Vitae

Professional Experience

Atalanta Therapeutics

Senior Bioinformatics Scientist	Apr 2023 - Present
Lead bioinformatics projects to enable transcriptomics, genomics, and other data-intensive analyses for pipeline enrichment. Mentor a team of talented junior scientists to enable bioinformatics and data-science efforts to improve drug safety and efficacy. Implement an in-house siRNA design algorithm with customized features to improve drug design focusing on chemistry and biology. Collaborate with lab teams on assay development to ensure scalable and high-quality data analysis. Deploy AWS cloud cyberinfrastructure for scalable data analysis and data security with external partner support.
Bioinformatics Scientist	Feb 2022 - Apr 2023
Lead bioinformatics projects to enable transcriptomics, genomics, and other data-intensive analyses for pipeline enrichment. Mentor a team of talented junior scientists to enable bioinformatics and data-science efforts to improve drug safety and efficacy. Implement an in-house siRNA design algorithm with customized features to improve drug design focusing on chemistry and biology. Collaborate with lab teams on assay development to ensure scalable and high-quality data analysis. Deploy cyberinfrastructure for scalable data analysis and data security with external partner support.

Greenlight Biosciences

Genomics Data Scientist	Apr 2021 - Jan 2022
Develop and maintain workflows to characterize the RNA molecules produced for human health projects, and collaborate with the NGS team to develop in-house assays for characterization using novel sequencing experiments and technologies. Actively develop and maintain workflows for discovery efforts and subsequent design of RNAs for crop protection products Design and implement cloud cyberinfrastructure to meet various team goals starting with secure web app development and deployment to auto-scaling turn-key HPC infrastructure. Develop dashboards to democratize data access of the experimental data to research scientists in plant and human health
Bioinformatics Software Developer	Nov 2020 - Apr 2021
Routinely analyze datasets generated by RNA-seq of single-stranded mRNAs produced for human health projects Run the proprietary pipelines to design RNAs for plant health projects Improve established pipelines into turn-key solutions tailored to HPC on the cloud (AWS and Azure) Develop dashboards to democratize data access to data to research scientists in plant and human health

SOPHiA Genetics

Bioinformatics Specialist

May 2019 - Oct 2020

Working on analyzing NGS data from probe-capture and amplicon panels on clinical samples to identify variants
Working on different assays used for Somatic and Germline samples ranging from small targeted panels to whole exome sequencing
Analyze data using proprietary pipelines developed for variant calling, assess the sensitivity on difficult samples and variants, and work with the team to optimize the pipelines
Summarize the data using R and Python and communicate results to team members, collaborators and clients
Adhere to high standards of analysis quality, attention to details, and meet demands of fast-paced analysis cycles and deadlines

Technical Skills

Computational Skills

Languages: R, Python, JavaScript, PHP, Perl, HTML, bash
Web Frameworks: Flask, Django, Angular, R-Shiny
Cloud: Amazon AWS and Microsoft Azure
Databases: MySQL/MariaDB, PostgreSQL, Neo4j
Containerization: Docker and Singularity
Other: Unix/Linux and Windows OS, Torque/PBS and Slurm HPC environments

Experimental Skills

Standard PCR techniques (PCR, and RT-PCR)
Experimental design, dissection and sample collection for NGS experiments
DNA/RNA extraction from fixed and fresh samples
BioAnalyzer, Fragment Analyzer, and Qubit for DNA/RNA Quantity and Quality
Illumina Library Construction and QC
Field experience in maize

Research Experience

Iowa State University

Gene Ontology Meta Annotator for Plants (GOMAP)	2016 - Present
Developed a new pipeline to annotate GO terms to plant protein sequences, which improves quality, quantity and reproducibility of GO annotations Currently finalizing the pipeline code, containerizing the pipeline and testing the pipeline before public release
Sequence-based methods to find the causal mutations in maize mutants	2014 - Present
Adapted and modified the existing GBS protocol, applied it to bulked segregants (BS-GBS) and analyzed data to find the causal locus of maize inflorescence mutants Currently desinging a pipline to analyze whole-genome sequencing data from maize mutants to generate a list of candidate causal mutations
Identifying transposon and transgene insertion locations in maize	2014 - Present
Collborative project using NGS to identify transposon and transgene insertion locations using flanking regions Analyzed Illumina and PacBio data produced by different target enrichment strategies
maize-GO Annotation Methods, Evaluation, and Review (maize-GAMER)	2012 - 2018
Generated a high-coverage and reproducible functional annotation dataset for maize protein coding genes using gene ontology (GO) terms, and evaluated the publicly available maize GO annotations using a manually curated dataset
Tools to design primers that amplify unique genomic targets	2017 - Present
Developed primerDAFT package to design PCR primers for a given target that can amplify unique targets for a given genome Mentored a computer engineering undergraduate student to build a web tool (PrimerServer) for the lab to design primers
The maize W22 genome sequencing project	2016 - 2017
Developed analysis pipeline to determine insertion locations of Ac/Ds Transposon collection, and compare the locations between maize W22 and B73 genomes
Effect of drought on early maize inflorescence development	2016 - 2017
Coordinated a multi-institutional effort to collect RNA-seq and SEM samples to study drought effects on maize inflorescences Extracted RNA, checked quality and outsourced the sequencing library preparation and sequencing efforts
Gene network variation and alternative paths to convergent evolution in turtles	2014 - 2016
Collaborative Volunteer project for the analysis of RNA-seq data from 3 different turtle species, which consisted of quantifying expression and de novo transcriptome assembly and analysis
MaizeGDB expression analysis tool	2011 - 2012
Built a web tool at MaizeGDB to visualize the expression dataset from the Maize Expression Atlas using MapMan web interface

Miami University

*Computational Analysis of Chlamydomonas reinhardtii* Promoters**	2016 - Present
Analyzed the C. reinhardtii promoters and identified putative core and distal promoter elements, and compared the identified promoter elements other existing elements
Visualizing Genetic Maps using Open Source Tools	2009 - 2011
Deployed a customized version of the genetic map viewer CMap as part of ConiferGDB Designed and developed modernized comparative map viewer (YouGenMap)

Education

PhD, Bioinformatics and Computational Biology	2011 - 2018
Iowa State University, Ames, Iowa, United States Advisors: Carolyn Lawrence-Dill & Erik Vollbrecht Experimental and computational methods to assign gene function in maize
MS, Botany	2009 - 2011
Miami University, Oxford, Ohio, United States Advisor: Chun Liang Genome-wide computational analysis of Chlamydomonas reinhardtii promoters
BSc, Bioinformatics	2005 - 2008
University of Colombo, Colombo, Sri Lanka Research Advisor: Shamala Tirimanne Honors Research: Implementing client-side bioinformatics algorithms using JavaScript

Teaching Experience

Iowa State University

Teaching Assistant	Spring 2018
Principles of Genetics
Workshop instructor	Spring 2016 Spring 2015
Introduction to Linux/Unix

Miami University

Course Instructor	Summer 2011
General Botany
Teaching Assistant	2009 - 2011
General Botany Plants and Environment

University of Colombo

Demonstrator (Teaching Assistant)	2008 - 2009
Introduction to bioinformatics Introduction to Molecular Biology Plant Systematics Genetics and Cell Biology

Talks

2019

Automatically Assigning GO Terms to Plant Gene Models

D. Psaroudakis*, K. Wimalanathan, H. Vu, P. Joshi, I. Friedberg, C. Dill. Plant and Animal Genome XXVII Conference (2019). San Diego, CA, USA

Automatically Assigning GO Terms to Plant Gene Models

We constructed a high-coverage and reproducible functional annotation dataset for wheat based on Gene Ontology (GO) term assignments, covering 100% of the 107,891 high-confidence gene models in IWGSC’s RefSeq 1.1 genome with a median of 10 annotations per gene model. To derive this annotation set, we used the GOMAP pipeline, which includes sequence similarity and protein domain presence methods as well as mixed-method pipelines that were developed for the Critical Assessment of Function Annotation (CAFA) challenge (https://biofunctionprediction.org/cafa/). Whereas application of the pipeline to maize was quality checked based on hand-curated functional annotations (Wimalanathan et al. 2018, DOI 10.1002/pld3.52), no such gold-standard exists for wheat so these predictions lack quality assessment. To build gold-standard datasets that would enable quality assessment for GOMAP annotations in wheat (as well as other genomes including rice, cotton, and soybean), we are building a platform to enable crowd-sourced review of computationally extracted gene-functional associations drawn from primary literature. The GOMAP pipeline is publicly available at https://github.com/Dill-PICL/GOMAP-singularity and the derived annotation datasets can be found at https://dill-picl.org/projects/gomap/gomap-datasets/.
Assigning GO Terms to Wheat Gene Models

D. Psaroudakis, K. Wimalanathan, C. Dill*. Plant and Animal Genome XXVII Conference (2019). San Diego, CA, USA

Assigning GO Terms to Wheat Gene Models

We constructed a high-coverage and reproducible functional annotation dataset for wheat based on Gene Ontology (GO) term assignments, covering 94% of the 107,891 high-confidence gene models in IWGSC’s RefSeq 1.1 genome with 9.5 annotations per gene model on average. To derive this annotation set, we used the GOMAP pipeline, which includes sequence similarity and protein domain presence methods as well as mixed-method pipelines that were developed for the Critical Assessment of Function Annotation (CAFA) challenge (https://biofunctionprediction.org/cafa/). Whereas maize annotations derived from the pipeline were quality checked (based on hand-curated functional annotations; https://doi.org/10.1002/pld3.52), no such gold-standard exists for wheat, so these predictions lack quality assessment. Ideas for how best to assemble a gold-standard dataset to enable quality assessments for these predictions will be discussed. The GOMAP pipeline is available at https://github.com/Dill-PICL/GOMAP-singularity. Wheat GOMAP annotations are available at https://dill-picl.org/projects/maize-gamer/maize-gamer-datasets/.

2018

GO-MAP Implements CAFA Tools: Improved Automated Gene Function Annotation for Plants

K. Wimalanathan, I. Friedberg, C. Andorf, C. Lawrence-Dill*. International Conference on Biomedical Ontology (2018). Corvallis, OR, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. International Conference on Intelligent Systems for Molecular Biology (2018). Chicago, IL, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. Maize Genetics Conference (2018). Saint Malo, France

2017

maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. Annual BCB Symposium (2017). Ames, IA, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. Maize Genetics Conference, Pre-conference workshop "Maize Tools & Resources" (2017). St Louis, MO, USA
An expression atlas of the maize shoot apex reveals signatures of TFs as important drivers for cell identity and sub-functionalization of key downstream factors

S. Knauer*, M. Javelle, L. Li, X. Li, K. Wimalanathan, S. Kumari, S. Leiboff, R. Johnston, D. Ware, C. Lawrence, P. Schnable, J. Yu, G. Muehlbauer, M. Scanlon, M. Timmermans. Maize Genetics Conference, Pre-conference workshop "Maize Tools & Resources" (2017). St Louis, MO, USA
Improved Methods for High-Confidence GO Annotation

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. Phenome 2017 (2017). Tucson, AZ, USA

2015

Bulked segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Unger-Wallace, E. Vollbrecht. ComBio2015 (2015). Melbourne, VIC, Australia
Ds mutagenesis and a de novo W22 genome sequence

E. Vollbrecht*, K. Ahern, E. Unger-Wallace, A. Studer, R. Mertz, J. Strable, K. Wimalanathan, T. Anderson, R. Saunders, G. Jander, J. Duvick, T. Brutnell. Maize Genetics Conference (2015). St Charles, IL, USA

2011

Genome-wide, Computational analysis of Chlamydomonas reinhardtii promoters

K. Wimalanathan*, C. Liang. Great Lakes Bioinformatics Conference 2011 (2011). Athens, OH, USA

Posters

2018

Primer Server - A web application to design primers for the amplification of unique DNA targets in complex genomes

T. Shibamoto*, K. Wimalanathan, E. Unger-Wallace, E. Vollbrecht. National Conference on Undergraduate Research 2018 (2018). Edmond, OK, USA
Bulked-segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Unger-Wallace, E. Vollbrecht. Maize Genetics Conference (2018). Saint Malo, France
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. Maize Genetics Conference (2018). Saint Malo, France
Natural variation in the molecular circuitry underlying cell type specification drives key plant architectural traits in maize

S. Knauer*, M. Javelle, L. Li, X. Li, K. Wimalanathan, X. Ma, S. Kumari, S. Leiboff, D. Ware, C. Lawrence-Dill, P. Schnable, J. Yu, G. Muehlbauer, M. Scanlon, M. Timmermans. 60^th Maize Genetics Conference (2018). Saint Malo, France
Maize annotation jamboree on last B73 RefGen_V4 assembly

C. Marco*, M. Tello-Ruiz, F. Hsu, H. Wu, K. Wimalanathan, J. Zhan, M. Stitzer, P. Qiao, R. Wasikowski, R. Khangura, S. Sapkota, Z. Brenton, M. Okoro, M. Munoz-Torres, U. Hilgert, J. Williams, D. Ware, D. Micklos. 60^th Maize Genetics Conference (2018). Saint Malo, France
Bulked-segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Unger-Wallace, E. Vollbrecht. American Society of Plant Biology - Midwest Section Meeting (2018). Ames, IA, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan, I. Friedberg, C. Andorf, C. Lawrence-Dill. American Society of Plant Biology - Midwest Section Meeting (2018). Ames, IA, USA

2017

Bulked-segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Unger-Wallace, E. Vollbrecht. 59^th Maize Genetics Conference (2017). St Louis, MO, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. 59^th Maize Genetics Conference (2017). St Louis, MO, USA
Bulked-segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, E. Unger-Wallace, R. Weeks, E. Vollbrecht. Plant and Animal Genome XXVI (2017). San Diego, CA, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. Plant and Animal Genome XXVI (2017). San Diego, CA, USA
Genetic interactions between JA and GA pathway genes and inflorescence branching in maize

E. Vollbrecht*, K. Wimalanathan, J. Strable, E. Unger-Wallace. Plant and Animal Genome XXVI (2017). San Diego, CA, USA

2016

Bulked-segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Unger-Wallace, E. Vollbrecht. 58^thMaize Genetics Conference (2016). Jacksonville, FL, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. 58^thMaize Genetics Conference (2016). Jacksonville, FL, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

C. Andorf, K. Ahern, F. Bai, O. Barad, W. Barbazuk, H. Bass, K. Baruch, G. Ben-Zvi, E. Buckler, R. Bukowski, R. Davenport, H. Dooner, L. He Du, C. Du, K. Easterling, C. Gault, J. Guan, G. Jander, Y. Jiao, K. Koch, G. Kol, T. Kudo, Q. Li, F. Lu, D. Mayfield-Jones, W. Mei, D. McCarty, J. Portwood, G. Ronen, M. Settles, D. Shem-Tov, I. Soifer, N. Springer, M. Suzuki, D. Vera, E. Vollbrecht, J. Vrebalov, D. Ware, K. Wimalanathan, W. Xiong, T. Brutnell*. 58^thMaize Genetics Conference (2016). Jacksonville, FL, USA
Sequencing, Assembly, and Annotation of Maize B104 : A Maize Transformation Resource

N. Manchanda*, C. Andorf, L. Ye, K. Wimalanathan, S. Rounsley, K. Wang, C. Lawrence-Dill. 58^thMaize Genetics Conference (2016). Jacksonville, FL, USA
Bulked-segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Unger-Wallace, E. Vollbrecht. Plant and Animal Genome XXVI (2016). San Diego, CA, USA
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, I. Friedberg, C. Andorf, C. Lawrence-Dill. Plant and Animal Genome XXVI (2016). San Diego, CA, USA
Sequencing, Assembly, and Annotation of Maize B104 : A Maize Transformation Resource

N. Manchanda*, C. Andorf, L. Ye, K. Wimalanathan, S. Rounsley, K. Wang, C. Lawrence-Dill. Plant and Animal Genome XXVI (2016). San Diego, CA, USA

2015

maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, C. Andorf, C. Lawrence-Dill. Australsian Genomic Technologies Association (2015). Hunter Valley, NSW, Australia
Bulked segregant-genotyping-by-sequencing: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Unger-Wallace, E. Vollbrecht. Australsian Genomic Technologies Association (2015). Hunter Valley, NSW, Australia
maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER)

K. Wimalanathan*, C. Andorf, C. Lawrence. 57^th Maize Genetics Conference (2015). St, Charles, IL, USA
Pooled GBS: Cost-effective and background independent genetic mapping of mutants and QTL

K. Wimalanathan*, R. Weeks, E. Vollbrecht. 57^th Maize Genetics Conference (2015). St, Charles, IL, USA
An expression atlas of the maize shoot apex

S. Knauer*, M. Javelle, L. Li, X. Li, K. Wimalanathan, S. Kumari, D. Ware, C. Lawrence, P. Schnable, J. Yu, G. Muehlbauer, M. Scanlon, M. Timmermans. 57^th Maize Genetics Conference (2015). St, Charles, IL, USA
Natural variation and drought responses in developing maize inflorescences

C. Trontin*, C. Lunde, K. Wimalanathan, H. Claeys, W. Feng, J. DInneny, Q. Dong, A. Eveland, S. Hake, D. Jackson, T. Rocheford, E. Vollbrecht. 57^th Maize Genetics Conference (2015). St, Charles, IL, USA
The Reinvention of MaizeGDB

J. Portwood*, E. Cannon, C. Andorf, B. Braun, L. Harper, D. Campbell, J. Gardiner, M. Schaeffer, J. Richter, A. Vinnakota, V. Sribalusu, W. Kokulapalan, T. Sen, C. Lawrence. 57^th Maize Genetics Conference (2015). St, Charles, IL, USA
Functional annotation of maize gene models: A machine learning approach

K. Wimalanathan*, C. Andorf, C. Lawrence-Dill. Pacific Symposium on Biocomputing (2015). Big Island, HI, USA

2014

Functional annotation of B73 gene models: A machine learning approach

K. Wimalanathan*, A. Carson, C. Lawrence. Maize Genetics Conference (2014). Beijing, China

2013

A SNP-based high-throughput genetic mapping data analysis tool for mapping mutants and QTL

K. Wimalanathan*, R. Weeks, E. Vollbrecht. 55 ^th Maize Genetics Conference (2013). St, Charles, IL, USA
Functional annotation of B73 gene models: A machine learning approach

K. Wimalanathan*, A. Carson, L. Carolyn. 55 ^th Maize Genetics Conference (2013). St, Charles, IL, USA
How to Access and Use the New MaizeGDB Website

L. Harper*, C. Andorf, E. Cannon, J. Richter, J. Portwood, K. Wimalanathan, D. Campbell, M. Schaeffer, J. Gardiner, T. Sen, C. Lawrence. 55 ^th Maize Genetics Conference (2013). St, Charles, IL, USA
Gene Expression Analysis Tools at MaizeGDB

J. Gardiner*, E. Cannon, K. Wimalanathan, C. Andorf, L. Harper, J. Richter, T. Sen, M. Schaeffer, C. Lawrence. 55^th Maize Genetics Conference (2013). St, Charles, IL, USA

2012

Gene Expression Resources Available from MaizeGDB

K. Wimalanathan*, G. Jack, B. Bremen, C. Ethalinda, S. Mary, H. Lisa, A. Carson, C. Darwin, B. Scott, S. Taner, P. Nicholas, L. Carolyn. International Symposium on Bioinformatics Research and Applications (2012). Dallas, TX, USA
Gene Expression Resources Available from MaizeGDB

K. Wimalanathan*, G. Jack, B. Bremen, C. Ethalinda, S. Mary, H. Lisa, A. Carson, C. Darwin, B. Scott, S. Taner, P. Nicholas, L. Carolyn. 54^th Maize Genetics Conference (2012). Portland, OR, USA

Awards and Fellowships

W. Young and W.E. Loomis Travel Award Department of Genetics, Development, and Cell Biology Iowa State University	2018 & 2014
PSI - Graduate Fellowship Competitive 4 year fellowship awarded to students interested in plant sciences Plant Sciences Institute, Iowa State University	2011 - 2015
Best Student-Poster Award AGTA 2015, Hunter Valley, NSW, Australia	2015
Leadership and Service Award Bioinformatics and Computational Biology Graduate Student Organization Iowa State University	2015
Research Award Bioinformatics and Computational Biology Graduate Student Organization Iowa State University	2015
Heimsch Graduate Award in Botany Award given to top performing departmental graduate students Botany Department, Miami University	2011
Graduate Achievement Award Award given to top performing graduate students Graduate College, Miami University	2011

Service

Taking the Road Less Traveled Volunteered at the one-day conference for middle school and high school girls to learn about STEM fields Iowa State University	Spring 2018
Maize Annotation Jamboree Workshop Participant Community maize genome curation for Gramene Cold Spring Harbor Lab	Fall 2017
Cricket Club President (2015) & Webmaster (2014 - 2017) Iowa State University	2014 - 2017
Losing Fear of the Command Line Workshop Volunteer for the Pre-conference workshop Maize Genetics Conference	Spring 2017
Introduction to Linux/Unix Workshop Instructor Bioinformatics and Computational Biology Graduate Student Organization Iowa State University	2016 & 2015
Graduate and Professional Student Senate Senator Bioinformatics and Computational Biology program Iowa State University	2013 - 2014
Sri Lankan Student Association Treasurer (2013) & Webmaster (2011 - 2013) Iowa State University	2011 - 2013

Professional Memberships

International Society of Computational Biology	2016-2018
Maize Cooperator	2012-2018