Lab News (Zhongming Zhao Biography, Keyword Cloud)
*** Multiple positions for postdoctoral fellows and students (GRAs) are available. Please contact to firstname.lastname@example.org.
An interesting AI hackathon on cancer data. It is free plus prize and cash! Try to join (the registration link and flyer).
Our latest publication, entitled "Integration of millions of transcriptomes using batch-aware triplet neural networks," is published in Nature Machine Intelligence! Nature Machine Intelligence is a new high-impact journal in machine learning and artificial intelligence. We developed INSCT, a novel deep learning algorithm to integrate millions of single-cell transcriptomes in a batch-aware manner. (06-21-2021)
Our latest COVID-19 research work, entitled " Association of CXCR6 with COVID-19 severity: Delineating the host genetic factors in transcriptomic regulation," has been published in Human Genetics! In this work, for the first time, we pinpointed the host genetic factor on C-X-C Motif Chemokine Receptor 6 (CXCR6) expression in immune cells is associated with the severity of COVID-19 symptoms. This finding was also reported by a medical media and mentioned by a few other studies, including - https://www.nature.com/articles/s41586-021-03767-x, https://www.biorxiv.org/content/10.1101/2021.01.25.428125v1.full.pdf (06-20-2021)
Dr. Zhao was a speaker in FaceBase Scientific Meeting 2021 (virtual). His talk title: “A developmental stage-specific network approach for studying dynamic co-regulation of transcription factors and microRNAs during craniofacial development”. (06-15-2021)
Dr. Zhao has been awarded nearly $4 million from the Cancer Prevention and Research Institute of Texas (CPRIT) to provide research training in cancer. The grant title: Biomedical Informatics, Genomics, and Translational Cancer Research Training Program (BIG-TCR) [News] (05-19-2021)
Dr. Zhao has received a new R01 grant from NIH/NICDR entitled "Deep learning for decoding genetic regulation and cellular maps in craniofacial development." (04-01-2021)
PhD candidate Astrid Manuel was awarded her NIH/NLM fellowship again! Great job and well done! Congrats Astrid! (04-06-2021)
Welcome Dr. Huihui Fan to join Dr. Zhao's lab and CPH as a Research Assistant Professor! (03-22-2021)
PhD candidate Fangfang Yan received the Doris Ross Scholarship at SBMI. Congrats, Fangfang! (01-26-2021)
Drs. Zhao and Pei’s abstract, “Gene expression imputation in human brain with spatiotemporal precision and cell-type specificity and its implications for 13 brain-associated disorders or traits,” was selected as the oral presentation in 2020 World Congress of Psychiatric Genetics (WCPG 2020) (10-20-2020)
Welcome Dr. Hyun-Hwan Jeong to join Dr. Zhao's lab and CPH as a Research Assistant Professor! (09-01-2020)
Dr. Zhao is a speaker in Biological Psychiatry and Single Cell Omics Networking Symposium, Gulf Coast Consortia for Quantitative Biomedical Sciences, Houston, TX, 08/27/2020
Dr. Zhao has received an R01 grant from NIH/NICDR entitled "Role of cellular metabolism in palate morphogenesis." (multiple PIs Dr. Junich Iwata and Dr. Zhao) (07-01-2020)
Congratulations, Astrid! Astrid has been selected by the UTHealth School of Biomedical Informatics Scholarship Committee to receive a prestigious SBMI Dean’s Excellence Scholarship award. The UTHealth School of Biomedical Informatics (SBMI) Dean’s Excellence Fund is awarded to current SBMI students who have strong informatics skills and are considered potential leaders in the informatics field.(05-14-2020)
Congratulations, Astrid! As a PhD student at SBMI, Astrid was recently named a fellow in the National Library of Medicine (NLM) Training Program in Biomedical Informatics and Data Science. The timeline for her fellowship is July 1, 2020 to June 30, 2021 and her project title is “Innovating Drug Repositioning Strategies for Drug Targets Linked Between Multiple Sclerosis and Blood Cancers.” Professor Zhongming Zhao, PhD and Assistant Professor Assaf Gottlieb, PhD serve as her fellowship mentors. (04-17-2020)
Congratulations, Astrid ! As a graduate student in the first year, Astrid has already had one first author manuscript accepted, and presented in the Schull Institute Symposium as an oral presentation last month. And now, she received the Schull Institute Summer Program scholarship. (04-03-2019).
Welcome Dr. Lukas Simon to join Dr. Zhao’s lab and CPH as a Research Assistant Professor. Lukas received his PhD in Structural and Computational Biology and Molecular Biophysics from Baylor College of Medicine in 2016 and then joined the Institute of Computational Biology, Germany as a postdoc. Lukas is an expert in single cell RNA sequencing (scRNA-seq). He has published three Nature Communications papers in the last four months, including one for scRNA-seq method and other for an atlas of the aging lung. (04-01-2019)
Our article "VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data" is among the top 10% most cited PLOS ONE articles with 12,682 viewed and 40 citations. (06-30-2017)
The supplement of “Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2015: systems biology” has been published in BMC Genomics and BMC Systems Biology. The full content of the supplement can be found at (https://bmcsystbiol.biomedcentral.com/articles/supplements/volume-10-supplement-3). (08-26-2016)
Our SZGR has been moved to the following address: https://bioinfo.uth.edu/SZGR since our lab moved to the University of Texas Health Science Center at Houston. The database has been updated. Users please contact us if you have any questions. (03.15.2016)
Dr. Feixiong Cheng was honored as one of the finalists for the 2014/2015 Vanderbilt Postdoc of the Year Award. Congratulations! (04-23-2015)
Our paper entitled "Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach" appeared in Genome Medicine was Editors' pick(10-17-2014).
Media report: "Bradfords' strong support bolsters melanoma research" appeared in the VUMC reporter (09-25-2014)
Media report: "VU study reveals shared pathways in psychiatric disorders" appeared in the VUMC reporter (09-18-2014)
Our paper entitled "VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data" was recommended by Faculty 1000 (09-12-2014)
Welcome three rotation students: Michaela Fooksa, Hunter Gibbons, and Gregory Salimando! (09-10-2014)
Media report: "Drug discovery clues in network map" appeared in the VUMC reporter (08-01-2014)
Dr. Sabrina Fritah, a visiting postdoc supported by INTER/MOBILITY Progamme, Luxembourg, arrived our lab. Welcome!(07-28-2014).
Santu's paper entitled "Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer" was accepted by RNA. Congratulations, Santu!(05-01-2014).
We welcome two new persons: Dr. Francisco Azuaje as a visiting scientist from Luxembourg, and Christen Parzych as our new Program Coordinator. Welcome!(05-01-2014).
Our paper entitled "Network-assisted prediction of potential drugs for addiction" was among the ~30 papers selected in AMIA TBI Translational Bioinformatics Year-in-Review (04-09-2014).
Media report: "Web tool speeds pulmonary hypertension discovery" by VUMC Reporter (03-05-2014)
Artwork from "An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis" in Molecular BioSystems was selected for the cover of Issue 4 (2014) of Molecular BioSystems. (02-19-2014)
Our recent paper entitled "An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis" in Molecular BioSystems was recommended by Faculty 1000. Congratulations, Min! (01-29-2014)
Vanderbilt School of Medicine moves into top 10 in NIH funding (01-23-2014)
Dr. Wei Jiang joined our lab as a postdoc fellow. Welcome! (01-16-2014)
Dr. Zhao delivered an invited talk in IEEE BIBM 2013 conference. The talk title: "A personalized mutation network approach for detecting putative cancer genes from next-generation sequencing data" (12-20-2013)
Dr. Jia's manuscript, entitled "VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-generation Sequencing Data," was accepted by PLoS Computational Biology. Congratulations! (12-17-2013)
"Molecular circuits in ovarian cancer" - our ovarian cancer regulatory network paper was highlighted by VUMC Reporter. (11-13-2013)
Our comparison of cancer somatic mutation callers has "Editor's Pick" by Genome Medicine and is one of the highly accessed papers since it was published online on October 11th. (10-15-2013)
Our work of pathway-based analysis of dental caries GWAS was highlighted by VUMC Reporter. (09-30-2013)
Dr. Zhao had a seminar talk entitled "Personal Genomics and Personalized Medicine: Current Approaches and Challenges" in Institute of Bioinformatics, University of Georgia (08-23-2013)
Our work published in Genome Research was highlighted as the cover story of the September issue and in VUMC Reporter. (09-13-2013)
Dr. Zhao had a seminar talk entitled "Personal Genomics and Personalized Medicine: Current Approaches and Challenges" in Institute of Bioinformatics, University of Georgia (08-23-2013)
Dr. Zhao received the Award for Outstanding Research, Department of Biomedical Informatics, Vanderbilt University (08-15-2013)
International Conference on Intelligent Biology and Medicine (ICIBM 2013), was successfully held on August 11-13, 2013, Nashville, TN, USA. Thanks for all the participants and volunteers. (08-13-13)
Dr. Zhao will present in upcoming Cold Spring Harbor Asia Conference on Frontiers in Bioinformatics and Computational Biology, The Second International Conference on Translational Biomedical Informatics (ICTBI 2013), etc. (08-09-2013)
The image/artwork was selected for the cover page of the September issue of Genome Research, in which our paper will be published (08-01-2013)
Dr. Zhao was an invited speaker in NGS Translate Boston, NGS Data Congress London, and Warwick University, UK. His talk topic: Application of NGS to Identify Actionable Mutations (06-21-2013)
Dr. Zhao was an invited lecturer in Network Medicine Nanocourse, The Harvard Clinical & Translational Science Center, Harvard University (06-04-2013)
Dr. Zhao was an invited speaker in The Society of Biological Psychiatry's 68th Annual Meeting in San Francisco (05-16-2013)
Mr. Tim O'Brien was awarded NIH Predoc Fellowship from the HGEN Training Program. Congratulations! (05-12-2013)
Two PhD students, Tim O'Brien and Morgan Harrell, joined our lab. Welcome! (05-02-2013)
Dr. Junfeng Xia started his faculty position after 2.5 years of postdoc work in our lab. Congratulations! (04-15-2013)
DBMI Bioinformatics Research Progress Seminar was inaugurated this Tuesday! Thanks for the support from DBMI (04-09-2013)
Dr. Feixing Cheng joined our lab as a postdoc. Welcome! (04-01-2013)
Dr. Carlos Lopez, an assistant professor of systems biology, visited our lab and delivered his talk in cancer systems biology. (03-26-2013)
Drs. Zhongming Zhao, Peilin Jia, Huy Vuoung and Qingguo Wang presented in the workshop "Tools and Applications for Next Gen Sequencing", 2013 UT-ORNL-KBRIN Bioinformatics Summit. Download the workshop program and see conference website here. Also, we had three other poster presentations. (03-25-2013)
Dr. Tony Capra, an assistant professor in CHGR, visited our lab and delivered his talk "Integrating Genome-scale Data to Predict the Effect of Human-specific Noncoding Mutations" (03-20-2013)
"Tools and Applications for Next-Generation Sequencing" workshop by Drs. Zhongming Zhao, Peilin Jia, Huy Vuong, and Qingguo Wang was held in Vanderbilt Medical Center (03-20-2013)
Dr. Jiang Qian, an associate professor of bioinformatics at Johns Hopkins University, visited us and delivered his talk "Global analysis of gene regulation and signaling networks" (03-13-2013)
Dr. Jay Shendure, an associate professor of genome sciences at University of Washington School of Medicine, delivered his talk "Next Generation Human Genetics" at Vanderbilt (03-12-2013)
Dr. Zhao was an invited speaker in the NSF EPSCoR Bioinformatics Workshop (03-05-2013)
Dr. Xingyi Guo joined our lab as a research assistant professor. Welcome! (03-01-2013)
Ms. Krystal Tsosie joined our lab for her rotation project. Welcome! (02-28-2013)
International Conference on Intelligent Biology and Medicine (ICIBM 2013), will be held on August 11-13, 2013, Nashville, TN, USA. Click here for Call for Papers(01-03-13)
Dr. Zhao was an invited speaker in The 23rd International Conference on Genome Informatics (12-14-12)
Dr. Zhao was a plenary speaker in The 1st International Conference on Translational Biomedical Informatics (ICTBI 2012) (12-10-12)
Dr. Zhao was an invited speaker in Department of Biostatistics Seminar Series, Virginia Commonwealth University (11-30-12)
Dr. Zhao was a platform speaker in The 62th Annual Meeting of The American Society of Human Genetics (11-08-12)
Dr. Zhao was an invited speaker in Bradley Department of Electrical & Computer Engineering, Virginia Tech (10-26-12)
Dr. Zhao was an invited speaker in Center for Health Informatics and Bioinformatics, New York University Langone Medical Center (10-25-12)
Dr. Zhao was an invited speaker in School of Informatics and Computing, Indiana University, Bloomington (10-16-12)
Dr. Zhao was an invited speaker in Center for Computational Biology & Bioinformatics, Indiana University School of Medicine (10-15-12)
Dr. Zhao was a keynote speaker in Workshop on Data-Mining of Next Generation Sequencing, IEEE BIBM'12 (10-04-12)
Mr. Timothy O'Brien joined our lab as a NIH Predoctoral Fellow for his rotation project. Welcome! (10-2012)
Mr. Junfeng Jiang from Soochow University joined our lab as a visiting PhD student. Welcome! (09-01-2012)
Dr. Huy Vuong from University of Michigan joined our lab as a NLH/NLM Postdoctoral Fellow. Welcome! (09-01-2012)
Mr. Darwin Fu joined our lab as a NIH Predoctoral Fellow for his rotation project. Welcome! (09-2012)
Dr. Ramkrishna Mitra from Stanford University joined our lab as a Postdoctoral Fellow. Welcome! (08-16-2012)
Dr. Zhao was an invited speaker in Lieber Institute for Brain Development, John Hopkins University (08-14-12)
"Network approach yields glioblastoma clues" -Our work recently published in PLoS Computational Biology was included in VUMC Reporter (08-09-2012).
Dr. Hui Yu from Key Laboratory of Systems Biology, Chinese Academy of Schience joined our lab as a Postdoctoral Fellow. Welcome! (08-01-2012)
Dr. Quan Wang from Beijing University joined our lab as a Postdoctoral Fellow. Welcome! (08-01-2012)
Ms. Morgan Harrell joined our lab as a NIH/NLM Predoctoral Fellow for her rotation project. Welcome! (07-16-2012)
Our recent paper, entitled "BRAF L597 mutations in melanoma are associated with sensitivity to MEK inhibitors", was chosen for cover page in the September issue in Cancer Discovery. (7-15-12), It was also cited, as "Uncommon BRAF Mutation In Melanoma Sensitive To MEK Inhibitor Drug Therapy" by MNT (Medical News Today) , MedicalXpress, EurekAlert AAAS Cancer Research News, VUMC Reporter, F1000 recommendation, among others.
Our recent whole genome sequencing based paper, entitled "BRAF L597 mutations in melanoma are associated with sensitivity to MEK inhibitors", was published in Cancer Discovery. Journal cover page, PubMed (7-13-12)
Dr. Zhao and three postdocs attended The 1000 Genomes Project conference. (7-13-12)
Dr. Zhao was recently interviewed by GenomeWeb and was featured in Genome Technology magazine's cover story on Genomics In the Clinic. (7-2-12)
Our manuscript entitled "Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives" was accepted by Briefings in Bioinformatics. Congrats, Qingguo. (6-29-12)
The Topical Issue on Systems Biology that Dr. Zhao and colleagues edited was published in Chem & Biodiversity. Click here for details. (6-14-2012)
Dr. Zhao was an invited speaker in the Society of Biological Psychiatry Symposium "Integration of Genomics, Epigenomics and Genetics for a Biological Understanding of Psychiatric Diseases", 67th Annual Scientific Convention & Program, Philadelphia, PA, USA (5-5-2012)
Dr. Bing Wang accepted a full professor faculty position in China. Congrats! (04-30-12)
The International Conference on Intelligent Biology and Medicine (2012) was successfully held on April 22-24, 2012 at Vanderbilt. Here is the link.
Our NGS Catalog database article was accepted by Human Mutation. Congratulations Junfeng for leading this effort! (03-09-2012)
Our recent work published in J Med Genetics (PubMed link here) was quickly featured on popular MedLinx site (12-27-2011)
Our rotation student Mr. Daniel Putman won the Second Prize in the Best Student Paper Award Competition, based on his rotation work in our lab, in the AMIA 2011 Annual Symposium, October 22-26, 2011. Congratulations! (10-23-2011)
Dr. Zhao was an invited speaker in University of Tennessee Health Science Center (11-03-2011)
Dr. Zhao was an invited speaker in University of Nebraska Medical Center (10-19-2011)
Dr. Zhao was a Plenary Speaker in The Informatics Day 2011, University of Missouri, Columbia, MO, October 17, 2011
Dr. Zhao was an invited speaker in the XIXth World Congress on Psychiatric Genetics (WCPG). (9-12-2011).
The paper based on the work by our former rotation student Mr. Dan Putman was selected as one of the finalists in the Student Best Paper competition in AMIA. Dr. Cindy Gadd, the director of DBMI training program, added "Your first research rotation project becomes an AMIA student paper finalist -- that's QUITE a first! Congratulations!"(9-8-2011).
Ms. Alex Fish joined our lab as an Vanderbilt IGP rotation student. Welcome! (9-7-2011)
Considering that our major research shifts to systems and translational medicine, we renamed our laboratory to Bioinformatics and Systems Medicine Laboratory (BSML). (9-2-2011).
Dr. Zhao was an invited speaker in the Department of Biomedical Informatics, Ohio State University. (8-30-2011).
Dr. Zhao was an invited speaker in the Cincinnati Children's Hospital Medical Center. (8-26-2011).
Dr. Bing Wang from University of Louisville joined our lab as a Postdoc Fellow. Welcome! (8-1-2011)
Dr. Zhao was an invited speaker in the International Workshop on Cancer Systems Biology (ICSB 2011). (7-3-2011).
The manuscript prepared by our rotation student Mr. Dan Putman was accepted by AMIA. Congratulations! (6-20-2011).
Dr. Zhao was a speaker in the Fourth Summit on Systems Biology, Richmond, VA (6-17-2011).
Mr. Paul Hart joined our lab as an NIH/NLM Summer Intern Fellow. Welcome! (6-15-2011)
Dr. Jingchun Sun was promoted to be a Research Instructor in DBMI. Congratulations! A celebration party will be held on June 23rd (5-16-2011)
Dr. Qingguo Wang from University of Missouri joined our lab as a Postdoc Fellow. Welcome! (5-16-2011)
Dr. Peilin Jia is one of the finalists for the 2010/2011 Vanderbilt Postdoc of the Year Award. Congratulations! (4-26-2011)
Dr. Siyuan Zheng had his oral presentation of his network analysis of HCC data in the 10th Annual UT-ORNL-KBRIN Bioinformatics Summit (4/2/2011)
Dr. Zhao was an invited speaker in the Greehey Children's Cancer Research Institute, The University of Texas at San Antonio (3-7-2011).
Dr. Zhao was an invited speaker in the Biostatistics Branch at the National Institute of Environmental Health Sciences (2-15-2011).
Our 2010 summer intern Mr. Jian Tian was a co-author of a recent paper appeared in IJCBDD. Congratulations! (1-20-2011).
Dr. Peilin Jia, postdoctoral fellow, in our lab was the recipient of the 2011 NARSAD Young Investigator Award Congratulations! (12-30-2010).
Dr. Jingchun Sun, postdoctoral fellow, in our lab was the recipient of the 2011 NARSAD Young Investigator Award Congratulations! (12-30-2010).
"Many needles in genetic haystack" -Our work recently published in Bioinformatics was included in VUMC Reporter (12-16-2010).
Our collaborative work recently published in Cancer Cell was documented in VUMC Reporter (12-10-2010).
Dr. Zhao joined Editorial Board of journal PLoS ONE (12-03-2010)
Our recent paper appeared in Bioinformatics was selected and evaluated by the Faculty of 1000 (F1000) who placed our work in their library of the top 2% of published articles in biology and medicine. See link here. (11-26-2010)
Congratulations to Ketaki, Bioinformatics intern at BRC for getting a job in Bioinformatics core at University of Illinois, Chicago. Her farewell was held on Wednesday (11-16-2010).
Professor John Quackenbush from Harvard University visited VICC and presented his work entitled "Network and state space models: Science and science fiction approaches to cell fate predictions" (11-12-2010).
Dr. Zhao was an invited speaker by the Wilmer Eye Institute and the Visual Neuroscience Training Program (VNTP) at the Johns Hopkins University School of Medicine (11-02-2010).
Dr. Zhao was chosen to receive the Nick Norgan Award 2010, as lead author of the best paper published in Annals of Human Biology during 2009 (10-14-2010).
Dr. Zhao was an invited speaker at the Department of Computer Science, Georgia State University (10-22-2010).
Cancer 2.0 - Harnessing computing power for cancer research and care (06-17-2010)
Schizophrenia data: one-stop-shopping (06-25-2010)
• Positions available now:
Bioinformatics Engineer I in BSBL (closed)
Postdoctoral Fellows in Bioinformatics in BSBL
• We welcome graduate and undergraduate students to join our lab.
Our new BRC (Bioinformatics Resource Center) office suite was renovated and is fully functional now. (7/19/2010)
We welcome four new members (Chunling Wan - Postdoc Fellow; Jian Tian - NIH/NLM Summer Intern Fellow; Satishkumar Ganakammal - Bioinformatics Engineer I; and Ketaki Bhide - Bioinformatics Engineer Intern). A welcome lunch meeting will be held on June 11, 2010 in the BRC room (6/8/2010)
Dr. Jingchun Sun was nominated the Vanderbilt Postdoc of the Year. Congratulations! (4/20/2010)
Two members (Peilin Jia and Zhongming Zhao) presented their work in the UT-ORNL-KBRIN Bioinformatics Summit (3/20/2010)
Our collaborator's Stand Up to Cancer (SU2C) grant was funded to support the next generation of cancer researchers VUMC Reporter (12/18/2009)
"Getting gene priorities in order". Our work appeared in Bioinformatics (Sun et al. 2009) was highlighted in the VUMC Reporter -Aliquots (11/20/09)
"If mice could speak". Our collaborator's work was highlighted by Nature reporter Erika Check Hayden on October 22, 2009, appeared in Nature Blog
Ms. Dedeepya Vaka joined the Bioinformatics Group in VMSR. Welcome! (11/1/09)
Dr. Anyuan Guo accepted a Full Professor position in Huazhong University of Science and Technology. Congratulations! (10/1/09)
Dr. Siyuan Zheng from Shanghai Institutes for Biological Sciences, Chinese Academy of Science joined our lab as a postdoc fellow. Welcome! (9/25/09)
Dr. Hung-Chung (Joe) Huang from Department of Systems Biology and Translational Medicine, Texas A&M Health Science Center joined the Bioinformatics Group in VMSR as a senior bioinformatician. Welcome! (10/1/09)
• The following databases are available now:
- Ethanol Related Gene Resource: ERGR
- Schizophrenia Gene Resource: SZGR
- Recent publications:
Sun J, Wan C, Jia P, Fanous AH, Kendler KS, Riley BP, Zhao Z (2010) Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample PubMedSun J, Jia P, Fanous AH, Webb BT, van den Oord EJCG, Chen X, Bukszar J, Kendler KS, Zhao Z (2009) A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases – Schizophrenia as a case. Bioinformatics 25:2595-2602 PubMed