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.

Bryce Kille

Algorithms & Software Engineer

Bryce received his MS in Bioinformatics and BS in Computer Science + Chemistry from the University of Illinois at Urbana-Champaign. As an undergraduate, he worked at Dow Agrosciences in both the computational biology and cheminformatics groups. His projects included developing software for phylogeny analysis and creating models for compound activity prediction. During his Master's program, Bryce worked in a biochemistry lab developing software for genome mining as well as a on research project for creating bit-wise algorithms for the C++ STL. One of his main interests is casting biological and chemical problems into theoretical computer science questions.

3rd 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.

3rd 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.

Nicolae Sapoval

2nd year PhD student

Program: Computer Science

Bio: Nick obtained a B.S. degree in Computer Science and a B.S. with Honors in Mathematics from the University of Chicago. Subsequently, he spent a year working in Chicago in financial software consulting. At the University of Chicago Nick worked in wireless networks research and later in computational biophysics focusing on transition pathway prediction for insulin degrading enzyme. His current interests are in the areas of computational biology with a focus on genomic data. Outside of the lab Nick likes to engage in educational projects and social games.

Yilei Fu

2nd year PhD student

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

2nd year PhD student

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

2nd year PhD student

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.

Kristen Curry

1st year PhD student

Program: Computer Science

Bio: Kristen obtained a B.A. in computer science from the University of California, Berkeley in 2015. She has since worked for a private biotech company that generates personalized health information by measuring proteins from a single blood sample. Her primary research interest is to better understand the holistic impacts of traumatic brain injury on the human body through genomic sequencing techniques. Outside of the lab, she enjoys backpacking, cycling and practicing yoga.

Lab alums

  • Dreycey Albin (PhD student at CU Boulder). Dreycey spent two years in the lab and completed his masters degree titled: "A novel computational platform for sensitive, accurate, and efficient screening of nucleic acids" and contributed to SeqScreen (www.gitlab.com/treangenlab/seqscreen) and DQT (database query tool).
  • Yongze Yin (PhD student @ Rice). Yongze spent two semesters in the lab working on novel methods for metagenomic misassembly detection and quantification (MASQ).
  • Abdelrahman Abouzeid (undergraduate research @ Rice). Abdel spent a semester in the lab working on primer/probe design for detection of coronaviruses.
  • Roger Wang (undergraduate research @ Rice). Roger spent a semester in the lab working on phylogenomic analyses and variant detect of FluA and FluB short read datasets.
  • Jacob Lu (undergraduate research @ Rice). Jacob spent a summer in the lab working on "Functional Genomic and Computational Assessment of Threats".
  • Erin Liu (undergraduate research @ Rice).
  • Jacob Diaz (undergraduate research @ Rice).
  • Viginesh Muraliraman (graduate research @ Rice). Vigi spent a semester and 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.

Contact info

Department of Computer Science

Rice University

(office) Duncan Hall 3099

(phone) 713-348-4724

(web) https://treangenlab.com

(twitter) @traingene