Liming Cai

Professor, Department of Computer Science and Institute of Bioinformatics

Research Information:

My research interests are in algorithms and theories for computation-intensive problems, with applications in structural boinformatics and genomics. In RNA-informatics, I investigate various issues related to the prediction of non-coding RNA genes and structures.

Russell Malmberg

Professor, Departments of Plant Biology, Genetics, and Institute of Bioinformatics; Fellow, AAAS

Research Information:

My bioinformatics research interests are primarily in modeling and searching genomes for non-coding RNAs; secondarily I have some interests in the phylogenetic analysis of gene families. I also have a biology wetlab project studying pitcher plants (Sarracenia species).

Zhibin Huang

Research Assistant
Ph.D Student, Department of Computer Science

Research Information:

Currently I am involved in the project of "Searching for Non-coding RNA Pseudoknot Structures in Genomes via Graph Tree Decomposition". This Research project is to search the special RNA secondary structure (pseudoknot) in genome. SCFG model for stem and PHMM model for loop are built from the training sequences. Based on this full probability model, candidates of the structure-pseudoknot are found. A conformational graph is also built based on the training sequence, treating arms of stem as nodes and loops as edges. Then the optimal structure-sequence alignment between RNA structure profile and a target sequence can be treated to be the sub-graph isomorphism problem. Tree decomposition-based dynamic programming is applied to go through all the combinations of candidates and calculate the energy score. I am responsible for the tree decomposition-based dynamic programming part.

Sal LaMarca

Teaching/Research Assistant
Ph.D Student, Department of Computer Science

slamarca@uga.edu

Research Information:

Currently, I am interested in applying artificial intelligence techniques to bioinformatics problems. In particular, I am working on GAMSA (Genetic Algorithm for Multiple Stem Alignment), which will be used to align and profile RNA stems that contain pseudoknots where some stems may not be present. I am also interested in using machine learning techniques to find genetic markers that are associated with certain phenotypes.

Deshen Lin

Research Assistant
MS Student, Department of Computer Science

lindeshen80@gmail.com

Research Information:

I'm interested in applying algorithms to bioinformatics problems, with current research focus on ncRNA tertiary structure profiling and search.

Amy Liu

Research/Teaching Assistant
Ph.D Student, Department of Computer Science

amyliu@uga.edu

Research Information:

My current research is to develop Pkfam, a database of non-coding RNA families with pseudoknot structural alignments, which is made possible by the RNATOPS, a profile-based RNA pseudoknot search program developed by this research group.

Amir Manzour

GSA Research Assistant
Ph.D Student, Institute of Bioinformatics

amanzour@uga.edu

Research Information:

Amirhossein Manzourolajdad (Amir Manzour) received his Master’s degree in Systems telecommunications from Isfahan University of Technology (IUT), Isfahan, Iran in 2007. His research background includes disease modeling, developing effective algorithms for population-based gene mapping of complex diseases and implementing such algorithms. His current research interest in general is further exploring the link between complex systems and molecular biology for the purpose of explaining biological phenomena such as epistasis. His areas of interest also include Data mining, algorithm design, complexity theory, information theory, and genetic diseases.

Here is my newest publication in epistatic models for studying disease association.

Sang Ngyuen

Research Assistant
Undergraduate Student, Department of Computer Science

snlildude87@gmail.com

Research Information:

I am interested in developing my programming skills as well as learning new languages such as Perl and Python all while learning about Bioinformatics. Currently, I am working alongside Tim Shaw to achieve this goal.

Ben Ngyuen

Research Assistant
Undergraduate Student, Department of Chemistry

benxten@uga.edu

Research Information:

RNA is known to function as a regulator in both transcription and translation. However, they also have many other undiscovered functions. I am interested in discovering and understanding these functions through examination of their structures in prokaryotic microorganisms using bioinformatic and experimental techniques.

Juber Patel

GSA Research Assistant
Ph.D Student, Institute of Bioinformatics

juberpatel@gmail.com

Research Information:

I received an MSc(Scientific Computing) from University of Pune, India. I worked for 2 years as a software engineer with Persistent Systems, Pune, India before joining UGA Bioinformatics PhD program. My research interests are fairly wide in the sense I would like to apply core computer science methods and techniques to unravel the code of life. In last several decades, computer scientists have delved deep into various problems that are very general in nature and they have gained valuable insights on how to approach these problems. If these insights could be applied to Bioinformatics, many hard problems will become easier to tackle. I plan to work on improving algorithms and programming methodologies as well as leveraging the latest technological advances in the quest for solutions in Bioinformatics. In particular, I am fascinated by graph theory and its wide applications.

Joseph Robertson

Presidential Graduate Fellow
Ph.D Student, Institute of Bioinformatics

Josephr@uga.edu

Research Information:

My interests are fairly broad in regard to the application of computational methods to biological problems, but my current focus is on tools to help elucidate the structure and function of bio-molecules, and in particular, work on RNA and protein tools that utilize structural information. In addition, using some of the same techniques, looking for SNP (single nucleotide polymorphism) markers for use in the detection of diseases. All these projects share the use of a graph to model relationships, and the use of tree-decomposition to limit time complexity.

Abdul Samad

Fulbright Graduate Fellow

Ph.D Student, Department of Computer Science

samad@uga.edu

Research Information:

Abdul Samad is interested in graph theory and algorithms with applications in solving biological and health problems. He is on the Fulbright Fellowship.

Timothy Shaw

Research Assistant
Ph.D. Student, Institute of Bioinformatics

gatechatl@gmail.com

Research Information:

When dealing with Genetic Research, one must realize that these problems are always multidimensional due to the various unknown influences acting upon it. As a Bioinformatician/Genetic Researcher, my job is to make sense of these complex systems via a combination of Biological and Computational resource. The current project that I am working on is to create a novel algorithm to identify ncRNA. Secondarily, I also have interest in the areas of RNA structural prediction and modeling of complex biological systems.

Pooya Shareghi

Teaching/Research Assistant
Ph.D Student, Department of Computer Science

Research Information:

I am interested in randomized algorithms, theory of computation, and problems in graph theory. Currently I am working on FPT algorithms for subgraph isomorphism with applications in computational biology.

Anuj Srivastava

GSA Research Assistant
Ph.D Student, Institute of Bioinformatics

Research Information:

ncRNA gene finding:

Computer gene-finding programs have been quite successful at locating protein-coding genes in both prokaryotic and eukaryotic genomes. However these programs - which use genomic features such as long open-reading-frames and codon signatures - are not designed to identify non-coding RNA (ncRNA) genes. As a result ncRNA-specific gene-finders have been required. My project is aimed at modeling noncoding RNA structures, and aligning RNA structures to genomes in order to find new instances of a given non-coding RNA gene family.

Mika Takata

GSA Research Assistant
Ph.D Student, Institute of Bioinformatics

mika@uga.edu

Research Information:

I have worked on protein folding classification and ab-initio tertiary structure prediction by using machine learning methods, like support vector machines, hidden Markov models and genetic algorithm. My current interests are RNA/protein structure prediction with computational algorithms and modeling of the complex structure, in particular by using low identical data set. Also, I am interested in obstinate or genetic diseases, such as HIV or Alzheimer's disease.

Yingfeng Wang

Research/Teaching Assistant
Ph.D Student, Department of Computer Science

Research Information:

Non-coding RNA (ncRNA) has recently been identified to be significant in biology. My current work focuses on ncRNA sequences structure analysis. The main purpose of my work is to develop methods for exploiting the conserved region of ncRNA that is critical for searching non-coding RNA genes in genomes.

Xingran Xue

Research Assistant
MS Student, Department of Computer Science

xrxue@uga.edu

Research Information:

Protein 3D structure visualization.