cited by: 5
Author(s): Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, André Reis, Rami Abou Jamra, Fulvia Ferrazzi
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-017-10930-w

Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis
Cited by: 69
Author(s): Maria Ryaboshapkina, Mårten Hammar
Software Mentions: 6
Published: over 6 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: over 9 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: almost 10 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: about 4 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: almost 4 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

10.1371/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 4 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: almost 5 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: over 10 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: almost 3 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

10.1371/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

10.1186/1471-2164-10-63

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

10.1371/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

10.7554/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: almost 6 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

10.1155/2020/2450569

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 3 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: almost 4 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

10.1371/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 3 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: about 3 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

10.1038/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

10.1038/srep21911

Transcriptional profiling of human smooth muscle cells infected with gingipain and fimbriae mutants of Porphyromonas gingivalis
Cited by: 6
Author(s): Boxi Zhang, Allan Sirsjö, Hazem Khalaf, Torbjörn Bengtsson
Software Mentions: 5
Published: about 8 years ago

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/s41598-019-48589-0

Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells
Cited by: 7
Author(s): Juan Bautista Menendez-Gonzalez, Samantha Sinnadurai, Alex Gibbs, Leigh-anne Thomas, Maria Konstantinou, Alfonso Garcia-Valverde, Magali Boyer, Zhengke Wang, Ashleigh S. Boyd, Allison Blair, Rhys G. Morgan, Neil P. Rodrigues
Software Mentions: 5
Published: over 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

10.1186/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.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/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

10.1371/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

10.1038/s41598-020-66721-3

Cardiac transcriptional and metabolic changes following thoracotomy
Cited by: 0
Author(s): Markus Heckmann, Ashraf Yusuf Rangrez, Daniel Finke, Andreas Jungmann, Julia S. Kreußer, Alexandra Rosskopf, Nesrin Schmiedel, Hugo A. Katus, Norbert Frey, Oliver Müller
Software Mentions: 5
Published: almost 4 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

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962