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Author Details

Amanda Birmingham
Center for Computational Biology & Bioinformatics , University of California
2004
33
22
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36059147Interleukin-18 signaling promotes activation of hepatic stellate cells in mouse liver fibrosis.Hepatology2023
34793695Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas.Curr Biol2022
35411350Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.medRxiv2022
35798029Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.Nature2022
36359808Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids.Cells2022
35332213The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.Sci Rep2022
33503434Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution.Cell Rep2021
32343490QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.Curr Protoc Bioinformatics2020
31344036Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.PLoS Comput Biol2019
28968701Interactive network visualization in Jupyter notebooks: visJS2jupyter.Bioinformatics2018
29659724Efficient population-scale variant analysis and prioritization with VAPr.Bioinformatics2018
29452643Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis.Mol Cell2018
28942920Adipose Tissue Macrophage-Derived Exosomal miRNAs Can Modulate In Vivo and In Vitro Insulin Sensitivity.Cell2017
28253908Normalization and microbial differential abundance strategies depend upon data characteristics.Microbiome2017
28495611HIV-1 TAT protein enhances sensitization to methamphetamine by affecting dopaminergic function.Brain Behav Immun2017
28319113Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.Nat Methods2017
26905627Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.ISME J2016
25800748Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference.Nucleic Acids Res2015
26530830Context and the human microbiome.Microbiome2015
26189696Systematic analysis of CRISPR-Cas9 mismatch tolerance reveals low levels of off-target activity.J Biotechnol2015
25777298The Power Decoder Simulator for the Evaluation of Pooled shRNA Screen Performance.J Biomol Screen2015
21677862Meeting report of the RNA Ontology Consortium January 8-9, 2011.Stand Genomic Sci2011
21610212Sharing and archiving nucleic acid structure mapping data.RNA2011
20702398NoiseMaker: simulated screens for statistical assessment.Bioinformatics2010
19644458Statistical methods for analysis of high-throughput RNA interference screens.Nat Methods2009
19622678The RNA structure alignment ontology.RNA2009
18367722Experimental validation of the importance of seed complement frequency to siRNA specificity.RNA2008
18431467Genome Reshuffling for Advanced Intercross Permutation (GRAIP): simulation and permutation for advanced intercross population analysis.PLoS One2008
17853862A protocol for designing siRNAs with high functionality and specificity.Nat Protoc2007
17708774PyCogent: a toolkit for making sense from sequence.Genome Biol2007
16682561Off-target effects by siRNA can induce toxic phenotype.RNA2006
164893373' UTR seed matches, but not overall identity, are associated with RNAi off-targets.Nat Methods2006
15317972BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences.RNA2004
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Collaborators

Rob Knight
University of California
Co-authored papers 9
Kathleen M Fisch
Center for Computational Biology and Bioinformatics, University of California
Co-authored papers 8
Daniel McDonald
University of California San Diego
Co-authored papers 5
Niema Moshiri
Bonita Vista High School, University of California San Diego, University of California, San Diego
Co-authored papers 4
Anastasia Khvorova
RNA Therapeutics Institute, University of Massachusetts Chan Medical School
Co-authored papers 4
Roman Sasik
Center for Computational Biology & Bioinformatics (CCBB), University of California
Co-authored papers 4
Sara Brin Rosenthal
Center for Computational Biology and Bioinformatics, University of California
Co-authored papers 3
Antonio Gonzalez
University of California San Diego School of Medicine
Co-authored papers 3
Adam Mark
Center for Computational Biology & Bioinformatics (CCBB), University of California
Co-authored papers 3
Gene W Yeo
University of California
Co-authored papers 3
Kristen Jepsen
Institute for Genomic Medicine, University of California San Diego
Co-authored papers 3
Neocles B Leontis
Bowling Green State University
Co-authored papers 3
Smruthi Karthikeyan
California Institute of Technology
Co-authored papers 2
Omid Bakhtar
University of Arizona Medical Center
Co-authored papers 2
Elizabeth H Simmons
University of California San Diego
Co-authored papers 2
Shirlee Wohl
The Scripps Research Institute
Co-authored papers 2
Pedro Belda-Ferre
University of California San Diego
Co-authored papers 2
Alexandre Bolze
The Rockefeller University
Co-authored papers 2
Clarisse Marotz
University of California San Diego
Co-authored papers 2
Ian McHardy
University of California, Davis Center for Valley Fever
Co-authored papers 2
Adam Buckley
Imperial College London Diabetes Centre
Co-authored papers 2
Jens Luebeck
University of California San Diego
Co-authored papers 2
Guorong Xu
Chinese University of Hong Kong
Co-authored papers 2
David T Pride
University of California San Diego
Co-authored papers 2
Stephen F Kingsmore
Rady Children's Institute for Genomic Medicine
Co-authored papers 2
Angela L Scioscia
University of California San Diego
Co-authored papers 2
Edyth Parker
The Scripps Research Institute
Co-authored papers 2
David Dimmock
Rady Children's Institute for Genomic Medicine
Co-authored papers 2
Alison Sanders
University of California San Diego
Co-authored papers 2
Steven L Gonias
University of California san francisco
Co-authored papers 2
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