• 7/2024 - Talk on detecting Alu exonization in the human genome with our deep learning model eXAlu, at the 6th World's Aging and Rejuvenation Conference (ARC2024), Paris, France
  • 1/2024 - Manuscript describing our new tool eXAlu, for predicting exonization of Alu elements, is on bioRxiv
  • 1/2024 - Manuscript describing MntJULiP and Jutils, our tools for differential splicing detection in the presence of covariates, is on bioRxiv


  • 11/2023 - Poster on the MntJULiP and Jutils tools for discovery of differential splicing events in complex data with covariates at ASHG 2023 (with Edward Wui Wang Lui and Guangyu Yang)
  • 10/2023 - Talk on our decades-long work on splice graph-based transcript reconstruction at the SorinFest: Phase Transitions conference honoring Sorin Istrail, at Brown University (YouTube)
  • 7/2023 - Talk on differential splicing analysis of human data with MntJULiP at SPLICING2023, Caparica, Portugal
  • 7/2023 - Collaborative paper on the transcriptomics of the interaction of B. burgdorferi and human dendritic cells (Mark Soloski's lab)
  • 5/2023 - Talk on the Deep Learning model of Alu exonization at WMESA2023, Penn State University
  • 4/2023 - Collaborative paper on a mouse model of Down syndrome (Roger Reeves' lab)



  • 11/2021 - Poster on our Probabilistic Deep Learning model of alternative splicing, at the CSHL's (Virtual) Genome Informatics Meeting (with Guangyu Yang and Zitong He)
  • 8/2021 - Our paper on Alubaster and Alu exonization events in frontal cortex is accepted in Frontiers Molecular Biosciences (with Kathy Burns, Lindsay Payer, Corina Antonescu and Guangyu Yang)
  • 5/2021 - Jutils paper on alternative splicing visualization tools is accepted in Bioinformatics (with Guangyu Yang, Leslie Cope and Zitong He)
  • 3/2021 - Zoom talk at University of Texas Southwestern, Department of Bioinformatics, Dallas, TX



  • 9/2019 - We received an NIH R01 grant to design tools for analyzing massive collections of RNA-seq data
  • 8/2019 - A collaborative paper on the molecular basis of telomere disorders (with Mary Armanios)
  • 6/2019 - A collaborative study on the the gut microbiome changes in medical weight loss (with GIM's Jeanne Clark and Clare Lee





  • 10/2015 - Accurate and efficient RNA-seq error correction with Rcorrector, with Li Song, in GigaScience
  • 7/2015 - More functional validation for the role of our novel HCV viral miRNA in hepatocellular carcinoma (with Ajit Kumar)
  • 5/2015 - Guangyu Yang (Clemson U) has joined the lab, and Dhruv Shankar (UNC) and Ankur Sundara (Nashua HS South) are joining us for the summer - welcome on board!


  • 11/2014 - An error correction algorithm for next generation sequences, in Genome Biology (with Li Song and Ben Langmead).
  • 8/2014 - We received NSF funding to extend our work on reconstructing alternative splicing variation from RNA-seq data (ABI-1356078)
  • 8/2014 ...And a new NSF award to develop software to improve plant genome assembly and gene and transcript annotations (IOS-1339134)
  • 7/2014 - An HCV virus-encoded small non-coding RNA modulates PTEN transport to the nucleus, in Infectious Agents and Cancer (with Ajit Kumar).
  • 2/2014 - A review I wrote with Steven Salzberg on genome-guided transcript assembly methods has appeared in TCBB.

We have openings for doctoral and postdoctoral positions.