C
Craig Smail
Researcher at Stanford University
Publications - 23
Citations - 632
Craig Smail is an academic researcher from Stanford University. The author has contributed to research in topics: Genome-wide association study & Genome. The author has an hindex of 9, co-authored 22 publications receiving 290 citations. Previous affiliations of Craig Smail include American Academy of Family Physicians & Children's Mercy Hospital.
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Journal ArticleDOI
Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
Laure Fresard,Craig Smail,Nicole M. Ferraro,Nicole A. Teran,Xin Li,Kevin S. Smith,Devon Bonner,Kristin D. Kernohan,Shruti Marwaha,Shruti Marwaha,Zachary Zappala,Brunilda Balliu,Joe R. Davis,Boxiang Liu,Cameron J. Prybol,Jennefer N. Kohler,Diane B. Zastrow,Chloe M. Reuter,Dianna G. Fisk,Megan E. Grove,Jean M. Davidson,Taila Hartley,Ruchi Joshi,Benjamin J. Strober,Sowmithri Utiramerur,Lars Lind,Erik Ingelsson,Erik Ingelsson,Alexis Battle,Gill Bejerano,Jonathan A. Bernstein,Euan A. Ashley,Kym M. Boycott,Jason D. Merker,Jason D. Merker,Matthew T. Wheeler,Matthew T. Wheeler,Stephen B. Montgomery +37 more
TL;DR: A diagnostic tool based on blood RNA-seq is shown to identify causal genes and variants linked to clinical phenotypes in individuals with rare diseases for which whole-exome genetic sequencing was uninformative.
Journal ArticleDOI
Transcriptomic signatures across human tissues identify functional rare genetic variation
Nicole M. Ferraro,Benjamin J. Strober,Jonah Einson,Nathan S. Abell,François Aguet,Alvaro N. Barbeira,Margot Brandt,Maja Bucan,Stephane E. Castel,Joe R. Davis,Emily Greenwald,Gaelen T. Hess,Austin T. Hilliard,Rachel L. Kember,Bence Kotis,YoSon Park,Gina M. Peloso,Shweta Ramdas,Alexandra J. Scott,Craig Smail,Emily K. Tsang,Seyedeh M. Zekavat,Marcello Ziosi,Aradhana,Kristin G. Ardlie,Themistocles L. Assimes,Themistocles L. Assimes,Michael C. Bassik,Christopher D. Brown,Adolfo Correa,Ira M. Hall,Hae Kyung Im,Xin Li,Xin Li,Pradeep Natarajan,Pradeep Natarajan,Tuuli Lappalainen,Pejman Mohammadi,Pejman Mohammadi,Stephen B. Montgomery,Alexis Battle +40 more
TL;DR: Watershed, a probabilistic model for personal genome interpretation that improves over standard genomic annotation–based methods for scoring RVs, is developed and integrated approaches to identify expression, allele-specific expression, and alternative splicing outliers, and characterized the RV landscape underlying each outlier signal.
Journal ArticleDOI
Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease.
Olivia M. De Goede,Daniel Nachun,Nicole M. Ferraro,Michael J. Gloudemans,Abhiram Rao,Craig Smail,Tiffany Eulalio,François Aguet,Bernard Ng,Jishu Xu,Alvaro N. Barbeira,Stephane E. Castel,Sarah Kim-Hellmuth,YoSon Park,Alexandra J. Scott,Benjamin J. Strober,Christopher D. Brown,Xiaoquan Wen,Ira M. Hall,Alexis Battle,Tuuli Lappalainen,Hae Kyung Im,Kristin G. Ardlie,Sara Mostafavi,Thomas Quertermous,Karla Kirkegaard,Stephen B. Montgomery +26 more
TL;DR: In this paper, the expression, genetic regulation, cellular contexts, and trait associations of 14,100 lncRNA genes across 49 tissues for 101 distinct complex genetic traits were identified, including associations between LncRNA quantitative trait loci and inflammatory bowel disease, type 1 and type 2 diabetes, and coronary artery disease.
Journal ArticleDOI
Properties of structural variants and short tandem repeats associated with gene expression and complex traits.
David Jakubosky,Matteo D’Antonio,Marc Jan Bonder,Craig Smail,Margaret K.R. Donovan,William W. Greenwald,Hiroko Matsui,Agnieszka D'Antonio-Chronowska,Oliver Stegle,Oliver Stegle,Erin N. Smith,Stephen B. Montgomery,Christopher DeBoever,Kelly A. Frazer +13 more
TL;DR: The study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits and finds properties, such as length of variation, that affect the association.
Journal ArticleDOI
Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.
Marc Jan Bonder,Marc Jan Bonder,Craig Smail,Craig Smail,Michael J. Gloudemans,Laure Fresard,David Jakubosky,Matteo D’Antonio,Xin Li,Nicole M. Ferraro,Ivan Carcamo-Orive,Bogdan Mirauta,Daniel D Seaton,Na Cai,Na Cai,Dara Vakili,Dara Vakili,Danilo Horta,Chunli Zhao,Diane B. Zastrow,Devon Bonner,Matthew T. Wheeler,Helena Kilpinen,Joshua W. Knowles,Erin N. Smith,Kelly A. Frazer,Stephen B. Montgomery,Oliver Stegle +27 more
TL;DR: In this paper, the authors integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells, and report hundreds of new colocalization events for human traits specific to iPSCs.