News

• [Oct 2025] The first Artificial Intelligence for Omics Research in Aging and Cancer (AI4OmicsAC) was a great success! Sincere thanks to all the speakers, attendees, and sponsors!
• [Oct 2025] Sergio Zamora-Erazo, PhD., will give a talk, ‘Quantitative modeling of DNA methylome using Global Peak Positioning System reveals peaks inversely correlate with patient survival’ at the NDC meeting.
• [Sept 2025] My lab members, Sergio Zamora-Erazo, PhD. & Sudheshna Bodapati, MS., will give a talk, ‘RNA-seq workflow for Immunotherapy Analysis,’ at Fox Chase Trainee Seminar Series (FTSS).
• [Aug 2025] We’re pleased to announce that our study, ‘Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans,’ in Nat Comm.
• [July 2025] Congratulations to Vahid on the acceptance of “MST-AI: Skin Color Estimation in Skin Cancer Datasets” in the Journal of Imaging!
• [June 2025] We are pleased to announce that Dr. Hayan Lee has been awarded a Director’s Discretionary allocation from Argonne National Laboratory, part of the U.S. Department of Energy (DOE), in support of the MELANOMA-ICB project—an initiative aimed at advancing research in melanoma immune checkpoint blockade.
• [May 2025] Sudheshna will present a poster titled, ‘Tumore Epimutation Burden as a Pan-Cancer Prognostic Marker: Integrating DNA Methylation and Survival Outcomes,‘ at the 89th Symposium on Senescence and Aging, Cold Spring Harbor Laboratory, 2025.
• [Apr 2025] Gabriela’s study on ‘Body mass index impacts blood-based markers signatures in advanced colorectal cancer’ has been selected for presentation at AACR 2025!
• [Mar 2025] We are pleased to announce that our manuscript, ‘Genome Assembly of Arctica islandica, the Longest-Lived Non-Colonial Animal Species,’ has been accepted for publication in MDPI Animals!
• [Feb 2025] We’re excited to welcome Sergio Zamora-Erazo to our lab!
• [Jan 2025]  I’m excited to give a talk, titled “Reliable, robust, and interpretable AI-based epigenetic aging clock models and service” at the Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University!
• [Dec 2024] It is my great honor to serve on the program committee of RECOMB 2025 (29th Annual International Conference on Research in Computational Molecular Biology)
• [Nov 2024] I’ll present the featured plenary session from 5:20-5:40 PM on Nov 7th at #ASGH24. My talk is titled “Methylome and Epigenome Dynamics during Polyps and Pre-colorectal Neogenesis.”
• [Nov 2024] We are pleased to announce that our manuscript, ‘Multiomics analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis’ has been accepted for publication in Nature Cancer!
• [Oct 2024] We are pleased to announce that our manuscript, ‘Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis’ has been accepted for publication in Nature Cancer!
• [Sept 2024] We’re excited to welcome Sudheshna Bodapati to our lab!
• [Mar 2024] Molly’s abstract was selected for the C. David Allis CEI Travel Award at the Fourth Annual Cancer Epigenetics Symposium!
• [Jan 2023] ‘Statistical analysis of methylation reveals epigenetic biomarkers for high-functioning autism spectrum disorder’ has been accepted in the Journal of Student Research!
• [Oct 2023] We are pleased to announce that our manuscript, ‘Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement,’ has been accepted for publication in Cell!
• [Jan 2023] ‘TET1 and TDG suppress the inflammatory response in intestinal tumorigenesis: implications for colorectal tumors with the CpG Island Methylator Phenotype‘ has been accepted in Gastroenterology!
• [Dec, 2022] Deep Neural Network Classifier for Alzheimer’s Disease has been published in the Journal of Student Research (http://dx.doi.org/10.47611/jsrhs.v11i3.3553).
• [Nov 9 – 12, 2022] I had a talk, “Epigenetic biomarkers for early CRC diagnosis from integrative multi-omics data analysis of Familial adenomatous polyposis (FAP) patients” at the Personalized Medicine and Biomarker session, Biological Data Science meeting, CSHL.
• [Sep 1, 2022] Officially announced is my joining the FCCC at the website and Twitter!
• [Aug 26, 2022] I’m happy to give a Science talk at the HTAN steering committee meeting. Thank Ultima Genomics for your support!
• [Aug 12, 2022] I start my own lab at Fox Chase Cancer Center! My lab focus on computational epigenetics in cancer and aging! (Northeast Times)
• I am looking forward to the 2022 HTAN Summer Meeting! OHSU Knight Cancer Research Building, Portland, OR. (June 27 – 28th, 2022)
• The AACR poster session was amazing! “Ultra-Low Input High-Fidelity (ULI-HiFi) long-reads uncover variants in genomic dark matter from pre-cancer polyp and tumor samples”, AACR annual meeting, New Orleans, LA, April 8-13, 2022.
• US Patent Application was filed! “Methylated DNA markers and assays for use in detecting colorectal cancer”. Thank you for being co-inventors at Stanford and Cedars-Sinai! (US Patent Application No: 63/315,895, filing Date: March 2, 2022)
• I had a poster “Ultra-Low Input High-Fidelity (ULI-HiFi) long-reads uncover variants in genomic dark matter from pre-cancer polyp and tumor samples”, HTAN Virtual Fall 2021 F2F Meeting. (Nov 18-19, 2021)
• My paper “Predictive Signatures for Lung Adenocarcinoma Prognostic Trajectory by Multi-omics Data Integration and Ensemble Learning” has been accepted for oral presentation at International Symposium On Mathematical And Computational Oncology (ISMCO’21) and won Best Paper Award! PDF is here! (Oct 11-13, 2021)
• Emmett, my intern from Amgen Scholars Program, Stanford Summer Research Program (SSRP) won “Best Presenter” award. (Aug 12, 2021)
• I’m attending HTAN VIRTUAL SPRING 2021 F2F Meeting. There are some posters very interesting. (May 13-14, 2021)
• I’m virtually attending the Biology of Genomes meeting. Please come and visit my poster#202 if you would like to know about methylation alteration in cancer. Methylation rules! (May 11-14, 2021)
• I am pleased to announce that I have been selected as a research mentor for an SSRP (Stanford Summer Research Program)-Amgen scholar. I can’t wait to meet Emmett! (May 12, 2021)
• “Candidate variants in TUB are associated with familial tremor” is published in PLoS Genetics. (Sept/21/2020)
• I was honored to serve as a planning committee for the 2020 HTAN Junior Investigators annual meeting (Aug 31, 2020)
• “Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma” is published in Nature Communications (Jul. 22, 2020)
• “Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding” is published in Giga Science. (July/10/2020)
• “Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world’s leading biomass crop” is published in Giga Science (Nov. 29, 2019)
• My poster has been selected for presentation at NCI HTAN (Human Tumor Atlas Network) CMCM (CANCER MOONSHOT COLLABORATIVE MEETING ) (Nov 18-20, 2019)
• “The human body at cellular resolution: the NIH Human Biomolecular Atlas Program” is published in Nature (Oct. 10, 2019)
• I am attending CMCM HTAN F2F meeting, Bethesda, Maryland. I will have highlight poster talk and poster(#32). (Nov 18-20, 2019)
• I attended HTAN Junior Investigator Meeting, Bethesda, Maryland. (Aug 26-27, 2019)
• I attended HTAN F2F meeting, Broad Institute, Cambridge, MA (June 25-26, 2019)
• I attended CEGS Meeting, Chicago, Il and had a poster presented. (Nov. 19-20, 2018)
• “Lifelong physical activity is associated with promoter hypomethylation of genes involved in metabolism, myogenesis, contractile properties and oxidative stress resistance in aged human skeletal muscle” is published in Scientific Reports. (03/01/2019)
• “Piercing the dark matter: bioinformatics of long-range sequencing and mapping” is published in Nature Reviews Genetics. (03/26/2018)
• I had a talk titled “MethylMarker: The Predictive DNA Methylation Marker Selection Algorithm for Liquid Biopsy”, Algorithmic Challenges in Genomics Reunion @ Simons Institute for the theory of computing, University of California, Berkeley. (Jun 27–30, 2017)
• I joined Snyder Lab @ Stanford University. (09/01/2016)
• I gave a talk about “DeepBind Method Details“, Deep Learning for Computational Biology. (04/08/2016)
• I gave a talk about “Spectral clustering“, Bioinformatics group meeting, JGI (03/29/2016)
• I gave a talk of “Long read sequencing technologies and its applications“, Genomics Program Biotechnology Companies Day. (03/15/2016)
• I am organizing “Genomics Program Biotechnology Companies Day“, Calvin Lab Auditorium, University of California, Berkeley. March 18th (9am-5pm). Here is the announcement at Lawrence Berkeley National Laboratory as well. (03/15/2016)
• “The pineapple genome and the evolution of CAM photosynthesis” is published online in Nature Genetics. (11/2/2015)
• “The resurgence of reference quality genomes” poster for the Genome Informatics meeting, CSHL is here. (10/31/2015)
• “The resurgence of reference quality genomes” slides for my talk at Probabilistic Modeling in Genomics meeting is here. (10/15/2015)
• “The resurgence of reference quality genomes” has been selected for a platform presentation for the Probabilistic Modeling in Genomics meeting. (09/17/2015)
• “The pineapple genome reveals the evolution of CAM photosynthesis” paper is accepted for publication by NG. (09/15/2015)
• MGM (Microbial Genomics & Metagenomics) workshop will be held on September 14 – 18, 2015 (09/03/2015)
• I started a new position at DOE Joint Genome Institute, Lawrence Berkeley National Laboratory as a postdoctoral fellow, funded by Simons Postdoctoral Fellowship (08/24/2015)
• I finished my defense successfully. Slides are here with annotations. (08/11/2015)
• Quality genome paper is submitted. (07/01/2015)
• My defense is scheduled on mid-August. (06/29/2015)
• Pineapple paper is submitted. (06/28/2015)
• I gave a talk in Graduate Student Symposium, CSHL. (05/18/2015)
• I successfully presented my thesis proposal “Long Read Sequencing Technology, Altorithms and applications”. (05/04/2015)
• My presentation slide about “MLE and its recent application in computational biology” is posted. (03/17/2015)
• I will give a presentation about “Sugarcane Genome De Novo Assemblly Challenges” at the Sugar Cane Sequencing Initiativeworkshop, PAG XXIII. (12/24/2014)
• ReadSim1.6 is released with improved speed and a new feature, dnasim, which simulates heterozygous polyploidy genome. (11/21/2014)
• My talk “Sugarcane genome de novo assembly challenges” is selected as a platform presentaion for data mining session, Biological Data Science Meeting, CSHL (11/05/2014-11/08/2014) All of the presentations and talks are listed I’ll serve as a program comittee member forCancer Panomics in Pacific Symposium on Biocomputing (PSB) 2015
• My internship in Microsoft Research, Redmond, WA started. (June – Aug, 2014)
• I’ll serve as a program comittee member for Cancer Panomics in Pacific Symposium on Biocomputing (PSB) 2014