LinkedIn +1 (312)883-5623 Wen-Ching Calvin Chan, Ph.D.

Lead Bioinformatics Scientist
COMPUTATIONAL BIOLOGIST • BIOINFORMATICS
Natera, CA

An enthusiastic and highly motivated research scientist with 10+ years of experience of focusing on Bioinformatics. Strong research professional with extensive skills of integrating multi '-omics' datasets using statistical, data mining, and machine learning techniques. An inspiring, productive employee possesses a keen ability for implementing and learning new emerging Bioinformatics technologies.

Education
National Yang Ming University & Academia Sinica TIGP
Taipei, Taiwan
PH.D. IN BIOINFORMATICS
July. 2006 - June. 2011
  • Dissertation: Systematic Identification of MicroRNA Genes and Clusters
  • Machine Learning • Data Mining • Bioinformatics • Genomics • MicroRNA Genes/Clusters
National Cheng Kung University
Tainan, Taiwan
M.S. IN COMPUTER SCIENCE AND INFORMATION ENGINEERING
July. 2001 - June. 2003
  • Thesis: Effective Location Mining and Prediction Mechanisms in Mobile Systems
  • Data Mining • Communicatoin Networking
National Chengchi University
Taipei, Taiwan
B.S. IN COMPUTER SCIENCE
July. 1997 - June. 2001
  • Project: A Recommendation System for an Online Auction Using Data Mining Approaches
  • Data Mining • Recommendation System
Experience
Lead Bioinformatics Scientist
San Carlos, CA
Biofx Team (Oncology & Organ Health), Natera
November 2019 - Present
  • Responsibilities:
    • Lead the development of an early detection panel using circulating tumor methylated DNA (ctmDNA).
    • Contribute to pipeline optimization, performance improvement, and code reviews for applications developed in the support of Oncology (solid cancers, liquid biopsy) products
    • Oversee the development of bioinformatics algorithms and pipelines for applications supporting Organ Health products using whole transcriptome (mRNAs) and small non-coding RNA (sncRNAs) sequencing data.
    • Before 2021
      • Develop and leverage computational methods to demultiplex (bcl2fastq), align (BWA MEM), detect (GATK4/Mutect2, VarScan2, Strelka2), manipulate (SAMtools, Picard), and annotate (VEP, snpEff) from whole exome/genome sequencing data and other complex multi-omics data (GDC/TCGA, dbSNP, COSMIC, 1000 Genomes).
      • Contribute to the development of automation bioinformatics pipelines (Docker, Conda) running in distribution/cloud systems (HPC, DNAnexus) for data analysis, integration, and management.
      • Collaborate closely with the Natera team of scientists and statisticians for diagnostic tests (Oncology and Organ Health), including variant detection, primer/experimental designs, and quality control (MSI, CNV, Homologous Recombination Deficiency/HRD, sample concordance).
      • Support to analyze experimental data and derive actionable biological conclusions and publications.
  • Achievements:
    • Ococks, E., A. Ng, G. Devonshire, S. Dashner, Wen-Ching Chan, S. Sharma, H.-T. Wu, et al. “1491P Bespoke Circulating Tumor DNA Assay for the Detection of Minimal Residual Disease in Esophageal Adenocarcinoma Patients.” Annals of Oncology 31 (September 1, 2020): S926. https://www.natera.com/wp-content/uploads/2021/04/ESMO-2020-Ococks-Esophageal-Poster-Aug-27-2020-Final.pdf.
  • Collaboration Achievements:
    • Li, Sung-Chou, Ho-Chang Kuo, Lien-Hung Huang, Wen-Jiun Chou, Sheng-Yu Lee, Wen-Ching Chan, and Liang-Jen Wang. “DNA Methylation in LIME1 and SPTBN2 Genes Is Associated with Attention Deficit in Children.” Children 8, no. 2 (February 2021): 92. https://doi.org/10.3390/children8020092.
Bioinformatics II
Chicago, IL
Center for Research Informatics, University of Chicago
November. 2015 - October, 2019
  • Responsibilities:
    • Develop and leverage computational methods to align (BWA, STAR), detect (DESeq2, limma, MACS2, DSS2), annotate (VEP, snpEff), and discover biological functions (Gene Ontology, KEGG) from NGS data and other complex multi-omics data (GDC/TCGA, dbSNP, COSMIC, 1000 Genomes).
    • Conduct variant-calling analyses (GATK4/Mutect2, VarScan2) and manipulations (SAMtools, Picard) using whole exome/genome sequencing data in human, mouse, and bacteria.
    • Contribute to the development of bioinformatics pipelines (Nextflow, Conda) running in distribution systems (HPC) for data analysis, integration, and management.
    • Support to analyze sequencing data and derive actionable biological conclusions and publications.
    • Collaborate closely with other scientists and research associates.
    • Assist collaborators with data access (GEO/SRA/dbGaP), analysis, and interpretation.
    • Interpret and present the results of the computational and statistical analyses to scientific team and management.
  • Achievements:
    • Guo, Y., A. A. Chomiak, Y. Hong, C. C. Lowe, Wen-Ching Chan, J. Andrade, H. Pan, et al. “Histone H2A Ubiquitination Resulting from Brap Loss of Function Connects Multiple Aging Hallmarks and Accelerates Neurodegeneration.” BioRxiv, January 9, 2021, 2020.10.22.341784. https://doi.org/10.1101/2020.10.22.341784.
    • Poropatich, Kate, Donye Dominguez, Wen-Ching Chan, Jorge Andrade, Yuanyuan Zha, Brian Wray, Jason Miska, et al. “OX40+ Plasmacytoid Dendritic Cells in the Tumor Microenvironment Promote Antitumor Immunity.” The Journal of Clinical Investigation 130, no. 7 (July 1, 2020): 3528–42. https://doi.org/10.1172/JCI131992.
    • Khalyfa, Abdelnaby, David Gozal, Wen-Ching Chan, Jorge Andrade, and Bharati Prasad. “Circulating Plasma Exosomes in Obstructive Sleep Apnoea and Reverse Dipping Blood Pressure.” European Respiratory Journal 55, no. 1 (January 1, 2020). https://doi.org/10.1183/13993003.01072-2019.
    • Domowicz, Miriam S., Wen-Ching Chan, Patricia Claudio-Vázquez, Judith G. Henry, Christopher B. Ware, Jorge Andrade, Glyn Dawson, and Nancy B. Schwartz. 2019. “Global Brain Transcriptome Analysis of a Tpp1 Neuronal Ceroid Lipofuscinoses Mouse Model.” ASN Neuro 11 (January): 1759091419843393. https://doi.org/10.1177/1759091419843393.
    • Baeten, Jeremy T., Michael R. Waarts, Margaret M. Pruitt, Wen-Ching Chan, Jorge Andrade, and Jill L. O. de Jong. 2019. “The Side Population Enriches for Leukemia Propagating Cell Activity and Wnt Pathway Expression in Zebrafish Acute Lymphoblastic Leukemia.” Haematologica, January, haematol.2018.206417. https://doi.org/10.3324/haematol.2018.206417.
    • Kline, Douglas E., Brendan W. MacNabb, Xiufen Chen, Wen-Ching Chan, Dominick Fosco, and Justin Kline. 2018. “CD8α+ Dendritic Cells Dictate Leukemia-Specific CD8+ T Cell Fates.” The Journal of Immunology, November, ji1801184. https://doi.org/10.4049/jimmunol.1801184.
    • Bhanvadia, Raj R., Calvin VanOpstall, Hannah Brechka, Nimrod S. Barashi, Marc Gillard, Erin M. McAuley, Juan Manuel Vasquez, Gladell Paner, Wen-Ching Chan, et al. 2018. “MEIS1 and MEIS2 Expression and Prostate Cancer Progression: A Role for HOXB13 Binding Partners in Metastatic Disease.” Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, May. https://doi.org/10.1158/1078-0432.CCR-17-3673.
    • Wang, Liang-Jen, Wen-Ching Chan, Miao-Chun Chou, Wen-Jiun Chou, Min-Jing Lee, Sheng-Yu Lee, Pao-Yen Lin, Yi-Hsin Yang, and Cheng-Fang Yen. 2017. “Polymorphisms of STS Gene and SULT2A1 Gene and Neurosteroid Levels in Han Chinese Boys with Attention-Deficit/Hyperactivity Disorder: An Exploratory Investigation.” Scientific Reports 7: 45595. https://doi.org/10.1038/srep45595.
    • Kach, Jacob, Tiha M. Long, Phillip Selman, Eva Y. Tonsing-Carter, Maria A. Bacalao, Ricardo R. Lastra, Larischa de Wet, Shane Comiskey, Marc Gillard, Calvin VanOpstall, Diana C. West, Wen-Ching Chan, et al. 2017. “Selective Glucocorticoid Receptor Modulators (SGRMs) Delay Castrate-Resistant Prostate Cancer Growth.” Molecular Cancer Therapeutics 16 (8): 1680–92. https://doi.org/10.1158/1535-7163.MCT-16-0923.
Senior Postdoctoral Fellow
Kaohsiung, Taiwan
Kaohsiung Chang Gung Memorial Hospital
January. 2015 - September. 2015
  • Responsibilities:
    • Developed a diagnostic model based on miRNA genes as biomarkers using a machine-learning (SVMs) approach in Kawasaki disease.
    • Conducted a genome-wide analysis study (GWAS; PLINK) using Affymetrix Genome-Wide Human SNP array data to detect susceptibility genes associated with Coronary Artery Aneurysm.
    • Revealed negatively associated interplay between DNA methylation and gene expression using Illumina HumanMethylation array data in Kawasaki disease.
  • Achievements:
    • Li, Sung-Chou, Wen-Ching Chan, Ying-Hsien Huang, Mindy Ming-Huey Guo, Hong-Ren Yu, Fu-Chen Huang, Hsing-Chun Kuo, and Ho-Chang Kuo. 2016. “Major Methylation Alterations on the CpG Markers of Inflammatory Immune Associated Genes After IVIG Treatment in Kawasaki Disease.” BMC Medical Genomics 9 (Suppl 1). https://doi.org/10.1186/s12920-016-0197-2.
    • Kuo, Ho-Chang, Sung-Chou Li, Mindy Ming-Huey Guo, Ying-Hsien Huang, Hong-Ren Yu, Fu-Chen Huang, Fuyong Jiao, Hsing-Chun Kuo, Jorge Andrade, and Wen-Ching Chan. 2016. “Genome-Wide Association Study Identifies Novel Susceptibility Genes Associated with Coronary Artery Aneurysm Formation in Kawasaki Disease.” PLOS ONE 11 (5): e0154943. https://doi.org/10.1371/journal.pone.0154943.
    • Kuo, Ho-Chang, Kai-Sheng Hsieh, Mindy Ming-Huey Guo, Ken-Pen Weng, Luo-Ping Ger, Wen-Ching Chan†, and Sung-Chou Li†. 2016. “Next-Generation Sequencing Identifies Micro-RNA–Based Biomarker Panel for Kawasaki Disease.” Journal of Allergy and Clinical Immunology 138 (4): 1227–30. https://doi.org/10.1016/j.jaci.2016.04.050.
Postdoctoral Fellow
Taipei, Taiwan
Academia Sinica
September. 2013 - December. 2014
  • Responsibilities:
    • Analyzed various NGS data; including RNA-seq, ChIP-seq, and BS-seq, to study the effects of aneuploidy in a model plant organism.
    • Applied variant calling methods on whole genome sequencing (WGS) data to study somatic variations in head and neck cancer.
    • Collaborated closely with interdisciplinary teams of plant biologists, computational biologists, and software engineers.
  • Achievements:
    • The 2nd Prize of Poster Competition in ICMDS, 2014
    • The 3rd Prize of Oral Competition in BIT, 2013
Research Associate
London, UK
University College London
October. 2011 - August. 2013
  • Responsibilities:
    • Leveraged integrative analysis approach in analyzing various NGS data, including RNA-seq, ChIP-seq, and HiC/4C-seq to study the fundamental function of a chromosome protein.
    • Developed an automated algorithm to rescue particular read data and enhanced the resolution of the experiment result.
    • Effectively engaged with labmates to formulate well-defined scientific questions.
  • Achievements:
    • Sofueva, Sevil, Eitan Yaffe, Wen-Ching Chan, Dimitra Georgopoulou, Matteo Vietri Rudan, Hegias Mira-Bontenbal, Steven M Pollard, Gary P Schroth, Amos Tanay, and Suzana Hadjur. 2013. “Cohesin-Mediated Interactions Organize Chromosomal Domain Architecture.” The EMBO Journal 32 (24): 3119–29. https://doi.org/10.1038/emboj.2013.237.
Skills
Bioinformatics
Genomics
RNA-Seq: STAR/kallisto, featureCounts, edgeR, DESeq2, limma
Extracellular RNA (exRNA): miRge3, sRNAbench, exceRpt, MirGeneDB
ChIP-Seq: MACS2, Q
Genetics
WXS/WGS: BWA, GATK4/Mutect2, VarScan2, Strelk2
GWAS: PLINK
Metagenomics
16S Amplicon: QIIME2
Whole Metagenome Shotgun (WMS): MetaPhlAn2, HUMAnN2
Epigenetics
BS-Seq/RRBS: Bismark, MethylDackel, DSS2, methylKit
Annotation
clusterProfiler, ChIPseeker, snpEff, ensemblVEP
DB
GDC/TCGA, dbSNP, 1000 Genomes, COSMIC, KEGG, GEO/SRA/dbGaP
Misc
BBMap, Trimmomatic, cutadapt
SAMtools, BEDTools, BEDOPS, vcflib, VCFtools, Picard
Computational Programming
Advanced Programming: R, Python, Perl
Intermediate Programming: C++/STL, JAVA, JavaScript, SAS
Machine Learning/Data Mining
SVMs (Support Vector Machines), Hidden Markov Model (HMM), Artificial Neural Network (ANN), FP-growth, Dimensionality Reduction
Management Platforms
Git, Conda, Docker/Singularity, Trello/Redmine
Data Sciences Platforms
Snakemake, Nextflow, WDL/Cromwell
Systems
UNIX/Linux, HPC, SGE, DNAnexus
Databases
MySQL, PostgreSQL
Porjects
An online database of homologous microRNA search in animal genomes.
A web service with Un-MAppable Reads Solution (UMARS) for NGS data
An online database of evolutionarily conserved miRNA clusters

Awards
Methods and kits for detecting Kawasaki disease
Using miRNAs to Develop the Molecular Diagnosis Method for Kawasaki Diseases
2nd Prize in the Poster Competition

Contact
Wen-Ching Calvin Chan
San Carlos, CA