Alex Bishara

Department of Computer Science
Stanford University

email: abishara (at) cs (dot) stanford (dot) edu

I am broadly interested in applications of machine learning to solve problems in life sciences. I was briefly a Postdoctoral Fellow at the Hooper Foundation within UCSF working under Peter Turnbaugh.

I completed my Ph.D. in Computer Science at Stanford advised by Serafim Batzoglou. I developed novel computational approaches for genome assembly that leveraged recent sequencing techniques such as 10x Genomics. My work has allowed sequence assembly of large nearly identical repeat genes within the human genome and for near reference-grade microbial genome drafts to be obtained using a single metagenomic sequencing experiment.

I completed my undergraduate degree in Electrical Engineering and Computer Science (EECS) at UC Berkeley in 2010. As an undergraduate, I worked in the Computer Architecture group in the Par Lab under Krste Asanovic. I worked for just under two years at Apple in the Mobile Silicon CPU group before coming to Stanford.

I also run, cycle, and play tennis.


High-quality genome sequences of uncultured microbes by assembly of read clouds.
A. Bishara*, E. Moss*, M. Kolmogorov, A. Parada, Z. Weng, A. Sidow, A. Dekas, S. Batzoglou, A. Bhatt.
Nature Biotechnology 2018 Article.

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis.
I. Fiddes, et al.
Cell 2018 Article.

Genome-wide reconstruction of complex structural variants using read clouds.
N. Spies, Z. Weng, A. Bishara, J. McDaniel, D. Catoe, J. Zook, M. Salit, R. West, S. Batzoglou, A. Sidow.
Nature Methods 2017 Article.

Read clouds uncover variation in complex regions of the human genome.
A. Bishara*, Y. Liu*, Z. Weng, D. Kashef-Haghighi, D. E Neuburger, R. West, A. Sidow, and S. Batzoglou
Genome Research 2015 Article.

Exploring the Tradeoffs between Programmability and Efficiency in Data-Parallel Accelerators.
Y. Lee, R. Avižienis, A. Bishara, R. Xia, D. Lockhart, C. Batten, and K. Asanović.
ACM Transactions on Computer Systems, 2013 and
International Symposium on Computer Architecture (ISCA-2011) 2011.

* denotes joint first author