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Barış Ekim

As seen in: BioRxiv, Cell Systems, Genome Research
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Articles

Graph-based deep reinforcement learning for haplotype assembly with Ralphi

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By Enzo Battistella, Anant Maheshwari, Barış Ekim, Bonnie Berger
| Genome Research
1,2 1Broad Clinical Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; 2Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; 3Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, USA; 4Department of Mathematics, MIT, Cambridge, Massachusetts 02139, USA Corresponding author: vpopic{at}broadinstitute.org Footnotes [Supplemental material is available for this article.] Article published online before print.
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mapquik: Efficient low-divergence mapping of long reads in minimizer space

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By Barış Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger
| BioRxiv
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
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Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

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By Barış Ekim, Bonnie Berger, Rayan Chikhi
| Cell Systems Verified
Highlights • We propose a novel graph representation for highly accurate and long sequencing reads • It improves the efficiency of genome assembly and pangenome graph construction • We construct for the first time a pangenome of 661,405 bacterial genomes Summary DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates.
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