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CBBG Students

Daniel Ayres
Cummings Lab

Domenick Braccia
New student; Rotations

Kuoyuan Cheng
Ruppin Lab
cancer omics, genetic interactions

Seth Commichaux
Pop Lab
Metagenomics, microbiome to phenotype, genomics of food safety

Matthew Conte
Kocher Lab
Population genomics and bioinformatics

Jonathan Goodson
Winkler Lab
microbiology/molecular genetics and computational biology focusing on transcriptomics

Johnathan Guest
Pierce & Scull Labs
Hepatitis C virus sequence analysis; Computational antibody-antigen modeling: Vaccine design

Rong Guo
Rotations

Keith Hughitt
El-Sayed Lab
Host-pathogen interactions, rna-seq, biological networks, gene regulation

Kunal Kundu
Moult Lab
SNPs and diseases, Disease mechanisms

Muzi Li
New student; Rotations

M. Senthil Kumar
Corrada Bravo Lab
Statistical genomics, evolutionary models, prokaryotic anti-phage defense, CRISPR.

 

Nate Olson
Corrada Bravo Lab
Metagenoics, bioinformatics, metrology

Nicholas Rachmaninoff
New student; Rotations

Shrutii Sarda
Hannenhalli Lab
Evolution of transcriptional regulation

Saul Sarria
New student

Yifei Shi
Mount Lab
RNA-seq, splicing, nano-exon

Sanju Sinha
Ruppin Lab
Fundamentals of cancer genomics and precision oncology

Sanju Sinha
Ruppin Lab
Fundamentals of cancer genomics and precision oncology

Steven Smith
Ravel & El-Sayed Labs
Integration of experimental and high-throughput sequencing datasets for use in systems biology approaches

Kun Wang
Cao & Hannenhalli Labs
Alternative splicing determinants

Haley Wight
Liu & Hannenhalli Labs
transcriptomics, fruit development, coexpression networks, web UI

Yizou Yin
Moult Lab
Protein Structure, SNPs and diseases

Reynold Yu
New student; Rotations


Recent publications by CBBG students

Conte, M. A., Gammerdinger, W. J., Bartie, K. L., Penman, D. J., & Kocher, T. D. (2017). A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics, 18, 341. http://doi.org/10.1186/s12864-017-3723-5

Goodson, J. R., Klupt, S., Zhang, C., Straight, P., & Winkler, W. C. (2017). LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens. Nature Microbiology, 2, 17003

Inbar, E., Hughitt, V. K., Dillon, L. A. L., Ghosh, K., El-Sayed, N. M., & Sacks, D. L. (2017). The Transcriptome of Leishmania major Developmental Stages in Their Natural Sand Fly Vector. mBio, 8(2), e00029–17. http://doi.org/10.1128/mBio.00029-17

Kundu K, Pal LR, Yin Y, Moult J. Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge. Hum Mutat. 2017 May 12. doi: 10.1002/humu.23249. [Epub ahead of print] PMID: 28497567

M. Senthil Kumar, Joshua B. Plotkin, and Sridhar Hannenhalli: Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution. PLoS Comp Bio, 2015, 11(11).

Shrutii Sarda, Avinash Das, Charles Vinson and Sridhar Hannenhalli,  Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters  Genome Res. 2017. 27: 553-566 Published in Advance February 21, 2017, doi:10.1101/gr.212050.116

Smith, S. B. and Ravel, J. (2017), The vaginal microbiota, host defence and reproductive physiology. J Physiol, 595: 451–463. doi:10.1113/JP271694

Kun Wang, Avinash Das, Zheng-Mei Xiong, Kan Cao and Sridhar Hannenhalli: 2014,Phenotype-dependent coexpression gene clusters: application to normal and premature ageing. Transactions on Computational Biology and Bioinformatics(TCBB) (doi: TCBB.2014.2359446)