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News in Bioinformatics and Machine Learning Laboratory (BML)

----2021----

9/2021. Max Highsmith defended his PhD dissertation. Congratulations, Dr. Highsmith.

6/2021. A new PhD student Frimpong Boadu joined our lab as graduate research assistant. Welcome!

4/30/2021. Dr. Cheng is featured in the College's Meet A Engineer series (news).

3/15/2021. Dr. Cheng received the Senior Faculty Research Award in the College of Engineering (news).

1/2021. Three new PhD students: Ashwin Dhakal, Nabin Giri, and Sajid Mahmud joined our lab. Welcome!

----2020----

12/2020. Our protein structure prediction method - MULTICOM - was ranked among top 10 methods (i.e. No. 3 in inter-domain protein structure predction and No. 7 in regular tertiary structure prediction) out of more than 130 predictors along with Google DeepMind's AlphaFold in the world-wide 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14). It also performed best in selecting best protein structural models in terms of GDT-TS score. (the CASP14 inter-domain protein prediction results, the CASP14 tertiary structure prediction results) [see MU's news]

11/2020. Meshal Alfarhood sucessfully defended his PhD disseration, Congratulations!

10/2020. Dr. Cheng started to co-edit a special research topics on deep learning methods for protein bioinformatics for Frontiers in Bioinformatics Journal ( Call for Papers).

9/10/2020. Dr. Cheng, as co-PI, received a Department of Energy (DOE) grant to apply high-performance computing to enhance deep learning methods for protein bioinformatics.

9/1/2020. Dr. Cheng, as PI, received an NIH R01 grant to study distance-based ab initio protein structure prediction. (see the story).

9/2020. Two new PhD students - Alex Morehead and Elham Soltanikazemi - joined the BML lab.

----2019----

11/2019. Dr. Cheng, as PI, received a grant of developing deep learning methods to study protein complex structures from the machine learning and artificial intelligence (AI) program of Department of Energy.

11/2019. Adil Al-Azzawi successfully defended his PhD dissertation.

9/2019. Dr. Cheng is a co-PI of an interdisciplinary research team (PI - Dr. James Umen at Danforth Plant Science Center) that received a grant from the genomics science program of Department of Energy.

7/2019. Jie Hou defended his PhD dissertation successfully.

5/2019. Yechan Hong defended his Master's thesis successfully.

5/2019. Tosin defended his PhD dissertation successfully.

3/2019. We collaborated with material scientists to pioneer the application of deep learning (the currently most powerful AI technology) to predicting the property of graphene. (news)

3/2019. Tosin accepted a tenure-track assistant professor position in the Department of Comptuer Science at University of Colorado, Colorado Springs. Congratulations!

3/2019. Jie accepted a tenure-track assistant professor position in the Department of Computer Science at Saint Louis University. Congratulations!

3/2019. Julia Wopata was admitted into the 2019 Mizzou '39 class as one of the 39 outstanding seniors at Mizzou.

2/2019. Jie won 2019 Outstanding PhD Student Award in Computer Science in the College of Engineering, University of Missouri. Congratulations!

1/2019. Dr. Cheng was named one of top 100 AI leaders in drug discovery and advanced healthcare in the world (news at LinkedIn).

----2018----

12/2/2018. Our MULTICOM protein structure predictors were ranked among the best in the 13th world-wide CASP competitions along with AlphaFold from Google’s DeepMind. MULTICOM was ranked 3rd in protein tertiary modeling, while DeepMind took no. 1 position. MULTICOM was ranked no.1 in ranking protein strucstural models. Read the news.

9/2018. Two new PhD students - Max Highsmith and Carlos Martinez Villar joined the BML lab. Welcome!

8/31/2018. Dr. Cheng gave a talk on deep learning for mapping protein sequences to folds at 2018 ACM-BCB conferences in Washington DC.

8/2018. Two new PhD students (Zhiye Guo and Farhan Quadir) joined our lab. Welcome!

7/23/2018. Dr. Cheng was named William and Nancy Thompson Missouri Distinguished Professor of Engineering (news).

7/2018. Dr. Cheng gavie a highlight talk on deep learning for protein contact prediction in 3DSig of ISMB 2018 conference, Chicago.

5/2018. Dr. Cheng received an NSF collaborative grant to develop deep learning methods for evaluating protein structural models (news).

3/2018. Dr. Cheng received an NSF grant to develop deep learning methods for protein bioinformatics.

2/2018. Dr. Cheng served on the program committee of ICIBM conference.

1/2018. Dr. Cheng served on the program committee of 2018 ISMB conference.

----2017----

12/2018. Dr. Cheng gave a talk about deep learning on protein structure prediction at Wuhan University, China.

12/2018. Dr. Cheng gave a talk about deep learning on protein structure prediction at Fudan University, China.

11/28/2017. Tuan Trieu successfuly defended his dissertation. Congratulations!

10/2017. Dr. Cheng gave a hightlight talk on 3D Genome Modeling in School of Medicine at Indiana University.

9/2017. Dr. Cheng gave a highlight talk on 3D Genome Modeling in ACM-BCB Conference in Boston.

8/11/2017. Badri Adhikari earned his PhD degree in computer science and went on to become an assistant professor in the Computer Science Department at University of Missouri - St. Louis. Congratulations!

5/4/2017. Tianshu Wei defended his Master's project successfully and earned his Master's degree in computer science. Congratulations!

4/2017. Dr. Cheng starts to serve as Associate Editor of IEEE/ACM Transaction on Computational Biology and Bioinformatics.

2/9/2017. Our deep learning research on protein structure prediction is mentioned in a main newspaper - the Economist (see the story).

1/2017. Dr. Cheng started to serve as workshop co-chair of ACM-BCB 2017 conference.

1/2017. Dr. Cheng started to serve as co-chair of 3DSig area of ISMB 2017 conference.

----2016---

12/9/2016 - 12/12/2016. Prof. Cheng talked about protein contact prediction and SAXS-data driven protein structure modeling in the round-table discussions of the CASP12 meeting, Gaeta, Italy.

12/6/2016. Pei Hu defended his Master's project sucessfuly and earned his Master's degree in computer science.

9/1/2016. Dr. Cheng was promoted to the rank of full professor.

8/2016. Two new PhD students: Siva and Soliman joined our lab. Welcome!

7/2016. Dr. Birchler (PI) and Dr. Cheng (Co-PI) received a five-year NSF plant genome grant to study the genome balance in maize using both experimental and bioinformatics methods.

7/20/2016. Renzhi Cao successfully defended his PhD dissertation and earned PhD degree in computer science. Congratulations! Renzhi will move on to be visiting assistant professor at Pacific Lutheran University, WA.

7/19/2016. Debswapna Bhattacharya successfully defended his PhD dissertation and earned PhD degree in computer science. Congratulations! Deb will move on to be an assistant professor at Wichita State University, KS.

7/10/2016. Prof. Cheng chaired a session for protein structure and function at 2016 ISMB conference held in Orlando, FL.

6/13/2016. Yunhao Tang successfully defended his Master's thesis and earned MS degree. Congratulations!

5/26/2016. Dr. Cheng co-organized a session for 18th International Conference on Bioinformatics and Biochemical Engineering in Tokyo, Japan. He also gave a talk about deep learning methods for predicting the protein stability change induced by amino acid mutations. His talk won the best presentation award.

5/2016. A high school intern in our lab - Hannah Chen's research on 3D genome structure modeling is reported in the news of Columbia Tribune. Hannha will attend MIT in the fall, 2016.

5/12/2016. Jilong Li successfully defended his PhD dissertation and earned his PhD degree in computer science.

5/2016. Tyler Banks successfully defended his Mater's project and earned Master's degree in computer science.

5/2016. Yuxiang Zhang successfully defended his Master's thesis and earned Master's degree in computer science.

3/5/2016. Renzhi won the first place in the student oral presentation competition during 2016 MCBIOS conference, and Haiou won the third place. Congratulations!

3/4/2016. Prof. Cheng chairs the Session of Protein Structure, Function, and Biological Networks for 2016 MCBIOS Conference, Memphis, TN.

1/1/2016. Prof. Cheng started to serve as co-chair of Protein Structure and Function Session of 2016 international conference on Intelligent Systems for Molecular Biology (ISMB).

----2015----

12/2015. Jilong Li accepted a senior bioinformatitian position at Omicsoft Corporation, North Carolina. Congratulations!

12/23/2015. Rui Xie defended his Master's thesis successfully and earned his Master's degree in computer science. Congratulations!

12/2015. Hannah Chen, a 2015 high school intern in our lab, was admitted by both MIT and Caltech. Congratulations!

12/11/2015. Alice Yang, a 2015 high school intern in our lab, was admitted by Stanford University. Congratulatioins!

12/10/2015, Xiao Zhou defended his Master's project sucessfuly and earned his Master's degree in computer science. Congratulations!

12/8/2015. Debswapna Bhattacharya accepted a tenure-track assistant professor position in the Computer Science Department at Wichita State University. Congratulations!

12/2015. Dr. Cheng gave a talk on de novo protein conformation sampling with Input-Output Hidden Markov Model (IOHMM) at the 3rd Protein Structure Prediction Conference.

11/2015. Kommidi Sai Ram defended his Master's project succesfully and earned his Master's degree. Congratulations!

11/3/2015. Rajani defended her Master's project succesfully and earned her Master's degree. Congratulations!

10/2015. Hannah Chen, a high school intern in our group, won a semi-finalist award of 2015 Siemens Scientific Competition. Her award-wining project is based on our 3D genome research funded by the NSF.

10/8/2015. Prof. Cheng gave a talk about deep learning for big data anaysis and protein structure modeling in the Physics Department at Missouri State University.

9/2015. Jilong Li and Jie Hou presented two posters about our protein structure prediction tool - MULTICOM and our RNA-Seq data analsyis tool - RNAMiner at 2015 ACM-BCB conference held in Atlanta, Georgia.

8/2015. Prof. Cheng gave a talk about computational modeling of 3D human genome at the Jackson Laboratory, CT, USA.

7/31/2015. Our lab received an NIH R01 grant to develop computational methods to predict protein structure in collaboration with Dr. Jack Tanner's group in the Department of Chemistry at MU.

7/2015. Prof. Cheng give a talk about our MULTICOM protein structure prediction method in 2015 International Conference on Intelligent Systems for Molecular Biology (ISMB), Dublin, Ireland.

7/2015. Prof. Cheng gave a talk about "CONFOLD: Residue-Residue Contact-guided ab initio Protein Folding" at 3DSig meeting associated with 2015 ISMB Conference, Dublin, Ireland.

5/2015. Prof. Cheng gave a talk about "CONFOLD: Residue-Residue Contact-guided ab initio Protein Folding" at the Great Lake Bioinformatics Conference (GLBIO) at Purdue University.

5/2015. Lingfei Xu, Xiaokai Qian, Vijender Koorella defended their MS projects successfullly and earned MS degree in computer science. Congratulations!

4/28/2015. Zhaolong Zhong defended his MS project successfully. Congratulations!

4/24/2015. Our RNA-Seq data analysis pipeline RNAMiner was discussed in RNA-Seq Blog.

4/20/2015. Our protein structure prediction paper was accepted by the prestigious 23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology (ISMB/ECCB) to be held in Dublin, Ireland, 2015. Congratulations, Renzhi, Deb, Badri, Jilong!

3/13/2015. Badri Adhari and Jie Hou each gave a talk about protein structure prediction in 2015 MCBIOS Conference. Badri won the first prize of student oral presentation. Congratulations!

3/13/2015. Prof. Cheng gave a talk about modeling 3D structure of human genome in 2015 MidSouth Bioinformatics Conference (MCBIOS), Little Rock, Arkansas.

3/10/2015. Jackson Nowotny presented his research to Missouri legislators in the state capitol Jefferson City. (a related news)

3/10/2015. Jilong Li passed his PhD comprehensive exam. He is one step away from earning his PhD degree.

2/19/2015. Our 3DRefine paper about protein struture refinement was ranked one of the most cited papers of 2013 in Proteins journal.

----2014----

12/9/2014. Prof. Cheng gave a talk entitled "MULTICOM - Large-Scale Sampling and Mining of Template Based Protein Models" at the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11), Cancun, Mexico. Renzhi Cao also demonstrated two posters about protein structure modeling and quality assessment during the meeting. Our protein structure prediction method MULTICOM was ranked among the best methods according to the official CASP11 assessment, 2014.

12/9/2014. The MU protein interaction and docking method led by Prof. Xiaoqin Zou with whom we collaborated was ranked as one of the best methods in 2014 Critical Assessment of Techniques for Protein Interaction (CAPRI) according to the CAPRI assessment.

11/20/2014. Jackson Nowotny was selected to present his genome research to Missouri state legislators at the state capital in March 2015.

11/18/2014. Deb Bhattacharya passed his MS thesis defense and earned the MS degree in CS.

10/13/2014. Badri Adhikari passed his qualifying exam for PhD degree in computer science with an emphasis on protein structure modeling.

9/29/2014. Tuan Trieu passed his qualifying exam for PhD degree in computer science with an emphasis on 3D genome structure modeling.

9/20/2014 - 9/23/2014. Prof. Cheng gave three talks at 2014 ACM-BCB Conference held in Newport Beach, California on three topics including (1) Deep Learning and its Application for Protein Structure Prediction (in the deep learning workshop), (2) Reconstruction of Gene Regulatory Networks from RNA-Seq Data (a highlight talk in the main conference), and (3) A Conformation Ensemble Approach to Protein Structure Prediction (in the CSBW workshop). Prof. Cheng also chaired a session on computational genomics and biological networks during the conference.

8/20/2014. Dr. Cheng's group (Badri, Deb, Renzhi, Jilong, Cheng) completed the CASP11 protein structure prediction experiment, which lasted for three and a half months.

8/14/2014. Prof. Cheng gave a talk about Deep Learning and its Application to Protein Structure Prediction at Tokyo Institute of Technology - Purdue Summer School, Purdue University, USA. Deb and Renzhi also gave poster presentations at the summer school.

7/24/2014. Zhiluo Gao defended his Master's project and earned the MS degree in computer science.

7/15/2014. Dr. Cheng gave a highlight talk about Modeling 3D Human Genome Structure at ISMB conference, Boston, 2014.

7/2014. Kishore Banala defended his Master's report successfully and earned his Master's degree.

5/17/2014. Prof. Cheng gave a highlight talk about reconstruction of 3D human genome structure in the Great Lake Bioinformatics Conference, Cincinnati, OH.

5/17/2014. Jilong Li presented his work about automatic reconstruction of metabolic networks using Bayesian probabilistic sampling and knowledge-based methods in the Great Lake Bioinformatics Conference, Cincinnati, OH.

5/2014. Sharif Ahmed defended his MS thesis successfully.

5/1/2014. Prof. Cheng's group started to participate in the 11th Critical Assessment of Techniques for Protein Structure Prediction (CASP11). The blind experiment will last for about three months.

3/7/2014. Dr. Taeho Jo gave a talk about a Random Forest Apporach to Protein Fold Recognition during the 12th MCBIOS conference.

3/7/2014. Prof. Cheng was elected to the Board of Directors of MCBIOS during the 12th MCBIOS conference.

2/2014. Deb won the Mizzou Honor graduate assistant award of the College of Engineering on behalf of the Computer Science Department.

2/2014. Prof. Cheng was appointed to the editorial board of the Scientific Report journal published by Nature Publishing Group.

2/2014. The graduate school's news about our alumni Dr. Zheng Wang.

2/11/2014. The department's news about our two alumni Drs. Jesse Eickholt and Zheng Wang.

1/6/2014. Prof. Cheng starts to serve as publicity chair of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB).

----2013----

12/4/2013. Prof. Cheng gave a talk about Contact-Based Ab Initio Protein Structure Prediction at Zing's conference on Protein and RNA Structures, Cancun, Mexico.

11/22/2013. Andrew Wilson successfully defended his Master's project and earned his MS degree. Congratulations, Andrew.

11/1/2013. Xin accepted a Research Scientist position at the Orlando's branch of the Reed Elsevier corporation - a Fortune 500 company in the world. She will use her expertise in machine learning and data mining to analyze the big health insurance data. Congratulations, Xin.

10/26/2013. Tuan, Badri and Renzhi won the first prize in the Computer Science Annual Programming Contest as a team. Pei, Xiaokai, and Rui Wu won the third prize.

9/24/2013. Dr. Cheng gave a highlight talk about 3D Conformation of Human Genome at 2013 ACM-BCB conference.

9/23/2013. Deb gave a talk entitled "Protein Structure Refinement by Iterative Fragment Exchange" at 2013 ACM-BCB conference. He also demonstrated a poster about our i3DRefine protein model refinement tool in the same conference. Deb also won a ACM-BCB travel award.

9/11/2013. Howard Luo succesfully defended his Master's project. Congratulations.

8/19/2013. Prof. Cheng started to develop a new graduate course "Computational Optimization Methods" as a part of his NSF CAREER project. More than 20 students are taking the class.

7/20/2013. Prof. Cheng gave a talk entilted "Associations between Gene Function and Spatial Gene-Gene Interaction in 3D Genome" at the Automated Function Annotation of Protein (AFP) satelite meeting of 2013 ISMB in Berlin, Germany.

7/14/2013. Prof. Cheng co-organized a one-day protein structure bioinformatics workshop at the 2013 AAAI conference in Seattle, USA.

6/21/2013. Our 2012 PhD graduate Zheng Wang accepted a tenure-track assistant professor position in the Computer Science Department at the University of Southern Mississipi. Congratulations, Zheng!

6/5/2013. Prof. Cheng's group had a BBQ party to honor two PhD graduates Jesse Eickholt and Xin Deng, say farewell to two group members Qi Qi and Zheng Wang, and celebrate the group's achievement in the past year.

5/31/2013. Jilong Li passed the PhD qualifying exam.

5/17/2013. Renzhi Cao passed the PhD qualifying exam.

5/17/2013. Xin Deng defended her dissertation successfully. Congratulations, Dr. Deng!

5/14-16/2013. Jilong Li, Qi Qi, Chenfeng He gave three poster presentations about RNA-Seq data analysis, genome structure visualization, and reconstruction of metabolic networks at 2013 Great Lake Bioinformatics Conference (GLBIO), Pittsburgh, PA.

5/15/2013. Prof. Cheng gave a highlight talk entitled "predicting protein residue-residue contacts using deep learning networks and boosting" at 2013 Great Lake Bioinformatics Conference (GLBIO), Pittsburgh, PA.

5/10/2013. Deb Bhattacharya passed the PhD qualifying exam.

5/7/2013. Prof. Cheng gave a talk about 2D and 3D genome structure at the 4th Biennial Joint Symposium between Gyeongsang National University (Korea) and University of Missouri, held in Columbia, MO, USA.

5/3/2013. Prof. Cheng gave a talk about protein structure prediction at University of Missouri, Kansas City.

4/26/2013. Jesse Eickholt successfully defended his PhD dissertation. Jesse is the second PhD who graduated from our group. He will leave for a tenure-track assistant professor position at the Central Michigan University in July. Congratulations, Dr. Eickholt.

4/9/2013. Prof. Cheng was appointed an editorial board member of the Journal, Current Synthetic & Systems Biology.

4/6/2013. Dr. Zheng Wang (a 2012 PhD graduate)'s talk about our human genome conformation project won the first place in the postdoctoral presentation category in 2013 Mid-South Computational Biology and Bioinformatics conference, Columbia, Missouri.

4/5/2013 and 4/6/2013. Seven group members (Badri, Renzhi, Deb, Jesse, Jilong, Qi, Tuan) gave oral presentations in 2013 Mid-South Computational Biology and Bioinformatics conference, Columbia, Missouri. Three group members (Xin, Chenfeng, Sharif) gave poster presentations in the same conference.

4/3/2013 and 4/4/2013. Prof. Jianlin Cheng gave two talks about 3D genome structure modeling and 3D protein structure modeling at Purdue University.

4/2013. Two chromosome research papers in collaboration with Prof. Jim Birchler were published in the Proceedings of National Academy of Science (PNAS), USA.

3/2013. PhD Student Jesse Eickholt accepted an offer of a tenure-track assistant professor position in the Computer Science Department at Central Michigan University. He will start his new position in July, 2013.

3/2013. Graduate students (Tuan, Chenfeng, Sharif) and undergraduate student (Avery) demonstrated our genome 3D modeling project and software to K12 students during the E-Week Exhibit of College of Engineering, University of Missouri, Columbia. They gave presentations, showed videos, and demonstrated the software.

3/2013 - 4/2013. As a program committee member, Prof. Cheng helped organize the Mid-South Bioinformatics conference. Several students (e.g., Xin, Chenfeng) in Cheng's group volunteered to help.

2/2013. Prof. Cheng was selected as one of Chancellor's top achievers, University of Missouri, Columbia.

2/2013. Dr. Taeho Jo joined our group as postdoctoral scientist.

1/2013. Matt Spencer joined our group as PhD student in bioinformatics.

1/2013. Four Students (Badri, Deb, Xin, Renzhi) and Dr. Zheng Wang (a 2012 PhD graduate) gave poster presentations in the Pacific Symposium on Biocomputing, the Big Island, Hawaii, 2013.

1/2013. Dr. Mingzhu Zhu took a postdoctoral position at Dartmouth College.

---- 2012 ----

12/2012. Our MULTICOM protein structure preditors were ranked high in protein teritary structure prediction, protein model quality assessment, protein model refinement, and protein residue-residue contact prediction during the 10th Critical Assessment of Techniques for Protein Structure Prediction (CASP10), Gaeta, Italy.

12/2012. A multi-group collaboration paper including our group's protein function predictioin method MULTICOM-PDCN ranked among top methods in the Critical Assessment of Protein Function Annotation (CAFA) was accepted by Nature Methods.

11/2012. Prof. Cheng started to serve as the publicity chair of the 2013 ACM-BCB conference.

11/2012. Prof. Cheng started to co-organize the Artificial Intelligence and Robotics Methods in Computational Biology Workshop of the 20th AAAI conference.

11/2012. Prof. Cheng gave a talk about reconstruction of biological networks and genome structure at Wayne State University.

11/2012. This news blog of Prof. Cheng's group started.