Kaiyuan Zhu

Contact

Department of Computer Science
Indiana University Bloomington
2033L Luddy Hall
700 N. Woodlawn Avenue
Bloomington, IN, 47408

Email: kzhu@indiana.edu

I'm currently visiting the Cancer Data Science Lab, National Cancer Institute.

About

Hi there, I'm a Ph.D. candidate at the Computer Science Department of Indiana University Bloomington, advised by Professor Cenk Sahinalp (and Professor Funda Ergun), working on algorithms and computational biology. I obtained my B.Sc.Eng. in Computer Science and Technology from Taishan College, Shandong University, China.

I'm interested in a diverse set of algorithmic problems from bioinformatics/computational biology, particularly in the context of genomic data compression, indexing and secure/privacy preserving computing. The main objective of my research is to develop computational methods that can reduce memory usage while analyzing large genomic data, or that directly make inference on the fly by processing genomic data on-line.

My research is funded by NSF CCF-1619081, NIH GM-108348 and IU's Precision Health Initiative.

CV is available upon request.

Publications

Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave
C Kockan, K Zhu, N Dokmai, N Karpov, MO Külekci, DP Woodruff, SC Sahinalp
[RECOMB 2019][BioRxiv][Code]

Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks
E Hodzic, R Shrestha, K Zhu, K Cheng, CC Collins, SC Sahinalp
[GigaScience][GigaDB][Supplementary][Code]

Genomic Data Compression
K Zhu, I Numanagić, SC Sahinalp
[Encyclopedia of Big Data Technologies]

Optimal Compressed Representation of High Throughput Sequence Data via Light Assembly
AA Ginart, J Hui, K Zhu, I Numanagić, TA Courtade, SC Sahinalp, DN Tse
[Nature Communications][Code]

Approximating Max NAE-k-SAT by anonymous local search
A Xian, K Zhu, D Zhu, L Pu, H Liu
[FAW 2015][Theoretical Computer Science]

Teaching

Fall 2014: B501 Theory of Computing (Associate Instructor)

Spring 2015: I201 Mathematical Foundations of Informatics (Associate Instructor)

Fall 2015: P536 Advanced Operating Systems (Associate Instructor)

Spring 2016: B503 Algorithms Design and Analysis (Associate Instructor)

Professional Expericence

Talks given: Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave
RECOMB, May 2019, Washington, DC, USA.

Optimal Compressed Representation of High Throughput Sequence Data via Light Assembly
RECOMB-Seq, May 2017, Hong Kong;
PHI meeting, IU, Dec 2017.

Reviewer: CPM 2017; RECOMB 2018; RECOMB 2019; Bioinformatics; BMC Bioinformatics; PLOS Computational Biology; Genome Biology

Computational Genomics Summer Institute 2017, UCLA

Links

[GitHub][dblp][Google Scholar][ORCID]