Yufeng Wu

Professor Computer Science and Engineering Department University of Connecticut 371 Fairfield Road, Unit. 2155 Storrs, CT 06269,  U.S.A.

Phone: +1 (860) 486-2234 Email: yufeng.wu (AT) uconn.edu Please note: I am no longer using ywu (AT) engr.uconn.edu. This email address seems still working but may take longer time for emails to reach me.

PhD, University of California, Davis, 2007.

I am a professor at Computer Science and Engineering Department, University of Connecticut. My research is on Computational Biology and Bioinformatics. Currently, my research is mainly on computational problems in population genomics. I am also interested in problems related to phylogenetics and high-throughput sequencing.

What is new?

• January 15, 2024. The latest publication from my research group, “A general approach for inferring the ancestry of recent ancestors of an admixed individual“, is now online at PNAS.

Software
Some of the software (including STELLS) were originally hosted in an old server that is unfortunately offline now. Please write to me by email if you want to have access to these software.

       PedMix2                Software accompaniment for our PNAS 2024 paper “A general approach for inferring the ancestry of recent ancestors of an admixed individual”.

       GTmix                Software accompaniment for my ISMB 2020 paper (to appear in proceedings of ISMB 2020 as special issue of Bioinformatics) “Inference of Population Admixture Network from Local Gene Genealogies: a Coalescent-based Maximum Likelihood Approach”.

       PedMix                Software accompaniment for our  paper (to appear in PLoS Computational Biology) “Inference of Ancestry of Parents and Grandparents from Genetic Data” (preprint), 2020.

       ScisTree                Software accompaniment for my paper (Bioinformatics, 2020) “Accurate and Efficient Cell Lineage Tree Inference from Noisy Single Cell Data: the Maximum Likelihood Perfect Phylogeny Approach” (preprint).

       STELLS                Software accompaniment for my paper (Evolution, 2012)
“Coalescent-based Species Tree Inference from Gene Tree Topologies Under Incomplete Lineage Sorting by Maximum Likelihood“.
There is also an extension called STELLSH which infers population split history from haplotypes.

        STELLS2              Software accompaniment for the paper (Bioinformatics, in press, 2017)
“STELLS2: Fast and Accurate Coalescent-based Maximum Likelihood Inference of Species Trees from Gene Tree Topologies”
by Jingwen Pei and Yufeng Wu. This paper develops an improved method for species tree inference on coalescents that is much faster than the original STELLS.

          RENTPlus             New on November 20, 2015. Software accompaniment for:
“RENT+: An Improved Method for Inferring Local Genealogical Trees from Haplotypes with Recombination”
by Sajad Mirzaei and Yufeng Wu, Bioinformatics, 2016. Software accompaniment for :inferring local trees with recombinant population sequences. This paper improves RENT (my TCBB paper) significantly.

         REPdenovo           Software for constructing consensus repeats directly from sequence reads without reference genomes or annotation.
Paper: “REPdenovo: Inferring de novo repeat motifs from short sequence reads“, PLoS One, 2016.

        SVseq                   Software accompaniment for our paper (with my student Jin Zhang, Bioinformatics, 2012)
“SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data“

        PIRN      A software program for constructing parsimonious hybridization networks, which was developed in: “Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees“.

08/02/2020: PIRN (and PIRNs) is now hosted in GitHub.

10/4/2012: Updated to version 2.0, which supports an approach for building exact parsimonious network for multiple trees.
10/28/2015: released a new software tool called PIRNs, which works better with large number of gene trees.

         SPRDist: a tool for computing the subtree-prune-and-regraft distance between two phylogenetic trees. Software accompaniment to Yufeng Wu, A practical method for exact computation of subtree prune and regraft distance, Bioinformatics, v.25, pp. 190-196, 2009.

Professional Services

Associate Editor, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013-now

Program committee members

2024: RECOMB 2024
2021: APBC 2021
2020: ISBRA 2020,  ACM BCB 2020
2019: ACM BCB 2019, WABI 2019, APBC 2019
2018: ISBRA 2018, WABI 2018, ACM BCB 2018
2017: ISBRA 2017, BIBM 2017
2016: ISBRA 2016, BIBM 2016, ICCABS 2016.
2015: ISBRA 2015, BIBM 2015, ICCABS 2015.
2014: ISBRA 2014, BIBM 2014.
2013: ISMB/ECCB 2013, ACM BCB 2013,  ISBRA 2013
2012: RECOMB 2012, ISMB 2012,  ISBRA 2012
2011: BICoB 2011, ISBRA 2011, BIOINFORMATICS 2011, ICCABS 2011, ACM-BCB 2011, ISMB/ECCB 2011
2010: ISMB 2010, CPM 2010, BICoB 2010, ISBRA 2010, BIBM 2010
2009: ISMB/ECCB 2009,  BICoB 2009, BIBM 2009,ISBRA 2009
2008: ISBRA 2008, BIBM 2008
2007: BIBM 2007