Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. - Yun S. Song; Yufeng Wu 001; Dan Gusfield (ISMB (Supplement of Bioinformatics), 2005)

Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event. - Yun S. Song; Yufeng Wu 001; Dan Gusfield (WABI, 2005)

Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. - Yun S. Song; Zhihong Ding; Dan Gusfield; Charles H. Langley; Yufeng Wu 001 (RECOMB, 2006)

A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem. - Yufeng Wu 001; Dan Gusfield (COCOON, 2007)

Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. - Yufeng Wu 001; Dan Gusfield (CPM, 2007)

Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms. - Yufeng Wu 001 (RECOMB, 2007)

Efficient Computation of Minimum Recombination with genotypes (not Haplotypes). - Yufeng Wu 001; Dan Gusfield (J. Bioinform. Comput. Biol., 2007)

A practical method for exact computation of subtree prune and regraft distance. - Yufeng Wu 001 (Bioinform., 2009)

The Three-state Perfect Phylogeny Problem Reduces to 2-SAT. - Dan Gusfield; Yufeng Wu 001 (Commun. Inf. Syst., 2009)

An analytical upper bound on the minimum number of recombinations in the history of SNP sequences in populations. - Yufeng Wu 001 (Inf. Process. Lett., 2009)

Bounds on the Minimum Mosaic of Population Sequences under Recombination. - Yufeng Wu 001 (CPM, 2010)

Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. - Yufeng Wu 001; Jiayin Wang 002 (ISBRA, 2010)

Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees. - Yufeng Wu 001 (Bioinform., 2010)

Exact Computation of Coalescent Likelihood for Panmictic and Subdivided Populations under the Infinite Sites Model. - Yufeng Wu 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Identifying interacting SNPs with parallel fish-agent based logic regression. - Jiayin Wang 002; Jin Zhang 038; Yufeng Wu 001 (ICCABS, 2011)

Haplotype Inference from Single Short Sequence Reads Using a Population Genealogical History Model. - Jin Zhang; Yufeng Wu 001 (Pacific Symposium on Biocomputing, 2011)

SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data. - Jin Zhang 038; Yufeng Wu 001 (Bioinform., 2011)

Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. - Jorge Duitama; Justin Kennedy; Sanjiv Dinakar; Yözen Hernández; Yufeng Wu 001; Ion I. Mandoiu (BMC Bioinform., 2011)

New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations. - Yufeng Wu 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. - Jin Zhang 038; Jiayin Wang 002; Yufeng Wu 001 (BMC Bioinform., 2012)

An SVM-based approach for genotyping deletions and insertions with population sequence reads. - Chong Chu; Jin Zhang; Yufeng Wu 001 (ICCABS, 2013)

An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. - Yufeng Wu 001 (RECOMB, 2013)

An SVM-based approach for discovering splicing junctions with RNA-Seq. - Chong Chu; Yufeng Wu 001 (ICCABS, 2014)

A coalescent-based method for population tree inference with haplotypes. - Yufeng Wu 001 (Bioinform., 2015)

SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data. - Chong Chu; Xin Li; Yufeng Wu 001 (BMC Bioinform., 2015)

Concod: Accurate consensus-based approach of calling deletions from high-throughput sequencing data. - Xiaodong Zhang; Chong Chu; Yao Zhang; Yufeng Wu 001; Jingyang Gao (BIBM, 2016)

An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree. - Yufeng Wu 001 (Bioinform., 2016)

Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. - Sajad Mirzaei; Yufeng Wu 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

GAPPadder: A sensitive approach for closing gaps on draft genomes with short sequence reads. - Chong Chu; Xin Li; Yufeng Wu 001 (ICCABS, 2017)

RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination. - Sajad Mirzaei; Yufeng Wu 001 (Bioinform., 2017)

STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies. - Jingwen Pei; Yufeng Wu 001 (Bioinform., 2017)

Concod: an effective integration framework of consensus-based calling deletions from next-generation sequencing data. - Lei Cai; Chong Chu; Xiaodong Zhang; Yufeng Wu 001; Jingyang Gao (Int. J. Data Min. Bioinform., 2017)

DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network. - Lei Cai; Yufeng Wu 001; Jingyang Gao (BMC Bioinform., 2019)

scSNVIndel. accurate and efficient calling of SNVs and indels from single cell sequencing using integrated Bi-LSTM. - Lei Cai; Yufeng Wu 001; Jingyang Gao (BIBM, 2020)

Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach. - Yufeng Wu 001 (Bioinform., 2020)

Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach. - Yufeng Wu 001 (Bioinform., 2020)

Inferring the ancestry of parents and grandparents from genetic data. - Jingwen Pei; Yiming Zhang 007; Rasmus Nielsen; Yufeng Wu 001 (PLoS Comput. Biol., 2020)

Detecting genomic deletions from high-throughput sequence data with unsupervised learning. - Xin Li 240; Yufeng Wu 001 (BMC Bioinform., 2022)

Bounding the Number of Reticulations in a Tree-Child Network that Displays a Set of Trees. - Yufeng Wu 001; Louxin Zhang (RECOMB-CG, 2023)

Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees. - Yufeng Wu 001; Louxin Zhang (J. Comput. Biol., 2024)

ScisTree2: An Improved Method for Large-Scale Inference of Cell Lineage Trees and Genotype Calling from Noisy Single Cell Data. - Haotian Zhang; Yiming Zhang 007; Teng Gao; Yufeng Wu 001 (RECOMB, 2025)

Bounding the number of reticulation events for displaying multiple trees in a phylogenetic network. - Yufeng Wu 001; Louxin Zhang (J. Comput. Syst. Sci., 2025)