Karchin Lab News

Date Description

OpenCRAVAT invited workshop at American Society for Human Genetics 2020 meeting, San Diego Convention Center, San Diego CA.


OpenCRAVAT web server now available!


Talk by Rachel at JHMI Cancer Chemical and Structural Biology meeting Evaluating Drivers with HotMAPS.


Webinar by Kym about OpenCRAVAT National Cancer Institute Data Science Seminar Series .


Talk by Rachel about tools for computational immuno-oncology at the UCSD Genetics, Bioinformatics and Systems Biology Symposium. San Diego.


Talk by Kym about OpenCRAVAT at the Walter J. Burdette Trainee Symposium on Human Genomics, Yale University, New Haven CT.


Talk by Rachel about tumor evolution at the Yale Center for Biomedical Data Science seminar series. New Haven.


Postdoc Kym Pagel presents the OpenCRAVAT framework at the American Society for Human Genetics annual meeting poster session in Houston.


Talk by Rachel about variant interpretation and 3D protein structure at Columbia University Department of Systems Biology Distinguished Speaker series. New York City.


Ph.D student Ashok Sivakumar and Postdoc Kym Pagel present at AGBT Precision Health meeting in San Diego.


Ph.D student Ashok Sivakumar defends his disssertation on tools for computational immuno-oncology, Malone Hall 107 2:30pm. Johns Hopkins Homewood campus.


Postdoc Kym Pagel presents a webinar for the National Cancer Institute on the OpenCRAVAT variant interpretation framework.


Rachel co-chairs RECOMB Cancer Computational Biology 2019 with Max Leiserson . Submit a paper to RECOMB CCB 2019 here


Hear Rachel talk about CHASMplus at the Integrative Omics meeting in Santa Fe, New Mexico


Single-cell mutation profiles support extensive early driver heterogeneity in human pancreatic neoplasms. Read about our joint work with the lab of pathologist at Hopkins Medicine.


CRAVAT/MuPIT tutorial workshop at American Society of Human Genetics annual meeting 2018. San Diego Convention Center Room 31, Upper Level. Friday 10/19/2018 at 7:15-8:45AM.


Dr. Karchin officially promoted to Full Professor of Biomedical Engineering, Oncology and Computer Science.


OpenCRAVAT beta released! Modular, open tools for Custom Ranked Analysis of VAriants Toolkit.


Gordon Research Conference on Human Genetic Variation and Disease, chaired by Dr. Karchin and Dr. Rita Casadio of Bologna, Italy.


Postdoc Violeta Beleva Guthrie's paper on network analysis of the functional impact of multiple adaptive mutations is published in the journal Molecular Biology and Evolution.

05/02/18 Poster session for Foundations of Computational Biology and Bioinformatics class. Clark 110 Homewood Campus, Johns Hopkins University 6-8pm.

Ph.D. student Collin Tokheim wins Martin and Carol Macht award for Young Investigator day at Hopkins Medicine.


Ph.D. student Collin Tokheim's paper on Driver Mutations in Cancer (co-first author with Matt Bailey and Eduard Porta-Pardo) is publisned in Cell.

10/20/17 CRAVAT/MuPIT tutorial workshop at American Society of Human Genetics annual meeting 2017 in Orlando, FL 7:15am Orange Ballroom FG - Lower Level/Hilton Orlando Hotel
9/11/17 CRAVAT/MuPIT web tools upgraded to version 5.0 with GRCh38 support.
08/15/17 Welcome to new lab members Lily Zheng (Ph.D. student Human Genetics) and Melody Xiaoshin Shao (Ph.D. student Biomedical Engineering)
06/02/17 Dr. Karchin presents keynote talk at New York University Department of Biology annual Genome Symposium.
05/15/17 Chris Douville and Noushin Niknafs receive doctoral degrees in Biomedical Engineering. Congratulations Chris and Noushin!
05/05/17 Foundations of Computational Biology II course poster session
02/10/17 Dr. Karchin and Dr. Masica give presentations about tools developed in our lab at the Gene Variation 3D meeting at the Institute for Systems Biology in Seattle, WA.
01/17/17 NAPA software from Postdoc Dr. Violeta Beleva Guthrie released. Python package to analyze the impact of multiple mutations in a protein evolving under selection. Designed to interpret mutations in pathogen proteins.
12/28/16 Ph.D students Noushin Niknafs, Rohit Bhattacharya and Postdoc Violeta Beleva-Guthrie do computational modeling of non-small cell lung cancer resistance to immunotherapy in Evolution of the Neoantigen Landscape During Immune Checkpoint Blockade in Non-Small Cell Lung Cancer published in Cancer Discovery.
12/16/16 Read about Ph.D student Collin Tokheim's latest paper in Science Daily.
11/13/16 Dr. Karchin presents Evaluating the Evaluation of Cancer Driver Genes at Canceromatics III Tumor Heterogeneity in Madrid, Spain.
11/07/16 New MuPIT v4.3.1 protein structure variant viewer released. Redesigned interface and fast 3D graphics.
09/27/16 Collin Tokheim presents Mutational hotspots in cancer: a protein structure-driver relationship to the JHU Lecture Series in Computational Biophysics.
08/18/16 PLoS Computational Biology launches Focus Feature on Genome Landscapes and Phenotype Prediction of Disease by Dr. Karchin and Dr. Ruth Nussinov.
08/11/16 David Masica presents webinar for Journal of American Medical Informatics Journal Club about "A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts", Masica et al. JAMIA 2016. https://knowledge.amia.org/
08/5/16 CRAVAT 4.3 released. Enhanced interactive results pages. New annotations. Dockerized CRAVAT/MuPIT available for local installation!
07/04/16 "Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants", Masica et al. PLoS Computational Biology, 2016 recommended by Faculty of 1000.
06/01/16 Karchin Lab receives ITCR U24 grant from the NCI for Cancer-Related Analysis of VAriants Toolkit.
04/07/16 Ph.D student Chris Douville presents poster "Within Sample Detection of Large Chromosomal Changes" at NHGRI's Research Training and Career Development Annual Meeting in Bethesda, Maryland.
04/04/16 Dr. Karchin presents keynote at ISCB NGS 2016 Genome Annotation meeting, Barcelona, Spain.
03/12/16 Ph.D student Noushin Niknafs presents SCHISM poster at Cancer as an Evolving and Systemic Disease meeting at Memorial Sloan Kettering Cancer Center, NYC.
02/14/16 New Docker image version of SCHISM released. The latest version features new mutation clustering methods.
12/18/15 A probabilistic model to predict clinical phenotypic traits from genome sequencing by Chen et al. named one of the best Translational Bioinformatics papers of the past year by the AMIA.
12/15/15 Inter-discplinary pancreatic cyst classification project featured in Hopkins In Health Article
12/10/15 Ph.D student Ashok Sivakumar presents a talk at the 13th Annual Rocky Mountain Bioinformatics Conference
10/18/15 Asst. Prof. David Masica receives prize for top oral presentation in session on Diagnosis and Treatment of Pancreatic Tumors at United European Gastroenterology meeting in Barcelona, Spain
10/08/15 Ph.D students Noushin Niknafs and Chris Douville present platform talks on their research at the American Society of Human Genetics annual meeting in Baltimore.
10/06/15 Dr. Karchin gives keynote talk at the Human Genome Variation Society annual meeting in Baltimore.
10/01/15 Ph.D student Collin Tokheim awarded a Ruth L. Kirschstein National Research Service Award (NRSA) F31 from the NCI.
09/09/15 Ph.D student Rohit Bhattacharya awarded the Jay D Samstag Engineering Fellowship.
08/30/15 SubClonial Hierarchy Inference from Somatic Mutations (SCHISM) automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing (Niknafs et al.) is in press at PLoS Computational Biology.
05/18/15 New version of mutation analysis pipeline CRAVAT released May 2015. Includes VEST pathogenicity scores for all non-silent mutation consequence types, improved report layouts, faster processing times.
05/15/15 Special issue of the Human Genetics journal on Computational Molecular Medicine, edited by Dr. Karchin and Dr. Melissa Cline published by Springer.
12/22/14 New release of Mutation Position Imaging Toolbox (MuPIT) interactive features visualization of clustered Cancer Genome Atlas somatic mutations in 21 tumor types and completely redesigned interface.
12/15/14 Dr. Karchin will teach Foundations of Computational Biology and Bioinformatics II, BME 580.688 during Spring semester 2015.
12/08/14 Paper by David Masica published Dec 8, 2014 in Human Molecular Genetics from Karchin Lab project with Cystic Fibrosis patient individualized care (inCF) initiative. Featured here in Johns Hopkins Engineering magazine.
11/15/14 Visualization of Ebola mutations. Mutation Position Imaging Toolbox for Ebola virus proteins released, in collaboration with the UCSC Ebola Portal
09/30/14 Congratulations to lab member Dr. Yun-Ching Chen, who received his Ph.D. in Biomedical Engineering! Dr. Chen is now a Postdoctoral Fellow at the NIH National Human Genome Research Institute.
08/03/14 Dr. Karchin presented a talk on new algorithms to predict phenotypes from genomic information at Gordon Research Conference on Human Single Nucleotide Polymorphisms & Disease at Stonehill College in Easton, MA.  Details
07/30/14 Ph.D. student Yun-Ching Chen defended his dissertation Methods for genome interpretation: causal gene discovery and personal phenotype prediction. July 30, 2014 at 1pm. Clark 210 JHU Homewood Campus.
07/13/14 Dr. Karchin co-chaired a Special Session on Post-genomic medical decision making in cancer at the 2014 Intelligent Systems for Molecular Biology (ISMB) meeting in Boston.  ISMB Sessions   Session Program
05/30/14 Dr. Masica is presented a study of computational tools to determine the prognostic significance of TP53 mutation in head and neck squamous cell carcinoma (HNSCC) at the 2014 American Society of Clinical Oncology (ASCO) meeting in Chicago.  Details
04/12/14 Dr. Karchin taught Foundations of Computational Biology and Bioinformatics II, BME 580.688, CS 600.688 during Spring semester 2014
03/01/14 CRAVAT and MuPIT web tools are now part of National Cancer Institutes Informatics Tools for Cancer Research Initiative and are supported by NIH NCI U01-CA180956-01
10/01/13 Lab alumn Hannah Carter (Ph.D. 2012) receives NIH Director's Early Independence Award.
09/19/13 Dr. Karchin named The William R. Brody Faculty Scholar in Whiting School of Engineering.
07/01/13 Dr. Masica promoted to Assistant Research Professor in the Department of Biomedical Engineering.
07/01/13 Dr. Karchin promoted to Associate Professor with tenure in the Department of Biomedical Engineering.
02/15/13 Dr. Karchin has received a National Science Foundation Advances in Biological Informatics Innovation Grant to study the impact of multiple mutations on protein adaptation.
02/24/12 Hannah Carter successfully defended her Ph.D. dissertation. Congratulations Dr. Carter!
08/11/11 Hannah Carter was awarded a Class of 2012 Siebel scholarship, in recognition of her academic excellence and leadership in the field of bioengineering. Congratulations Hannah!
04/13/11 Jean Fan was awarded a 2011 Provost's Undergraduate Research Award for her project "Improving computational models of the biological consequences of mutation through limiting the phylogenetic distances of orthologous sequences". Congratulations Jean!
03/03/11 Jodi Chapman (Art as Applied to Medicine graduate student at JHMI) was awarded the 2011 Alan W. Cole Scholarship, the top scholarship prize from the Vesalius Trust, for her work collaborating with the Karchin Lab on an educational computer video game to introduce high school students to protein evolution, genetics and cancer biology. Congratulations Jodi!
02/10/10 Karchin Lab receives a MOLLY award at the 2010 Critical Assessment of Genome Interpretation (pre-pro-CAGI) meeting.
11/04/09 BME/ICM research intern Debattama Sen named as Semifinalist in the Intel Science 2009 Talent Search. Congratulations, Deb!
09/01/08 BME/ICM Ph.D. student Hannah Carter awarded three-year NDSEG fellowship to study impact of mutant phosphoinositidyl kinase signaling in cancer. Congratulations, Hannah!