Author

Alex Bishara

Stanford Medicine

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 2 Bioinformatics· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Organism:human· 4 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Assay:metagenomics· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2

Frequent Co-Authors

Serafim BatzoglouiD· 3 shared Ziming WengiD· 3 shared Ami Siddharth BhattiD· 2 shared Arend SidowiD· 2 shared Eli L. Moss· 2 shared Adam D. EwingiD· 1 shared Adam M. NovakiD· 1 shared Alex A. PolleniD· 1 shared

Activity by Year

2016-2020 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersGenomics

Serafim BatzoglouORCID

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Author profile →

4 papers

Recent·Most cited

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

Alex Bishara, Eli L. Moss, Ekaterina Tkachenko, Joyce B. Kang, Soumaya Zlitni, Rebecca Neal Culver, Tessa M. Andermann, Ziming Weng, Christina M. Wood-Bouwens, Christine Handy, Hanlee P. Ji, Serafim Batzoglou, Ami Siddharth Bhatt

This study uses read cloud sequencing to identify mobile elements in Bacteroides caccae that contribute to antibiotic resistance in a patient's microbiome over time.

Genome Medicine · May 29, 2020Peer-reviewedBioinformatics

Culture-free generation of microbial genomes from human and marine microbiomes

Alex Bishara, Eli L. Moss, Mikhail Kolmogorov, Alma E. Parada, Ziming Weng, Arend Sidow, Anne Dekas, Serafim Batzoglou, Ami Siddharth Bhatt

This paper introduces a read cloud metagenomic sequencing approach combined with a new assembler, Athena, to generate high-quality microbial genome drafts from human and marine microbiomes without culturing.

Nature Biotechnology · Oct 15, 2018Peer-reviewedGenomics

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis

Ian T. Fiddes, Gerrald A. Lodewijk, Meghan Mooring, Colleen M. Bosworth, Adam D. Ewing, Gary L. Mantalas, Adam M. Novak, Anouk van den Bout, Alex Bishara, Jimi L. Rosenkrantz, Ryan Lorig-Roach, Andrew R. Field, Maximilian Haeussler, Lotte Russo, Aparna Bhaduri, , David H. Haussler

The paper identifies human-specific NOTCH2NL genes linked to neurodevelopmental disorders and shows they affect cortical neurogenesis through Notch signaling.

Cell · May 1, 2018Peer-reviewedNeuroscience

Genome-wide reconstruction of complex structural variants using read clouds

Noah Spies, Ziming Weng, Alex Bishara, Jennifer McDaniel, David Catoe, Justin M Zook, Marc Salit, Robert B West, Serafim Batzoglou, Arend Sidow

This paper introduces GROC-SVs, a method for detecting and assembling structural variants using read cloud data, showing improved specificity and enabling complex breakpoint reconstruction in cancer samples.

bioRxiv · Sep 10, 2016Genomics