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Bioinformatics and Mathematical Biosciences Lab

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Bioinformatic tools development and Omic data mining & modeling

  • Comparative and functional genomics analysis
  • Biclustering of large-scale (meta-)transcriptomic data
  • Discovery, scanning and comparison of cis-regulatory motifs
  • Dynamic programming for chromosomal folding structure prediction

Computational systems biology in microbial and plant genomes

  • Prediction of metabolic networks and associated regulatory systems
  • Meta-genomics data analysis of plant–microorganism interactions
  • Elucidation and application of organizing principles of bacterial genomes
  • Identification and evolutionary study of plant cell-wall related genes

Openings

Graduates

Students with biology, computer science and statistics/mathematics background are all welcome to contact me at qin.ma@sdstate.edu with a letter of interest and information about your GPA, GRE, TOEFL (if internationals) scores.

Undergraduates

Students interested in doing bioinformatics research are welcome to contact me directly at qin.ma@sdstate.edu or 605-688-6315, and should read here before contact.

Lab News

  • [21 April 2017] Mr. Shuai Li, an undergraduate student from Department of Computer Science, was hired in BMBL. He also received the BioSNTR Summer Undergraduate Research Grant.
  • [12 April 2017] The paper 'Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes' was officially accepted by Briefings in Bioinformatics. (IF=8.399)
  • [10 April 2017] The paper 'DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses' was officially accepted by Bioinformatics(IF=5.766)
  • [27 March 2017] Yiran Zhang received the “Meeting the Grand Challenges” Award for 2017 from SDSU!
  • [08 March 2017] The paper An algorithmic perspective of de-novo cis-regulatory motif finding based on ChIP-seq data was published in Briefings in Bioinformatics. (IF=8.399)
  • [06 October 2016] The paper QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data was published in Bioinformatics(IF=5.766)
  • [Oct 2016] A new grant was received from NSF. (Link)
  • [Oct 2016] A new biclustering R package was published in Bioinformatics.
  • [Aug 2016] Ms. Juan Xie, a master student from Department of Mathematics and Statistics, was hired in BMBL.
  • [June 2016] 'DMINDA2 web server: regulatory DNA motif identification and analyses', has been accepted to the ISMB 2016 - Technology Track.
  • [May 2016] Mr. Xiaozhu Jin received the BioSNTR Summer Undergraduate Research Grant.
  • [May 2016] The Research/Scholarship Support Fund received from SDSU.
  • [April 2016] Mr. Xiaozhu Jin, an undergraduate student from Department of Computer Science, was hired in BMBL.
  • [April 2016] Mr. Adam McDermaid, a Ph.D. student from Department of Mathematics and Statistics, was hired in BMBL.
  • [14 Match 2016] Dr. Dong Xu is invited to visit our lab.
  • [Match 2016] A paper regarding regulon identification was published in Scientific Reports.
  • [Feb 2016] Mr. Yiran Zhang, an undergraduate student from Department of Computer Science, was hired in BMBL.
  • [Jan 2016] A new grant was received from BioSNTR Seed Opportunity Program.
  • [Jan 2016] Mr. Jinyu Yang, a master student from Department of Mathematics and Statistics, was hired in BMBL.
  • [Oct 2015] Scholarly Excellence Funds was received from SDSU.
  • [26 May 2015] The paper Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum was published in Nucleic Acids Research(IF=9.202)