Mark D. Robinson

According to our database, Mark D. Robinson authored at least 24 papers between 2002 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

<i>DESpace</i>: spatially variable gene detection via differential expression testing of spatial clusters.

Peiying Cai, Mark D. Robinson, Simone Tiberi

Bioinform., February, 2024

Ten simple rules for computational biologists collaborating with wet lab researchers.

Mark D. Robinson, Peiying Cai, Martin Emons, Reto Gerber, Pierre-Luc Germain, Samuel Gunz, Siyuan Luo, Giulia Moro, Emanuel Sonder, Anthony Sonrel, Jiayi Wang, David Wissel, Izaskun Mallona

PLoS Comput. Biol., 2024

On the identification of differentially-active transcription factors from ATAC-seq data.

Felix Ezequiel Gerbaldo, Emanuel Sonder, Vincent Fischer, Selina Frei, Jiayi Wang, Katharina Gapp, Mark D. Robinson, Pierre-Luc Germain

PLoS Comput. Biol., 2024

Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.

Yu-Ning Huang, Michael I. Love, Cynthia Flaire Ronkowski, Dhrithi Deshpande, Lynn M. Schriml, Annie Wong-Beringer, Barend Mons, Russell Corbett-Detig, Christopher I Hunter, Jason H. Moore, Lana X. Garmire, T. B. K. Reddy, Winston A. Hide, Atul J. Butte, Mark D. Robinson, Serghei Mangul

CoRR, 2024

2021

Censcyt: censored covariates in differential abundance analysis in cytometry.

Reto Gerber, Mark D. Robinson

BMC Bioinform., 2021

2020

TreeSummarizedExperiment: a S4 class for data with hierarchical structure.

Ruizhu Huang, Charlotte Soneson, Felix G. M. Ernst, Kevin C. Rue-Albrecht, Guangchuang Yu, Stephanie C. Hicks, Mark D. Robinson

F1000Research, 2020

An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data.

Helena L. Crowell, Stéphane Chevrier, Andrea Jacobs, Sujana Sivapatham, Tumor Profiler consortium, Bernd Bodenmiller, Mark D. Robinson

F1000Research, 2020

2019

Financializing epistemic norms in contemporary biomedical innovation.

Mark D. Robinson

Synth., 2019

12 Grand Challenges in Single-Cell Data Science.

David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth

PeerJ Prepr., 2019

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms.

Jochen T. Bick, Shuqin Zeng, Mark D. Robinson, Susanne E. Ulbrich, Stefan Bauersachs

Database J. Biol. Databases Curation, 2019

2018

A systematic performance evaluation of clustering methods for single-cell RNA-seq data.

Angelo Duò, Mark D. Robinson, Charlotte Soneson

F1000Research, 2018

Towards unified quality verification of synthetic count data with countsimQC.

Charlotte Soneson, Mark D. Robinson

Bioinform., 2018

2013

Chromothripsis-like patterns are recurring, but heterogeneously distributed features in cancer: A survey of 22, 347 genomic copy number profiles.

Haoyang Cai, Nitin Kumar, Homayoun C. Bagheri, Christian von Mering, Mark D. Robinson, Michael Baudis

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

2012

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

Marc Fiume, Eric J. M. Smith, Andrew Brook, Dario Strbenac, Brian Turner, Aziz M. Mezlini, Mark D. Robinson, Shoshana J. Wodak, Michael Brudno

Nucleic Acids Res., 2012

2010

<tt>Repitools</tt>: an R package for the analysis of enrichment-based epigenomic data.

Aaron L. Statham, Dario Strbenac, Marcel W. Coolen, Clare Stirzaker, Susan J. Clark, Mark D. Robinson

Bioinform., 2010

<tt>edgeR</tt>: a Bioconductor package for differential expression analysis of digital gene expression data.

Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth

Bioinform., 2010

2009

Differential splicing using whole-transcript microarrays.

Mark D. Robinson, Terence P. Speed

BMC Bioinform., 2009

2008

FIRMA: a method for detection of alternative splicing from exon array data.

E. Purdom, Ken M. Simpson, Mark D. Robinson, J. G. Conboy, A. V. Lapuk, Terence P. Speed

Bioinform., 2008

2007

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.

Mark D. Robinson, David P. De Souza, Woon Wai Keen, Eleanor C. Saunders, Malcolm J. McConville, Terence P. Speed, Vladimir A. Likic

BMC Bioinform., 2007

A comparison of Affymetrix gene expression arrays.

Mark D. Robinson, Terence P. Speed

BMC Bioinform., 2007

Moderated statistical tests for assessing differences in tag abundance.

Mark D. Robinson, Gordon K. Smyth

Bioinform., 2007

2005

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model.

Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes

Proceedings of the Research in Computational Molecular Biology, 2005

2004

MyMed: A database system for biomedical research on MEDLINE data.

Kimberly N. Lewis, Mark D. Robinson, Timothy R. Hughes, Christopher W. V. Hogue

IBM Syst. J., 2004

2002

FunSpec: a web-based cluster interpreter for yeast.

Mark D. Robinson, Jörg Grigull, Naveed Mohammad, Timothy R. Hughes

BMC Bioinform., 2002