News (since July 2008)

RNA Informatics Lab alumna Dr. Chunmei Liu Won the NSF Faculty Early CAREER Award. (Additional note: Chunmei joined Howard University in 2006 and was promoted to Associate Professor in 2010.)

August

31

Where have all our recent graduates gone?

Yingfeng Wang has joined as a Postdoctoral Research Associate in the Computer Science and Mathematics Division of Oak Ridge National Laboratory; Pooya Shareghi is now a software engineer with turn.com in California, and Mika Takata is a research staff with the Hitachi Ltd. in Japan. Congratulations!!!

 

May

4

Abdul has a new born baby boy. Congratulations!

Beautiful baby. Both the mother and the baby are doing just fine. Congratulations!!

April

24

Mika, Pooya, and Yingfeng have passed their defenses, Congratulations!

Mika Takata MS (Bioinformatics) thesis is "Analyese for Protein Structure Prediction", Pooya Shareghi's Ph.D (CS) dissertation has the title "Graph Generating Systems for Predicting Biological Structures" and Yingfeng Wang's Ph.D (CS) dissertation is "Separating Structural Non-coding RNAs From Genomic Backgrounds". Their degrees will be conferred on May 11 at Stegeman Coliseum. Congratulations!!

October

31

Anuj passed his dissertation defense. Congratulations!

Anuj Srivastava successfully defended Ph.D his dissertation "Evolution and detection of non-coding RNA, and transcriptome analyses of two non-coding systems", under the direction of Russell Malmberg. He joined UGA bioinformatics in 2007 and will join The Jackson Laboratory, a leading genetics research lab in Maine after Christmas, as a research scientist. Congratulations!!

August

20

Liang Ding joins the group

Mr. Liang Ding joins RNA Informatics Lab. He graduated from Univ of Texas, Pan American with an MS in computer science. His research interests include bioinformatics, design and analysis of algorithms, and computational complexity.

August

9

Alumnus Tim Shaw receives ARCS Foundation Global Impact Award

RNA Informatics Lab alumnus Tim Shaw receives ARCS Foundation Global Impact Award (2011-2012). Selected by the BHSI at UGA, Tim's application for this fellowship was partly based on his previous work in non-coding RNA research with RNA Informatics Lab. Congratulations!

May

20

Zhibin received his Ph.D. Congratulations!

Zhibin got it, a Ph.D in computer science. His is leaving our lab and joining a software company in Atlanta. Well done, Zhibin!

May

4

Yingfeng awarded Doctoral Dissertation Completion Award.

Yingfeng Wang has been awarded the Doctoral Dissertation Completion Award by the UGA graduate school with a full-year fellowship beginning the fall 2011. Congratulations!

April

7

Anuj awarded Doctoral Dissertation Completion Award.

Anuj Srivastava has been awarded the Doctoral Dissertation Completion Award by the UGA graduate school with a full-year fellowship beginning the fall 2011. Congratulations!

Feb

16

Yingfeng awarded an NSF travel fund by ICCABS

Yingfeng and Pooya traveled to Orlando, FL to attend the ICCABS 2011 conference; Yingfeng presented at the podium the paper which they co-authored with Amir, Pooya, Tim, Ying-Wai, Russell, and Liming: "Stable stems enabled Shannon entropies distinguish ncRNA from random viagra generico background". Yingfeng was also awarded an NSF travel fund by the conference. Congratulations! Click to enlarge pictures -- it is not difficult to find Yingfeng from the crowd!

August

20

Tim and Zhibin presented papers at CSB2010

Tim and Zhibin traveled to Stanford University to present their papers at the podium at the CSB2010 Conference, Stanford University (Palo Alto, CA). August 16-18, 2010. (click to enlarge the pictures)

August

20

Russell visited Chinese Universities

Russell visited and gave colloquia at Beijing University and Jinlin University in China in Mid August, 2010. (click to enlarge the pictures)

July

19

Angelina Jianing Wang was born July 19. Congratulations!

Yingfeng's baby Angelina Jianing Wang was born in the morning of July 19. Both the mother and the baby have been doing well. Congratulations!

June

15

Juber is awarded the Amazon AWS Education research grant, Congratulations!

Juber's research project: "DawgPack - Analyzing Multiple Human Genomes in The Cloud for Clues to Cancer" is a collaboration with Dr. Shaying Zhao of the IOB and Biochemistry and Molecular Biology Department. The awarded grant will allow us to use cloud computing facilties at AWS (free for one year and possibly renewable) for this project that requires extensive computing resources. Congratulations!

May

5

Two papers from the group are accepted to CSB 2010 -- Congratulations!

Zhibin and Mohammad's paper "RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism" and Tim, Amir and Yingfeng's paper "ANALYZING MODULAR RNA STRUCTURE REVEALS LOW GLOBAL STRUCTURAL ENTROPY IN MICRORNA SEQUENCES" are both accepted to Life Science Society Computational Systems Bioinformatics Conference (CSB2010) to be held in Stanford Univ in August. This is an annual conference of the society. Congratulations!

April

26

Zhibin receives Doctoral Dissertation Completion Award - Congratulations!

Zhibin is awarded the Doctoral Dissertation Completion Award by the UGA graduate school with a full-year fellowship beginning the fall 2010. Congratulations!

January

20

Amanda, John, Mohammad and Qi joined the group

Mohammad Mohebbi is a Ph.D. student in computer science, with an MS degree in CS from the Sharif University of Iran and teaching experience. With a BS in forestry science from UGA, Amanda Bouffier is currently a IOB graduate student pursing her MS degree. Qi Li is an MS student in computer science, with a BS degree. John Kerry is a CS undergraduate student, with a short term goal to pursue bioinformatics/plant biology graduate program.

October

15

Undergraduate students joined the group

Ben Ngyuen, a Biochemistry undergraduate student, and Sang Ngyuen, a Computer Science undergraduate student, joined our research group to train in and to contribute to the research.

October

12

Abdul Samad joins the group

Abdul Samad, a CS Ph.D student with the Fulbright Fellowship has joined the group. Abdul is interested in graph theory and algorithms for computational biology.

September

5

Juber Patel and Deshen Lin join the group

Juber Patel and Deshen Lin have joined the group. Juber is a new Ph.D student in the Institute of Bioinformatics; he has a MS in computer science. Deshen is a second year MS student in the Department of Computer Science, with 5 years of industry experience.

August

17

RNA Informatics Lab alumna Dr. Chunmei Liu won the NSF CAREER award

RNA-Informatics Group alumna Chunmei Liu won the 2009 NSF CAREER award for her project titled, "CAREER: A Complete System for Protein Identification with Computational Approaches". Chunmei received her Ph.D. in Computer Science at University of Georgia in 2006 and is currently an assistant professor at Howard University, Washington DC. The NSF CAREER award is the most prestigious award to faculty in their early careers. Chunmei completed her doctoral dissertation research under the supervision of Liming and Russell.

Congratulations, Chunmei!

August

14

Mika Takata joined the group

Mika is a new Ph.D student of the Institute of Bioinformatics at UGA. She holds an MEng in Computer Science awarded by Waseda University, Japan (in 2009). Her research interests include ab initio prediction of protein tertiary structures and protein classification.

August

8

Liming and Russell attended Benasque RNA Workshop

Liming and Russell attended the Computational Methods for RNA Analysis Workshop, Benasque, Spain Jul 26 -- Aug 08. The RNA Workshop is dedicated to RNA informatics research, organized every three years in the same place, and by invitation only. Liming gave a talk "Homology Search for Pseudoknots and Beyond". The workshop site Benasque is a small village within the Pyrenee mountain about 5 hour bus ride from Barcelona.

May

25

Anuj and Yingfeng attended RECOMB2009

Anuj presented a poster "Phylogenetic study of Three Bacterial RNA Secondary Structures" in RECOMB 2009 (Tucson, Arizona, May 18-21).

May

8

Congratulations Dong and Yong.

Dong and Yong were awarded with MS. in Computer Science and graduated from UGA on May 8, 2009. Congratulations!

April

14

Sal LaMarca joins the group.

Sal LaMarca joined the group. He is a CS PhD student with experience in machine learning and evolutionary computation.

February/h1>

24

TRFolder released.

TRFolder is a utility program capable of searching for the core structure (including pseudoknots and triple helices) of telomerase RNAs. It consists of a set of functions for telomerase RNA (TR) specific structure prediction. Unlike existing general purpose structure prediction programs, TRFolder works progressively to predict core TR elements pseudoknots, triple helices, telomere repeat template boundary elements, and core-closing stems that occur in TRs.

January/h1>

10

Amir Manzour and Timothy Shaw joining the group.

Amir Manzour and Tim Shaw, graduate students of the Bioinformatics program in the IOB have joined our group. Amir's research experience is in information theory based study of disease association and has just published a paper in that area. Tim has a BS in Computer Science from GaTech and is interested in evolution and RNA folding energy functions.

December

18

Dr. Malmberg elected a Fellow of AAAS. Congratulations!

Dr. Russell Malmberg has been named Fellow of the American Association for the Advancement of Science. Election as a fellow is an honor bestowed upon AAAS members by their peers. Dr. Malmberg has made distinguished contributions to the field of plant biology, and for studies of biochemical genetics, evolution and bioinformatics. Congratulations! See Frankin News.

November

6

Ying Zheng is visiting the group.

Ying Zheng, a computer science Ph.D student at CSU is visiting the RNA-Informatics group. She will do research with us until next November. Her research experience is in parameterized algorithms, complexity theory, and computer networks.

October

31

RNATOPS-W web server is online!

RNATOPS-W based on RNATOPS versions 1.2 has been released with the additional functions of automatic and manual HMM and substructure filter selections.

September

1

Amy Liu and Xingran Xue joined the group.

New Computer Science graduate students Amy Liu and Xingran Xue have joined the RNA-Informatics group.

August

15

RNATOPS v1.1 and v1.2 are available!

RNATOPS (versions 1.1 and 1.2) have been released with the additional function of automatic HMM filter selection. Version 1.1 still needs to manually handl the transition from filtering to whole structure search; while version 1.2 makes the connection fully automatic.

August

2

Congratulations, Dr. Che!

Our former group member, Dongsheng Che received his Ph.D. degree in Computer Science on August 2. He will join East Stroudsburg University as an assistant professor in Computer Science in the Fall.

Click to see full size pictures.

July

27

RNATOPS publicized!

RNATOPS (version 1.0) was initially posted on the web site in June and is now formally publicized with the acceptance of our paper [Huang et al., 2008] to Bioinformatics journal. Version 1.1 will be released soon with the additional function of automatic HMM filter selection.

July

18

Yong's new born baby boy, Congratulations!

Brayden Wu was born at Athens Regional Medical Center at 3:45pm, July 18th, 2008. He was 8 lbs, 4 oz and 20 inches.

Click to enlarge the pictures.