Nature Search

Unsupervised detection of cancer driver mutations with parsimony-guided learning

Runjun Kumar, S. Joshua Swamidass and Ron Bose present an unsupervised parsimony-guided method, ParsSNP, for prioritizing candidate cancer driver mutations. They apply ParsSNP to a gastric cancer data set and predict potential driver mutations not detected by other methods, including truncations in known tumor-suppressor genes and previously confirmed drivers.

Runjun D Kumar
S Joshua Swamidass
Ron Bose
Research12 Sept 2016
Nature Genetics

Volume: 48, P: 1288-1294
Initiatives to bridge faith and science

S. Joshua Swamidass
Correspondence29 Jul 2015
Nature

Volume: 523, P: 531
Understanding and mitigating the impact of race with adversarial autoencoders

Sarullo and Swamidass use an adversarial variational autoencoder (AVAE) to remove race information from computer models while retaining essential data for accurate predictions, effectively reducing bias. This approach highlights the importance of developing tools to manage bias, ensuring fairer and more trustworthy technology.

Kathryn Sarullo
S. Joshua Swamidass
ResearchOpen Access23 Oct 2024
Communications Medicine

Volume: 4, P: 1-8
A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data

A machine learning approach for refinement of somatic variant calls automates this process and reduces bias stemming from inter-reviewer variability.

Benjamin J. Ainscough
Erica K. Barnell
Obi L. Griffith
Research05 Nov 2018
Nature Genetics

Volume: 50, P: 1735-1743
Accounting for proximal variants improves neoantigen prediction

Including patient-specific information about nearby somatic and germline alterations improves the accuracy of neoantigen prediction, potentially impacting cancer vaccine design.

Jasreet Hundal
Susanna Kiwala
Malachi Griffith
Research03 Dec 2018
Nature Genetics

Volume: 51, P: 175-179
Erratum: Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity

Yanchun Pan
Takuji Daito
Hiroko Yano
Amendments and CorrectionsOpen Access21 Sept 2016
Scientific Reports

Volume: 6, P: 1-2
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples

Erica K. Barnell
Peter Ronning
Obi L. Griffith
ResearchOpen Access05 Oct 2018
Genetics in Medicine

Volume: 21, P: 972-981
Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity

Yanchun Pan
Takuji Daito
Hiroko Yano
ResearchOpen Access12 Aug 2016
Scientific Reports

Volume: 6, P: 1-18

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