translating genomics to the clinic (selected publications)
Abadie, Daza et al. Reversible, tunable epigenetic silencing of TCF-1 generates flexibility in the T cell memory decision. Cell Press (2024)
PMID: 38301652
Srivatsan et al. SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing. Clinical Chemistry (2021)
PMID: 32511368
(with Seattle Flu Study)
Choi, Chen et al. Precise genomic deletions using paired prime editing. Nature Biotechnology (2022)
PMID: 34650269
Bedford, Greninger, Roychoudhury, Starita, Famulare et al. Cryptic transmission of SARS-CoV-2 in Washington state. Science (2020)
PMID: 32913002
Srivatsan, McFaline-Figueroa, Ramani et al. Massively multiplex chemical transcriptomics at single-cell resolution. Science (2020)
PMID: 31806696
(with Trapnell Lab)
Chu et al. Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform. NEJM (2020)
PMID: 32356944
Rentzsch et al. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research (2019)
PMID: 30371827
(with Kircher Lab)
Starita et al. A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function. AJHG (2018)
PMID: 30219179
(with Parvin Lab)
Findlay et al. Accurate classification of BRCA1 variants with saturation genome editing. Nature (2018)
PMID: 30209399
(with Starita Lab)
Starita et al. Variant Interpretation: Functional Assays to the Rescue. AJHG (2017)
PMID: 28886340
Underhill et al. Fragment Length of Circulating Tumor DNA. PLoS Genetics (2016)
PMID: 27428049
(with Underhill Lab)
Neveling, Mensenkamp et al. BRCA Testing by Single-Molecule Molecular Inversion Probes. Clinical Chemistry (2017)
PMID: 27974384
(with Nelen, Hoischen Labs)
Snyder, Kircher et al. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell (2016)
PMID: 26771485
Roach et al. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota.PLoS Genetics (2015)
PMID: 26230489
(with Salipante Lab)
Starita et al. Massively Parallel Functional Analysis of BRCA1 RING Domain Variants. Genetics (2015)
PMID: 25823446
(with Fields Lab)
Kumar, Ryan et al. Whole genome prediction for preimplantation genetic diagnosis. Genome Medicine (2015)
PMID: 26019723
Snyder, Simmons et al. Copy-Number Variation and False Positive Prenatal Aneuploidy Screening Results. New England Journal of Medicine (2015)
PMID: 25830323
(with Gammill Lab)
Salipante, Roach et al. Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains. Genome Research (2014)
PMID: 25373147
Kumar et al. Genome sequencing of idiopathic pulmonary fibrosis in conjunction with a medical school human anatomy course. PLoS One (2014)
PMID: 25192356
Kumar et al. Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes. Genome Biology (2014)
PMID: 25608559
(with Rostomily Lab)
Kircher, Witten et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics (2014)
PMID: 24487276
(with Cooper Lab)
Kitzman et al. Noninvasive whole-genome sequencing of a human fetus. Science Translational Medicine (2012)
PMID: 22674554
Snyder et al. Noninvasive fetal genome sequencing: a primer. Prenatal Diagnosis (2013)
PMID: 23553552
Vasta V et al. Next generation sequence analysis for mitochondrial disorders. Genome Medicine (2009)
PMID: 19852779
(with Hahn Lab)
Cooper, Shendure. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews Genetics (2011)
PMID: 21850043