The Shen Lab at Columbia University studies human biology and diseases using genomic and computational approaches. We are interested in two broad questions: identify genetic causes of human diseases, and understand the dynamics of human adaptive immune system. To study these questions, we develop computational and statistical methods and analyze data generated by high-throughput genomic technologies.
Nov 2019, Alex H. successfully defended his PhD thesis. Congratulations Dr. Hsieh!
Nov 2019, Our paper describing genetic analysis of a large pulmonary arterial hypertension study is now published at Genome Medicine. Congratulations to Na who led the analysis and all collaborators at Columbia and CCHMC!
Oct 2019, Alex K got a best poster award at Systems Biology department retreat. Congrats!
Sept 2019, 1st year PhD student Guojie Zhong started a rotation in our group. Welcome Guojie!
August 2019, our paper on SPARK pilot project is now published. Congratulations to Xueya who led the analysis and our collaborators in the SPARK consortium!
June 2019, Yige Zhao formally joined our group as a PhD student. Welcome aboard!
June 2019, Our paper single cell RNA-seq analysis of dendritic cell progenitors is now published. Congratulations to Wenji and our collaborators!
April 2019, Yufeng's promotion to tenured associated professor has been approved.
April 2019, Zicheng Wang (PhD from Tsinghua University) recently joined the lab as a postdoc research scientist, taking on computational immunology. Jake Hagen joined us as a bioinformatician to help our collaboration on medical genetics with Dr. Wendy Chung's group. Welcome Zicheng and Jake!
April 2019, we were recently awarded a new grant from Simons Foundation on genomics analysis for autism risk variants in SPARK . SPARK is a large autism research project aiming for recruitment and analysis of 50,000 individuals with autism.
Dec 2018, our paper on genetics of congential diaphragmatic hernia is accepted by PLOS Genetics, Congratuations to Xueya, Hongjian, and Lan!
Oct 2018, we have multiple open postdoc positions in computational genomics and immunogenomics. If you are interested in joining our team, please send a CV, a statement of interest, and contact information for three references to Yufeng.
Oct 2018, we are looking forward to the ASHG meeting in San Diego. Xueya will give a talk in CDH genetics. Haicang will have a reviewer's choice poster on MVP.
July 2018, we have another paper on pulmonary arterial hypertension genetic published: Zhu et al Genome Medicine, "Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease". Congratulations to Na, Jiayao, and collaborators in Chung lab!
July 2018, Somaye and Xiao joined our group as postdocs jointly mentored by Dr. Wendy Chung. Welcome Somaye and Xiao!
June 2018, our paper on modeling of alloreactive T cell clones is accepted by JCI Insight ("Quantifying size and diversity of the human T cell alloresponse"). Congratulations to our collaborator Susan from Megan Sykes group and lab alum Boris!
May 2018, Our paper on Episcore is published by Nature Communications: Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders. Congratulations, Xinwei, Siying, and friends of the lab Elise, Shuang, and Dana!
April 2018, Lu joined our group as a postdoc jointly mentored by Dr. Wendy Chung. Welcome Lu!
April 2018, Our manuscript on MVP led by Hongjian and Chen is now on bioRxiv: MVP: predicting pathogenicity of missense variants by deep learning
April 2018, Our collaboration with Dr. Wendy Chung group on pulmonary arterial hypertension is published at Circulation: Genomic and Precision Medicine: Exome Sequencing in Children With Pulmonary Arterial Hypertension Demonstrates Differences Compared With Adults The analysis was led by Na. Congratulations!
Feb 2018, Jiayao got an offer from the DBMI PhD program. Congratulations!
Feb. 2018, The SPARK consortium published a preview paper on Neuron: SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research
Oct. 2017, Hongjian presented his work on MVP in ASHG as a Reviewer’s Choice poster.
Sept. 2017, Our collaboration with Dr. Donna Farber group on human resident memory T cells is published at Cell Reports: Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Congratulations, Wenji and Brahma!
June 2017, our R01 on integrating cancer and functional genomics data in genetic studies of developmental disorders is funded by NIGMS for five years!
June 2017, Our collaboration with Dr. Kang Liu group on dendritic cell lineage specification is published at Nature Immunology: Lineage specification of human dendritic cells is marked by IRF8 expression in hematopoietic stem cells and multipotent progenitors. Congratulations, Wenji and Josh!