Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

Luciane T. Kagohara https://orcid.org/0000-0003-1706-0950 https://www.wikidata.org/entity/Q90014353

Jacob T. Mitchell Orian Stapleton Kavita Krishnan Sushma Nagaraj Dmitrijs Lvovs Christopher Cherry Amanda Poissonnier Wesley Horton Andrew Adey Varun Rao Amanda Huff Jacquelyn W. Zimmerman Luciane T. Kagohara Neeha Zaidi Lisa M. Coussens Elizabeth M. Jaffee Jennifer H. Elisseeff Elana J. Fertig Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal. 2026 42 Bioinform. 3 https://doi.org/10.1093/bioinformatics/btag089 db/journals/bioinformatics/bioinformatics42.html#MitchellSKNLCPHARHZKZCJ26 streams/journals/bioinformatics

Daniel R. Bergman Jeanette A. I. Johnson Marwa Naji Max Booth Heber L. Rocha Atul Deshpande Dimitrios N. Sidiropoulos Tamara Lopez-Vidal Randy W. Heiland Luciane T. Kagohara Robert A. Anders Lei Zheng Elizabeth M. Jaffee Genevieve L. Stein-O'Brien Paul Macklin Elana J. Fertig BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells. 2025 41 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btaf571 db/journals/bioinformatics/bioinformatics41.html#BergmanJNBRDSLH25

Thomas Sherman Luciane T. Kagohara Raymon Cao Raymond Cheng Matthew Satriano Michael Considine Gabriel Krigsfeld Ruchira Ranaweera Yong Tang Sandra A. Jablonski Genevieve L. Stein-O'Brien Daria A. Gaykalova Louis M. Weiner Christine H. Chung Elana J. Fertig CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. 2019 15 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1006935 https://www.wikidata.org/entity/Q90014360 db/journals/ploscb/ploscb15.html#ShermanKCCSCKRT19

Bahman Afsari Theresa Guo Michael Considine Liliana Florea Luciane T. Kagohara Genevieve L. Stein-O'Brien Dylan Kelley Emily Flam Kristina D. Zambo Patrick K. Ha Donald Geman Michael F. Ochs Joseph A. Califano Daria A. Gaykalova Alexander V. Favorov Elana J. Fertig Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. 1859-1867 2018 34 Bioinform. 11 https://doi.org/10.1093/bioinformatics/bty004 https://www.wikidata.org/entity/Q47561950 db/journals/bioinformatics/bioinformatics34.html#AfsariGCFKSKFZH18

Andrew Adey Bahman Afsari Robert A. Anders Daniel R. Bergman Max Booth Joseph A. Califano Raymon Cao Raymond Cheng Christopher Cherry Christine H. Chung Michael Considine Lisa M. Coussens Atul Deshpande Jennifer H. Elisseeff Alexander V. Favorov Elana J. Fertig Emily Flam Liliana Florea Daria A. Gaykalova Donald Geman Theresa Guo Patrick K. Ha Randy W. Heiland Wesley Horton Amanda Huff Sandra A. Jablonski Elizabeth M. Jaffee Jeanette A. I. Johnson Dylan Kelley Gabriel Krigsfeld Kavita Krishnan Tamara Lopez-Vidal Dmitrijs Lvovs Paul Macklin Jacob T. Mitchell Sushma Nagaraj Marwa Naji Michael F. Ochs Amanda Poissonnier Ruchira Ranaweera Varun Rao Heber L. Rocha Matthew Satriano Thomas Sherman Dimitrios N. Sidiropoulos Orian Stapleton Genevieve L. Stein-O'Brien Yong Tang Louis M. Weiner Neeha Zaidi Kristina D. Zambo Lei Zheng Jacquelyn W. Zimmerman