# overview
Our work focuses on the application of computational techniques to solve problems in biology. Current research projects cover diverse areas in computational biology, including multiple sequence alignment, motif finding with applications to predicting transcription factor binding sites, biological network analysis, and identification of gene clusters within genomes.

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Networking And Information Technology R&d

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3102 Bioinformatics And Computational Biology

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Reverse Transcriptase Polymerase Chain Reaction

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Intracellular Signaling Peptides And Proteins

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3102 Bioinformatics And Computational Biology

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1.1 Normal Biological Development And Functioning

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3102 Bioinformatics And Computational Biology

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Pennsylvania State University - (State College, Pennsylvania, United States)

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University of Southern California - (Los Angeles, California, United States)

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Chinese University of Hong Kong - (Shatin, Hong Kong, China)

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Gene expression correlates of facultative predation in the blow fly Chrysomya rufifacies (Diptera: Calliphoridae).

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Identifying clusters of functionally related genes in genomes.

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GRAPHLET ALIGNMENT IN PROTEIN INTERACTION NETWORKS

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Institute of Electrical and Electronics Engineers (IEEE)

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Identifying gene clusters within localized regions in multiple genomes.

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Parameterized and approximation algorithms for maximum agreement forest in multifurcating trees

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Finding alignments of conserved graphlets in protein interaction networks.

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Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus

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Machine learning performance in a microbial molecular autopsy context: A cross-sectional postmortem human population study.

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Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton.

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Accurate prediction of maize grain yield using its contributing genes for gene-based breeding.

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De novo transcriptome sequencing and analysis revealed the molecular basis of rapid fat accumulation by black soldier fly (Hermetia illucens, L.) for development of insectival biodiesel.

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Querying pathways in protein interaction networks based on hidden Markov models.

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Improved Algorithms for Path, Matching, and Packing Problems

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Path matching and graph matching in biological networks.

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Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

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Greedy localization and color-coding: Improved matching and packing algorithms

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Integrating sample-driven and pattern-driven approaches in motif finding

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Iterative Expansion and Color Coding: An Improved Algorithm for 3D-Matching

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Association for Computing Machinery (ACM)

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A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de bruijn graphs of RNA-seq data

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Institute of Electrical and Electronics Engineers (IEEE)

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Identification of the syr-syp box in the promoter regions of genes dedicated to syringomycin and syringopeptin production by Pseudomonas syringae pv. syringae B301D.

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A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data.

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Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements.

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Large-scale analysis of gene clustering in bacteria.

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Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment.

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Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues.

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Gene hunting without sequencing genomic clones: finding exon boundaries in cDNAs.

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Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains.

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Combinatorial approaches to finding subtle signals in DNA sequences.

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Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development.

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Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei.

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A polynomial time solvable formulation of multiple sequence alignment.

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Multiple sequence alignment based on profile alignment of intermediate sequences

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Recent Developments in Alignment and Motif Finding for Sequences and Networks

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Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.

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American Association for the Advancement of Science (AAAS)

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A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms.

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Developmental and gene expression analyses of a cotton naked seed mutant.

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A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms.

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Corepressor-dependent silencing of chromosomal regions encoding neuronal genes.

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American Association for the Advancement of Science (AAAS)

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High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop.

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A 24-48 h fed Amblyomma americanum tick saliva immuno-proteome.

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Parameterized and Approximation Algorithms for the MAF Problem in Multifurcating Trees

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Identifying complexes from protein interaction networks according to different types of neighborhood density.

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Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection.

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Computational Approaches for Studying Alternative Splicing in Nonmodel Organisms from RNASEQ Data

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Heuristic pairwise alignment of de Bruijn graphs to facilitate simultaneous transcript discovery in related organisms from RNA-Seq data.

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Algorithms and software for support of gene identification experiments.

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A de novo transcriptome assembly of Lucilia sericata (Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms and transcript expression estimates.

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Functional characterization of calliphorid cell death genes and cellularization gene promoters for controlling gene expression and cell viability in early embryos.

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Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection.

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RANDOMIZED DIVIDE-AND-CONQUER: IMPROVED PATH, MATCHING, AND PACKING ALGORITHMS

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Society for Industrial & Applied Mathematics (SIAM)

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Finding pathway structures in protein interaction networks

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A polynomial time solvable formulation of multiple sequence alignment

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Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

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Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata.

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Improved pattern-driven algorithms for motif finding in DNA sequences

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Supervised protein family classification and new family construction.

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Multiple sequence alignment based on profile alignment of intermediate sequences.

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Splicing graphs and EST assembly problem.

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Genome Sequence of a Providencia stuartii Strain Isolated from Luciliasericata Salivary Glands.

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Las Vegas algorithms for gene recognition: suboptimal and error-tolerant spliced alignment

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Proteomic and microRNA markers of fly development: Stable correlates of insect age to improve forensic entomology casework

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United States Department of Justice - (Washington D.C., District of Columbia, United States)

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Texas A&M University; Computer Science & Engineering; 3112 TAMU

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Yang, Qingwu (2007-12). Finding conserved patterns in biological sequences, networks and genomes. Doctoral Dissertation.

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Lu, Songjian (2009-12). Randomized and Deterministic Parameterized Algorithms and Their Applications in Bioinformatics. Doctoral Dissertation.

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Lu, Yue (2008-12). Improving the quality of multiple sequence alignment. Doctoral Dissertation.

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Zhao, Xiaoyan (2010-12). Improved Algorithms for Discovery of Transcription Factor Binding Sites in DNA Sequences. Doctoral Dissertation.

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Fan, Jia-Hao (2013-08). Cuts and Partitions in Graphs/Trees with Applications. Doctoral Dissertation.

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Chin, See Loong (2003-12). Incomplete gene structure prediction with almost 100% specificity. Master's Thesis.

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Yi, Gang Man (2011-05). Algorithms for Gene Clustering Analysis on Genomes. Doctoral Dissertation.

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Fu, Shuhua (2015-05). Genomic and Transcriptomic Studies on Non-Model Organisms. Doctoral Dissertation.

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Yi, Gang Man (2006-12). An algorithm for identifying clusters of functionally related genes in genomes. Master's Thesis.