Lab News

Keep up to date with Wang Genomics lab

The 2019 International Conference on Intelligent Biology and Medicine (ICIBM 2019) will be held on June 9-11, 2019 in Columbus, Ohio, USA. Kai will co-chair the steering committee. You are invited to submit papers and abstracts with unpublished original work describing recent advances on all aspects of bioinformatics, Systems Biology and intelligent Computing. The easychair conference link is being set up and will be available soon.

 

The  Mid-Atlantic Bioinformatics Conference (MABC) 2018, organized by Laura Almasy, Kai Wang, Deanne Taylor, Kai Tan and several colleagues at DBHi, is held at the Colket Translational Research Building.

The MABC 2018 is presented by the Department of Biomedical and Health Informatics (DBHi) at the Children's Hospital of Philadelphia and Penn's Institute for Biomedical Informatics (IBI).  A distinguished line-up of internationally recognized speakers will discuss the challenges in genetic analysis of complex diseases, and present how novel bioinformatics and genomics approaches can help address these challenge.

The book "Copy Number Variants", edited by Dr. Derek M. Bickhart as part of the Methods in Molecular Biology book series, is published today. Li and Kai wrote the first chapter titled "Identification of Copy Number Variants from SNP Arrays Using PennCNV", which can be downloaded at https://www.springer.com/us/book/9781493986651. The entire book is available at Amazon at https://www.amazon.com/Copy-Number-Variants-Protocols-Molecular/dp/1493986651/.

 

Our collaborative article with Chuanle Xiao and other colleagues titled "N6-Methyladenine DNA Modification in the Human Genome" is published online at Molecular Cell today. It can be accessed at https://www.cell.com/molecular-cell/fulltext/S1097-2765(18)30460-X. We showed evidence that DNA 6mA and N 6-demethyladenine modification in the human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively, and that decrease of genomic DNA 6mA promotes human tumorigenesis. See GenomeWeb Sequencing News here.

Our collaborative article with Dr. Chunhua Weng's group and other Columbia and Mayo Clinic colleagues, titled "Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes", is published online at American Journal of Human Genetics. It can be accessed at https://www.cell.com/ajhg/fulltext/S0002-9297(18)30171-X. In the paper, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. See press release from Columbia here, from CHOP here, and GenomeWeb Informatics News here.

The Wang Genomics Lab is moved to the Center for Cellcular and Molecular Therapeutics at the Children's Hospital of Philadelphia, and Dr Kai Wang is appointed as an Associate Professor of Pathology at the University of Pennsylvania, after a short stint at Columbia University. We are actively recruiting undergraduate research students, graduate students and postdocs in the lab. If you want to have fun playing with cutting edge development of genomics and bioinformatics methods, please feel free to contact Kai.

Our InterVar paper ("InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines") was selected as one of the ten Best Papers published in AJHG in 2016-2017, unveiled at the American Soceity of Human Genetics meeting. What a pleasant surprise when I open the special issue and saw the InterVar paper as the first paper right in the special issue! See details on the special collection at https://www.cell.com/bestof.

Yunfei Guo became the first student to get a PhD in Biostatistics from the lab, and it is also Kai's first time attending a hooding ceremony. It is been a great pleasure working with a group of young and brilliant graduate students such as Yunfei, Coco and Hui at USC (it is a pity that Kai did not attend the other hooding ceremonies after he moved to the east coast). Best of luck to this group of USC trainees at Roche, Goldman Sachs and Amazon!

We had a lab celebration for Kai's recent tenure approval and the promotion to Associate Professor, at one of our favorate restuarants Beijing Tasty House. Great thanks to all lab members for your hard work to make this happen.

 

Our lab won best costome design in ZNI Halloween party again!

Radiation by the UV light resulted in a base pair change in a personal genome, causing coding change to a gene that may impact health conditions. Baymax came up and used CRISPR to fix the base pair change, so that the personal genome is healthy again.

Special thanks to Coco for the design and implementation!

 

Kai is the 1st place winner of the first ever ZNI Art Contest! His creative design skillfully and artistically represented the collaborative and innovative work being done here at ZNI! T-shirts with the winning design will be given out during the holiday party.

 

We had a lab summer party with lab members and guests at Dr. Wang's home. We had food, drinks and enjoyed charade games.

"Science" turns out to be the hardest category, yet "Game" is one of the easiest categories to guess.

KEEP CALM IT'S TEATIME!

The Wang Lab will host this week's tea time, at the 2nd floor bridge between ZNI and BCC. You are welcome to join and enjoy watermelons!

We had a lab party at Kai's home in Agoura Hills, filled with yummy food and lively conversations.

 

Our lab members and two guests from Jeannie's lab won the best costume/performance award in the ZNI Halloween Party! In fact, many consider this as the best performance ever that they saw in ZNI Halloween party. Thanks Lingling for designing and directing the show titled "Gangnam style DNA sequencing".

ZNI tea time is hosted by Wang lab today!

Come enjoy snack, ice cream, watermelon, and most importantly, live discussion with Wang lab members!

The Wang lab presented in the ZNI dinner night on June 14. Four members each described their current project in progress and the preliminary results of their projects:

  • Xiao Chang: wANNOVAR: annotating genetic variants for personal genomes via the web
  • Lingling Shi: Modeling NLGN4X deletions in neurodevelopment
  • Fan Gao: Landscape of DNA Methylation in Meningiomas
  • Yunfei Guo: Automated annotation pipeline for Mendelian disorder

Thanks to all who participated in the dinner night!

 

Dr. Wang hosted the 2nd Annual ZNI New Technology Symposium together with Dr. Robert Chow. The symposium was created to promote awareness of the new technologies being applied by biomedical researchers across USC!

In the symposium, four speakers from USC presented their research on developing new technologies. Dr. Wang gave a lecture titled "interpreting personal genomes", describing our recent work on developing sequence annotation pipelines and web servers.

After the symposium, we had a wine and cheese session, filled with lively discussions.

 

Dr. Wang hosted the inaugural ZNI New Technology Symposium together with Dr. Robert Chow. The symposium was created to promote awareness of the new technologies being applied by biomedical researchers across USC!

In the symposium, four speakers from USC presented their research on developing new technologies and applying them on biological problems. These include:

  • Dr. Benjamin Berman discussed the use of bisulfite sequencing for cancer epigenomics 
  • Marcelo Coba discussed systems biology approaches for the study of signaling networks
  • Don B. Arnold discussed tools for visualizing endogenous proteins in vivo
  • Robert Chow discussed super-resolution optical microscopy of transmembrane molecules and molecular complexes

After the symposium, we had a wine and cheese session, filled with lively discussions.

We started the Wang Genomics Lab officially on 9/1/2010, at the Zilkha Neurogenetic Institute of the University of Southern California. We share the lab (ZNI 221) with a great colleague Bill Mack and subsequently had a few collaborative projects.