Members

Todd Treangen, PhD

Assistant Professor, Computer Science

Bio: Todd J. Treangen, Ph.D. is an Assistant Professor in the Department of Computer Science at Rice University. Before joining Rice, Dr. Treangen was a Research Scientist at the University of Maryland College Park. He received his Ph.D. in Computer Science in 2008 from the Polytechnic University of Catalonia (Barcelona, Spain). His research group focuses on solving large-scale computational problems specific to computational biology, with a focus on developing robust software tools targeted towards biothreat screening, infectious disease monitoring, and microbial forensics.

Leo Elworth, PhD

Postdoctoral Scientist

Bio: Leo Elworth recently received his PhD in Computer Science at Rice University working on statistical modeling of DNA sequence evolution. He was advised by Dr. Luay Nakhleh, the J.S. Abercrombie Professor and Chair of the Department of Computer Science at Rice. Since joining at Rice, Leo was awarded a graduate research fellowship from the National Library of Medicine, has published work in computational biology in journals such as Bioinformatics, presented research at scientific conferences like RECOMB-CG in Barcelona and WABI in Helsinki, and contributed to a soon to be released book on computational modeling of evolutionary histories of genomes.

Dreycey Albin

2nd year PhD student

Program: Systems, Synthetic, and Physical Biology (SSPB)

Bio: Dreycey obtained B.S. degrees in both Chemistry and Biology from the University of Northern Colorado. While at the University of Northern Colorado, he was a McNairs Scholar and an Honors student. Subsequently, he did a post baccalaureate in the lab of Dr. Gabriele Varani at the University of Washington, focusing on computational and experimental approaches to RNA structure elucidation. His interests are in the areas of applied mathematics, lab automation, and computational biology. For fun Dreycey likes to spend his time outdoors either running, backbacking/camping, or skateboarding.

2nd year PhD student

Program: Computer Science

Bio: Advait obtained a dual degree, B.E Computer Science and MS Biological Sciences from BITS, Pilani in India. During his undergraduate degree, he received the Khorana Scholarship (2016) from the Indo-US Science and Technology Forum and also a thesis fellowship (2017-18) to work at Icahn School of Medicine, Mount Sinai, NY. At Mount Sinai, he worked on creating a Sub-cellular process-based ontology that predicts whole cell function using Natural Language Processing. His research interests are at the intersection of genomic data science and designing efficient algorithms to analyze genomic data.

2nd year PhD student

Program: Systems, Synthetic, and Physical Biology (SSPB)

Bio: Qi obtained B.S. degrees in Biotechnology from Hong Kong Baptist University and MS in Biotechnology from Northwestern University. During her undergraduate, she did research in University of Chinese Academy of Sciences, Beijing University of Chemical Technology and Capital Medical University, focusing on using bioinformatics and experimental approaches to solve various life science problems, including synthetic biology, developmental biology, oncology and drug discovery. Her interest is to improve human health and environment by understanding complex biology data.

Yilei Fu

1st year PhD student (COMP 590)

Program: Computer Science

Bio: Yilei obtained B.E. degrees in Computer Science and Technology from Harbin Institute of Technology, China. During his undergraduate procedure, he receive National People's Scholorship for 3 times. In the meantime, he also worked on detecting SV(structure variation) on human genomes using third generation sequencing data. His research interest can be briefly discribed as exploring gene-carried information using third/next generation sequencing data.

Chunxiao Liao

1st year PhD student (COMP 590)

Program: Computer Science

Bio: Chunxiao received her MS in Computer Science from the University of Nebraska Lincoln. Her previous research includes microRNA targets prediction and premature infants sucking signal analysis and their brain development prediction. After graduation, she was working on gas chromatography image processing as a software engineer in industry. She always interested in building tools to solve the problems in bioinformatics and biomedical engineering. In her spare time, she likes to play with her two children.

Yunxi Liu

1st year PhD student (COMP 590)

Bio: Yunxi obtained a B.S. degree in Computer Science from the University of Houston and a B.S. degree in Pharmacology from China Pharmaceutical University. During his undergraduate in UH, he did research in the Pattern Analysis Laboratory on image feature extraction. His research interests include Bioinformatics, Data Science, and Machine Learning.

Yongze Yin

1st year PhD student (COMP 590)

Program: Computer Science

Bio: Yongze double majored in Computer Science and Statistics and received his B.S. degree from University of North Carolina at Chapel Hill. His research interests include analyzing high throughput sequencing genomic data and developing bioinformatics tools for biological research. During his undergrad, he developed pipelines to fix mouse reference genome and worked on an optical mapping simulator for Bionano in Dr. Leonard McMillan’s lab. Currently, Yongze is striving to delve into metagenomic assembly, specifically, tools for error detection and assembly validation.

Erin Liu

COMP 390 student.

Bio: Erin is an undergraduate student majoring in Computer Science. She did research in Harvard University, Department of Chemistry and Chemical Biology, where she helped improve the design of the nanoscale injectable electronic used for neuron signal recoding. Her research interest is to use the state-of-the-art computational methods and efficient algorithms to solve interesting biological problems.

Jacob Diaz

COMP 390 student.

Bio:

Viginesh Muraliraman

COMP 590 student.

Bio: Vigi is from Chennai, India and currently enrolled in the Master’s in Computer Science program at Rice. Vigi did his undergraduate degree in Computer Science and Engineering at Sastra University, which is located at Thanjavur, India. Vigi's research interests include Data Science, Machine Learning, and developing solutions for problems in the real world using ideas from these areas.

Lab alums

  • Jacob Lu (undergraduate research @ Rice). Jacob spent a summer in the lab working on "Functional Genomic and Computational Assessment of Threats".
  • Viginesh Muraliraman (graduate research @ Rice). Vigi spent a summer in the lab working on sensitive and efficient read mapping of PacBio/Nanopore read data (collaboration with Fritz Sedlazeck from Baylor HGSC).
  • Josie Garza (undergraduate research @ Rice). Josie spent a semester in the lab analyzing sequencing data to track flu transmission on a university campus. Now a Junior in the CS department.
  • Daniel Nasko Ph.D (Postdoctoral Scientist). Dr. Nasko spent two years in the lab and contributed to several projects, including IARPA FunGCAT and investigating the influence of reference databases on taxonomic classification. Now a Senior Data Scientist at Biota.
  • Bernard Fongang, Ph.D. (Bioinformatic Scientist). Dr. Fongang joined us from UTMB Galveston and worked on protein-protein interaction prediction. Now an Assistant Research Professor University of Texas San Antonio.
  • Shilpa Roy (Intern) - Shilpa joined as a senior from Eleanor Roosevelt HS and worked on comparing/contrasting Illumina MiSeq, HiSeq, PacBio RS II and Oxford Nanopore data in her research practicum titled "Mapping the effectiveness of genome sequencing technologies". Now an undergraduate student at University of Maryland College Park.

Collaborators

  • Sarah Allard (University of Maryland College Park, College Park, MD)
  • Nick Bergman (National Biodefense and Countermeasures Center, Frederick, MD)
  • Sharon Bewick (University of Maryland College Park, College Park, MD)
  • Aaron Darling (University of Technology Sydney, Sydney, Australia)
  • Judson Hervey (National Research Lab, Washington D.C.)
  • Scott Jackson (National Institute for Standards in Technology, Gaithersburg, MD)
  • Chris Jermaine (Rice University, Houston, TX)
  • Sergey Koren (NHGRI/NIH, Bethesda, MD)
  • Don Milton (University of Maryland College Park, College Park, MD)
  • Luay Nakhleh (Rice University, Houston, TX)
  • Brian Ondov (NHGRI/NIH, Bethesda, MD)
  • Adam Phillippy (NHGRI/NIH, Bethesda, MD)
  • Hendrik Poinar (McMaster University, Hamilton, Ontario, Canada))
  • Mihai Pop (University of Maryland, College Park, MD)
  • Eduardo Rocha (Institute Pasteur, Paris, France)
  • Steven Salzberg (Johns Hopkins University, Baltimore, MD)
  • Fritz Sedlazeck (Baylor Human Genome Sequence Center, Houston, TX)
  • Sara Vieira-Silva (KU Leuven, Leuven, Belgium)
  • Sonia Villapol (Houston Methodist Research Institute, Houston, TX)
  • Tandy Warnow (University of Illinois Urbana-Champaign, Champaign, IL)

Contact info

Department of Computer Science

Rice University

(office) Duncan Hall 3099

(phone) 713-348-4724

(web) https://treangenlab.com

(twitter) @traingene