A. Birmingham

发表

The RNA structure alignment ontology.

James W. Brown, R. Knight, E. Westhof, 2009, RNA.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

Sophie J. Weiss, J. Raes, L. Ursell, 2016, The ISME Journal.

3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets

Anastasia Khvorova, Amanda Birmingham, Elena Maksimova, 2006, Nature Methods.

Statistical methods for analysis of high-throughput RNA interference screens

Aideen Long, Dermot Kelleher, Peter Ghazal, 2009, Nature Methods.

Normalization and microbial differential abundance strategies depend upon data characteristics

Jesse R. Zaneveld, Sophie J. Weiss, R. Knight, 2017, Microbiome.

Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data

Jesse R. Zaneveld, Sophie J. Weiss, R. Knight, 2015 .

Context and the human microbiome

R. Knight, D. McDonald, A. Birmingham, 2015, Microbiome.

Systematic analysis of CRISPR-Cas9 mismatch tolerance reveals low levels of off-target activity.

Z. Strezoska, A. Birmingham, E. Anderson, 2015, Journal of biotechnology.

Sharing and archiving nucleic acid structure mapping data.

Craig L. Zirbel, R. Knight, D. Mathews, 2011, RNA.

BayesFold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences

R. Knight, M. Yarus, A. Birmingham, 2004 .

PyCogent: a toolkit for making sense from sequence

R. Knight, M. Hamady, C. Lozupone, 2007, Genome Biology.

A protocol for designing siRNAs with high functionality and specificity

A. Reynolds, D. Leake, Q. Boese, 2007, Nature Protocols.

Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference

R. Barrangou, S. Wiemann, R. Beijersbergen, 2015, Nucleic acids research.

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions

Aaron N. Chang, Lei S. Qi, T. Ideker, 2017, Nature Methods.

Off-target effects by siRNA can induce toxic phenotype.

Anastasia Khvorova, Amanda Birmingham, Angela Reynolds, 2006, RNA.

BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences.

Rob Knight, Amanda Birmingham, Michael Yarus, 2004, RNA.

Meeting report of the RNA Ontology Consortium January 8-9, 2011

Eric P. Nawrocki, Craig L. Zirbel, J. Clemente, 2011, Standards in genomic sciences.

Simulated clustering accuracy if rarefying is not penalized for removing the lowest 15th percentile samples

Zaneveld, S. Peddada, C. Lozupone, 2015 .

All normalization techniques on key microbiome datasets, unweighed UniFrac distance

Zaneveld, S. Peddada, C. Lozupone, 2015 .

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Christine M. Aceves, Kristian G. Andersen, S. Kingsmore, 2022, Nature.

Addendum: 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets

A. Reynolds, D. Leake, W. Marshall, 2006, Nature Methods.

Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution.

J. Venter, L. Alexandrov, S. Rosenthal, 2021, Cell reports.

Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis.

Christian M. Metallo, T. Ideker, A. Birmingham, 2018, Molecular cell.

Adipose Tissue Macrophage-Derived Exosomal miRNAs Can Modulate In Vivo and In Vitro Insulin Sensitivity

Jong Bae Seo, A. Birmingham, J. Olefsky, 2017, Cell.

Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids

R. Weinreb, Manan Chopra, A. Birmingham, 2022, Cells.

Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas

M. Hiller, T. Capellini, A. Birmingham, 2021, Current Biology.

Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion

M. Hiller, A. Birmingham, Virag Sharma, 2019, bioRxiv.

Combinatorial CRISPR-Ca s 9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP 1-NRF 2 Regulatory Axis

Christian M. Metallo, T. Ideker, A. Birmingham, 2018 .

Experimental validation of the importance of seed complement frequency to siRNA specificity.

Anastasia Khvorova, Amanda Birmingham, Elena Maksimova, 2008, RNA.

Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools

Kenneth E Curewitz, Kristian G. Andersen, R. Garfein, 2023, The Lancet Regional Health - Americas.

Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project

Kenneth E Curewitz, R. Garfein, Ameen Akel, 2021, medRxiv.

The Power Decoder Simulator for the Evaluation of Pooled shRNA Screen Performance

Jesse Stombaugh, Abel Licon, Michael Banos, 2015, Journal of biomolecular screening.

Context and the human microbiome

R. Knight, A. Birmingham, Daniel McDonald, 2015, Microbiome.

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

Christine M. Aceves, Kristian G. Andersen, S. Kingsmore, 2021, medRxiv.

The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction

A. Birmingham, K. Jepsen, K. Fisch, 2022, Scientific Reports.

HIV-1 TAT protein enhances sensitization to methamphetamine by affecting dopaminergic function

A. Birmingham, S. Semenova, D. Dulcis, 2017, Brain, Behavior, and Immunity.

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Rob Knight, Qiyun Zhu, Evan Bolyen, 2020, Current protocols in bioinformatics.

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

Ilkay Altintas, Niema Moshiri, Rob Knight, 2019, PLoS Comput. Biol..

Interactive network visualization in Jupyter notebooks: visJS2jupyter

Sara Brin Rosenthal, Amanda Birmingham, Julia Len, 2018, Bioinform..

Interleukin‐18 signaling promotes activation of hepatic stellate cells in mouse liver fibrosis

S. Loosen, F. Tacke, C. Trautwein, 2022, Hepatology.

Corrigendum: 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets

Anastasia Khvorova, Amanda Birmingham, Elena Maksimova, 2007, Nature Methods.

Ten Simple Rules for Reproducible Research in Jupyter Notebooks pdf

Ilkay Altintas, Niema Moshiri, Rob Knight, 2018, ArXiv.

Bioinformatics Applications Note Data and Text Mining Noisemaker: Simulated Screens for Statistical Assessment

A. Birmingham, P. Kwan, 2022 .

Experimental validation of the importance of seed complement frequency to siRNA specificity.

A. Reynolds, D. Leake, A. Khvorova, 2008, RNA.