• [12/17/2024] Our SAT-based, exact algorithm for computing the DCJ distance has been accepted to RECOMB 2025. Congratulations to Aaryan, Ke, and Austin!
• [12/17/2024] Our EquiRep work, an accurate approach for reconstructing the repeating unit from error-prone sequences, has been accepted to RECOMB 2025. Congratulations to Zhezheng, Tasfia, and Xiang!
• [11/20/2024] Tasfia passed her comprehensive exam. Congratulations!
• [10/04/2024] Aaryan traveled to attend the 2024 Mid Atlantic Bioinformatics Conference and presented a poster “An exact SAT formulation for computing DCJ distance in genome with duplicate genes”.
• [10/01/2024] Mingfu will serve as the publication chair of GLBIO 2025.
• [09/01/2024] Carl traveled to Royal Holloway, UK, for attending WABI 2024 and presenting his accepted Anchorage work.
• [08/09/2024] The entire group participated in and helped the organization of the 2024 workshop on sequence analysis (WEMSA’24). Ke gave a wonderful talk titled “Sequence similarity estimation by random subsequence embedding”; Carl, Zhezheng, Aaryan, Xiang, and Ke presented posters.
• [08/08/2024] Carl received the Huck Travel Award to support his trip to UK for WABI 2024. Congratulations, Carl!
• [08/08/2024] Aaryan has transitioned into the CSE PhD program, effective this Fall. Congratulations, Aaryan!
• [07/11/2024] Several of us will travel for ISMB 2024, in Montreal, Canada. Xin will present proceeding paper “Learning locality-sensitive bucketing functions” in HitSeq COSI; Qian will present proceeding paper “Accurate assembly of multiple RNA-seq samples with Aletsch” in iRNA COSI; Carl will present poster “Anchorage accurately assembles full-length anchor-flanked synthetic long reads” in HitSeq COSI; Zhezheng will present poster “Accurate detection of tandem repeat in error-prone long reads” in HitSeq COSI.
• [07/09/2024] Our TERRACE work, previously accepted to RECOMB 2024, has now been accepted to Genome Research. Congratulations to Tasfia, Qian, and Carl.
• [07/01/2024] Mingfu has been promoted to associate professor (with tenure), effective today.
• [06/30/2024] The Anchorage work, an assembler for anchor-enabled synthetic long reads data, has been accepted to WABI 2024. Congratulations to Carl, Xiang, and Element Biosciences co-authors!
• [06/24/2024] Xin received the ISMB 2024 travel award! Congratulations, Xin!
• [05/14/2024] Mingfu gave a keynote address at GLBIO 2024 titled “Transcript assembly for modern RNA-seq data”.
• [04/26/2024] Many of us are traveling for RECOMB. Mingfu will co-chair RECOMB-seq; Tasfia will present the TERRACE work (proceeding paper); Qian, Qimin, and Xin will present posters.
• [04/18/2024] Qimin successfully defended her PhD dissertation. Congratulations, Dr. Zhang!
• [04/05/2024] Qian passed her comprehensive exam. Congratulations!
• [04/02/2024] Both conditionally accepted papers have been now accepted to ISMB 2024.
• [03/07/2024] Congratulations to Xin, Ke, Xiang, and Qian for their work on learning LSB functions (conditionally) accepted to ISMB 2024
• [03/07/2024] Congratulations to Qian and Qimin for their Aletsch work that assembles multiple RNA-seq samples being (conditionally) accepted to ISMB 2024!
• [12/22/2023] Congratulations to Tasifa, Qian, and Carl, for having their work on a new assembler for circular RNAs (named TERRACE) accepted to RECOMB 2024!
• [12/21/2023] Our work on studying the divergence of annotations and its impact on transcript assembly has been published in PLOS Computational Biology. Congratulations to Qimin!
• [07/17/2023] Qimin’s poster about her work on studying different annotations for transcript assembly was accepted to WABI 2023; congratulations!
• [07/13/2023] Two (short) papers have been accepted to ACM-BCB 2023. Congratulations to Leran, Ke, and Xiang!
• [06/01/2023] Zhezheng Song, MS student of CSE at Penn State, joined us as a graduate research assistant. Welcome Zhezheng!
• [05/24/2023] The entire group participated in and helped the organization of the 2023 workshop on emerging methods for sequence analysis. Tasfia gave a great talk about her work on assembling circular RNAs!
• [04/26/2023] Xiang passed his comprehensive exam. Congratulations!
• [04/11/2023] The SubseqHash work has been accepted at ISMB/ECCB 2023 (conference proceeding). Congratulations to Xiang, Qian, and Ke!
• [01/09/2023] Sanchal Thakkar, an MS student graduated from Penn State, joined us as a graduate research assistant. Welcome Sanchal!
• [10/17/2022] Welcome Dr. Chenglin Fan, joining us as a postdoc! Chenglin obtained his PhD from University of Texas, Dallas, followed by one-year postdoc training at Sorbonne University, France.
• [09/06/2022] Congratulations to Qimin on being one of the winners of the annual CSE outstanding TA award!
• [09/01/2022] Welcome Dr. Xin Yuan! Xin graduated from Waseda University, Japan, and joined us as a postdoc in CSE and Biology.
• [06/13/2022] Our work titled locality-sensitive bucketing functions has been accepted to WABI’22. Congratulations, Ke!
• [05/14/2022] Our Scallop2 work has been accepted for a talk at HitSeq COSI of ISMB’22. Qimin will present this work. Six members of the lab will travel for this conference.
• [04/26/2022] Carl passed his comprehensive exam. Congratulations Carl!
• [04/21/2022] Congratulations to Austin on being accepted to BG PhD program!
• [04/14/2022] Qimin passed her comprehensive exam. Congratulations Qimin!
• [03/14/2022] Mayank successfully defended his MS thesis. Congratulations Mayank!
• [02/16/2022] Our Scallop2 paper has been accepted for publication in Nature Computational Science (in press). Congratulations to Qimin and Qian!
• [02/03/2022] We received the NSF CAREER award for developing allele-specific assembly methods. Grateful to the NSF for the generous support!
• [09/20/2021] Dr. Ke Chen from U. Wisconsin, Milwaukee has joined our group as a Postdoctoral Scholar. Welcome Ke!
• [03/01/2021] Xiang successfully defended his MS thesis. Congratulations Xiang!
• [02/12/2021] We received an NIH R01 grant for developing efficient algorithm to assemble large-scale RNA-seq data. Grateful to the NIH for the generous support!
• [01/20/2021] Mayank Murali, from CSE MS program, has joined our group. Welcome Mayank!
• [12/11/2020] Raj Pandey, from CSE MS program, has joined our group. Welcome Raj!
• [09/01/2020] Carl (Xiaofei) Zang, from BG PhD program, has joined our group. Welcome Carl!
• [06/02/2020] We received an NSF grant to develop computational methods to construct regulatory infrastructure using single-cell RNA-seq data. Thanks to the NSF for the generous support!
• [10/31/2019] Xiang Li, from CSE MS program, has joined our group. Welcome Xiang!
• [07/30/2019] Qimin Zhang, from CSE PhD program, has joined our group. Welcome Qimin!
• [11/16/2018] Qian Shi, from CSE PhD program, has joined our group. Welcome Qian!
• [07/01/2018] Our research group at CSE has started!