Detecting and annotating genetic variations using the HugeSeq pipeline
Hugo Y. K. Lam,Cuiping Pan,Michael J. Clark,Phil Lacroute,Rui Chen,Rajini R Haraksingh,Maeve O'Huallachain,Mark Gerstein,Jeffrey M. Kidd,Carlos Bustamante,Michael Snyder +10 more
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This research presents a meta-modelling architecture that automates the very labor-intensive and therefore time-heavy and expensive and therefore expensive and expensive process of designing and implementing nanofiltration systems.Abstract:
volume 30 number 3 march 2012 nature biotechnology Liege, Belgium. 31The Babraham Institute, Cambridge, UK. 32Genomatix Software GmbH, Munich, Germany. 33Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. 34Christian-Albrechts-Universitaet Zu Kiel, Kiel, Germany. 35Cellzome AG, Heidelberg, Germany. 36Institut National de la Sante et de la Recherche Medicale, Marseille, France. 37Weizmann Institute of Science, Rehovot, Israel. 38Barcelona Supercomputing Center, Barcelona, Spain. 39Centro Nacional de Investigaciones Oncologicas, Madrid, Spain. 40University Medical Centre Groningen, Groningen, The Netherlands. 41University of Saarland, Saarbruecken, Germany. 42Oxford Nanopore Technologies Ltd., Oxford, UK. e-mail: h.stunnenberg@ncmls.ru.nlread more
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Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes
Rui Chen,George I. Mias,Jennifer Li-Pook-Than,Lihua Jiang,Hugo Y. K. Lam,Rong Chen,Elana Miriami,Konrad J. Karczewski,Manoj Hariharan,Frederick E. Dewey,Yong Cheng,Michael J. Clark,Hogune Im,Lukas Habegger,Suganthi Balasubramanian,Maeve O'Huallachain,Joel T. Dudley,Sara Hillenmeyer,Rajini R Haraksingh,Donald Sharon,Ghia Euskirchen,Phil Lacroute,Keith Bettinger,Alan P. Boyle,Maya Kasowski,Fabian Grubert,Scott Seki,Marco Garcia,Michelle Whirl-Carrillo,Mercedes Gallardo,Maria A. Blasco,Peter L. Greenberg,Phyllis Snyder,Teri E. Klein,Russ B. Altman,Atul J. Butte,Euan A. Ashley,Mark Gerstein,Kari C. Nadeau,Hua Tang,Michael Snyder +40 more
TL;DR: This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity and reveals extensive heteroallelic changes during healthy and disease states and an unexpected RNA editing mechanism.
Journal ArticleDOI
Toward better understanding of artifacts in variant calling from high-coverage samples
TL;DR: By investigating false heterozygous calls in the haploid genome, the erroneous realignment in low-complexity regions and the incomplete reference genome with respect to the sample are identified as the two major sources of errors, which press for continued improvements in these two areas.
Journal ArticleDOI
A survey of tools for variant analysis of next-generation genome sequencing data
Stephan Pabinger,Andreas Dander,Maria Fischer,Rene Snajder,Michael Sperk,Mirjana Efremova,Birgit Krabichler,Michael R. Speicher,Johannes Zschocke,Zlatko Trajanoski +9 more
TL;DR: A comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers.
Journal ArticleDOI
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
Jason O'Rawe,Jason O'Rawe,Tao Jiang,Guangqing Sun,Yiyang Wu,Yiyang Wu,Wei Min Wang,Jingchu Hu,Paul Bodily,Lifeng Tian,Hakon Hakonarson,W. Evan Johnson,Zhi Wei,Kai Wang,Kai Wang,Gholson J. Lyon,Gholson J. Lyon,Gholson J. Lyon +17 more
TL;DR: The results suggest that more caution should be exercised in genomic medicine settings when analyzing individual genomes, including interpreting positive and negative findings with scrutiny, especially for indels.
The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.
Atul J. Butte,Null Null +1 more
TL;DR: The three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses are described, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.
References
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