Alistair Ward
Boston, Massachusetts, United States
715 followers
500+ connections
About
My background is in theoretical physics, but I have worked in computational biology since…
Activity
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Josh Bonkowsky, Mark Yandell and I are thrilled to lead this amazing team that will revolutionize precision/genomic medicine throughout the…
Josh Bonkowsky, Mark Yandell and I are thrilled to lead this amazing team that will revolutionize precision/genomic medicine throughout the…
Liked by Alistair Ward
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We are thrilled to welcome Gage Black to our Computational team! With his extensive expertise in computational genetics, gained through his PhD…
We are thrilled to welcome Gage Black to our Computational team! With his extensive expertise in computational genetics, gained through his PhD…
Liked by Alistair Ward
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The summary of the successful #UndiagnosedHackathon2024! Thank you to all children and adults with undiagnosed diseases, clinicians…
The summary of the successful #UndiagnosedHackathon2024! Thank you to all children and adults with undiagnosed diseases, clinicians…
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Experience
Education
Publications
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Tangram: a comprehensive toolbox for mobile element insertion detection
BMC Genomics
Mobile elements (MEs) constitute greater than 50% of the human genome as a result of repeated insertion events during human genome evolution. Although most of these elements are now fixed in the population, some MEs, including ALU, L1, SVA and HERV-K elements, are still actively duplicating. Mobile element insertions (MEIs) have been associated with human genetic disorders, including Crohn's disease, hemophilia, and various types of cancer, motivating the need for accurate MEI detection…
Mobile elements (MEs) constitute greater than 50% of the human genome as a result of repeated insertion events during human genome evolution. Although most of these elements are now fixed in the population, some MEs, including ALU, L1, SVA and HERV-K elements, are still actively duplicating. Mobile element insertions (MEIs) have been associated with human genetic disorders, including Crohn's disease, hemophilia, and various types of cancer, motivating the need for accurate MEI detection methods. To comprehensively identify and accurately characterize these variants in whole genome next-generation sequencing (NGS) data, a computationally efficient detection and genotyping method is required. Current computational tools are unable to call MEI polymorphisms with sufficiently high sensitivity and specificity, or call individual genotypes with sufficiently high accuracy.
Other authorsSee publication -
MOSAIK: A hash-based algorithm for accurate next-generation sequencing short-read mapping
PLoS ONE
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the…
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).
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More activity by Alistair
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Excited to announce that I successfully defended my PhD dissertation yesterday! My time at the University of Utah has been an incredible experience…
Excited to announce that I successfully defended my PhD dissertation yesterday! My time at the University of Utah has been an incredible experience…
Liked by Alistair Ward
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The possibilities brought about by collaboration have never been more obvious to me than in the extraordinary initiative, that is the brainchild of…
The possibilities brought about by collaboration have never been more obvious to me than in the extraordinary initiative, that is the brainchild of…
Liked by Alistair Ward
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Congratulations to the "Space team" on 3 diagnoses at the UDNI hackathon! #udni #hackathon #undiagnosedhackathon2024
Congratulations to the "Space team" on 3 diagnoses at the UDNI hackathon! #udni #hackathon #undiagnosedhackathon2024
Shared by Alistair Ward
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The 2nd Undiagnosed Hackathon began today with a Tools worksho. It's a collaboration between Wilhelm Foundation and Professor Wendy van Zelst-Stams…
The 2nd Undiagnosed Hackathon began today with a Tools worksho. It's a collaboration between Wilhelm Foundation and Professor Wendy van Zelst-Stams…
Liked by Alistair Ward
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Kudos to our collaborator Dr. Alistair Ward who is presenting at the Undiagnosed Disease Network International (UDNi) in the Netherlands this week on…
Kudos to our collaborator Dr. Alistair Ward who is presenting at the Undiagnosed Disease Network International (UDNi) in the Netherlands this week on…
Liked by Alistair Ward
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I'm really proud to be representing Frameshift at the Undiagnosed Hackathon in Nijmegen. A fantastic group of dedicated people from across the globe…
I'm really proud to be representing Frameshift at the Undiagnosed Hackathon in Nijmegen. A fantastic group of dedicated people from across the globe…
Shared by Alistair Ward
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For Wilhelm Foundation there is no diagnostic dead end! We can’t lean back when we know that 60% of the Undiagnosed Diseases that can’t to solved…
For Wilhelm Foundation there is no diagnostic dead end! We can’t lean back when we know that 60% of the Undiagnosed Diseases that can’t to solved…
Liked by Alistair Ward
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I am honored to be elected as a Fellow of the AAAS “for distinguished contributions by an exceptional individual who possesses a unique combination…
I am honored to be elected as a Fellow of the AAAS “for distinguished contributions by an exceptional individual who possesses a unique combination…
Liked by Alistair Ward
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In my recent Form Bio blog post - Removing the Multiomics Data Analysis Bottleneck to Advance Life Science Research and Development - I explore how…
In my recent Form Bio blog post - Removing the Multiomics Data Analysis Bottleneck to Advance Life Science Research and Development - I explore how…
Liked by Alistair Ward
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Really excited to announce that Form Bio goes Academic! Form Bio has developed a point and click bioinformatics platform to empower researchers to do…
Really excited to announce that Form Bio goes Academic! Form Bio has developed a point and click bioinformatics platform to empower researchers to do…
Liked by Alistair Ward
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Great talk from Steve Bleyl on implementing WGS for infants in the CICU at Intermountain Primary Children’s Hospital. I appreciate the acknowledgment…
Great talk from Steve Bleyl on implementing WGS for infants in the CICU at Intermountain Primary Children’s Hospital. I appreciate the acknowledgment…
Posted by Alistair Ward
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Nice summary of Utah's process for analyzing rapid whole-genome negative cases!!
Nice summary of Utah's process for analyzing rapid whole-genome negative cases!!
Liked by Alistair Ward
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My colleague Dr. Steven Bleyl will discuss our Utah experience with substituting clinical microarrays for whole-genomes in infants undergoing…
My colleague Dr. Steven Bleyl will discuss our Utah experience with substituting clinical microarrays for whole-genomes in infants undergoing…
Liked by Alistair Ward
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At the NIH today for the Advancing Genomic Medicine Research symposium; we presented an update on our software tools for promoting team-based…
At the NIH today for the Advancing Genomic Medicine Research symposium; we presented an update on our software tools for promoting team-based…
Liked by Alistair Ward
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