About

Hello. My name is Alan. I am a Computational Research Scientist and Senior Software Engineer at the National Center for Genome Resources. In my spare time I enjoy downhill skiing, rock climbing, and mountain biking. I also play guitar when I can.

Ph.D. Computer Science, Montana State University, 2018 (Dr. Brendan Mumey)
B.A. Computer Information Science, Western State College of Colorado, 2012
B.A. Mathematics, Western State College of Colorado, 2012

Contact

Google Scholar | Linkedin | ResearchGate | ORCID | dblp | GitHub

National Center for Genome Resources
2935 Rodeo Park Dr E
Santa Fe, NM, 87505
E-mail: acleary (at) ncgr.org

Research

Generally, I am interested in algorithms for hard, practical problems, though my main focus is on Computational Biology. Recently I have been working on methods for visually exploring and mining data from genomic databases and developing algorithms for pan/population genomcics, with an eye towards parallelism and high performance computing.

2024

Cleary, Alan M., Joseph Winjum, Jordan Dood, Shunsuke Inenaga. “Revisiting the Folklore Algorithm for Random Access to Grammar-Compressed Strings.” String Processing and Information Retrieval (SPIRE). Lecture Notes in Computer Science, vol 14899. Springer, 2024.

Kahanda, Indika, Joann Mudge, Buwani Manuweera, Thiruvarangan Ramaraj, Alan Cleary and Brendan Mumey. “Graph-Based Machine Learning Approaches for Pangenomics.” Machine Learning Methods for Multi-Omics Data Integration. Springer Nature, 2024.

2023

Kahanda, Indika, Joann Mudge, Buwani Manuweera, Thiruvarangan Ramaraj, Alan Cleary and Brendan Mumey. “Genotype-to-Phenotype Associations with Frequented Region Variants.” 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Istanbul, Turkey, 2023.

Ramaraj, Thiruvarangan, Brendan Mumey, Alan Cleary, Indika Kahanda, Nathaniel Lane, Buwani Manuweera, Snehaa Durairaj, Azalea Mendoza, Joia Capocchi, Avery Phillips, Niveditha Bala, Mateo Amador and Joann Mudge. “Pangenomic analysis with FindFRs3: A case study in Medicago truncatula.” 17th Annual Sequencing, Finishing, and Analysis in the Future Meeting. LANL SFAF, 2023.

Dood, Jordan and Alan Cleary. “Novel Grammar-Based Compression Algorithms for Pangenome Analysis.” 17th Annual Sequencing, Finishing, and Analysis in the Future Meeting. LANL SFAF, 2023.

Cleary, Alan M. and Andrew D. Farmer. “Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes.” Nucleic Acids Research (2023): gkad391.

Cleary, Alan and Jordan Dood. “Constructing the CDAWG CFG using LCP-Intervals.” Data Compression Conference. DCC, 2023. (Capocelli Prize for outstanding student-authored paper)

2022

Durant, Eloi, Mathieu Rouard, Eric W. Ganko, Cedric Muller, Alan M. Cleary, Andrew D. Farmer, Matthieu Conte, and Francois Sabot. “Ten simple rules for developing visualization tools in genomics.” PLOS Computational Biology. Public Library of Science, 2022.

Redsun, Sven, Sam Hokin, Connor T. Cameron, Alan M. Cleary, Joel Berendzen, Sudhansu Dash, Anne V. Brown, Andrew Wilkey, Jacqueline D. Campbell, Wei Huang, Scott R. Kalberer, Nathan T. Weeks, Steven B. Cannon, and Andrew D. Farmer. “Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources.” Plant Bioinformatics. Springer US, 2022, pp. 81-100.

2021

Berendzen, Joel, Anne V. Brown, Connor T. Cameron, Jacqueline D. Campbell, Alan M. Cleary, Sudhansu Dash, Samuel Hokin, Wei Huang, Scott R. Kalberer, Rex T. Nelson, Sven Redsun, Nathan T. Weeks, Andrew Wilkey, Andrew D. Farmer, and Steven B. Cannon. “The legume information system and associated online genomic resources.” Legume Science. Wiley, 2021.

Al Khleifat, Ahmad, Jenny L. Smith, Brandon M. Blobner, Sierra D. Miller, Kymberleigh Pagel, Annie Nadkarni, Melanie Gainey, Patrick Campbell, Olaitan I. Awe, Manuel Belmadani, Alan M. Cleary, Nicholas P. Cooley, Shamika Dhuri, Virginie Grosboillot, Brian Haas, Samuel Hokin, Ekaterina Orlova, Meghana Pagadala, Stephen Price, Adelaide Rhodes, Janice Kyla, Nascimento Smith, Chaitanya Srinivasan, Barry Zorman, and Ben Busby. “SnpReportR: A Tool for Clinical Reporting of RNAseq Expression and Variants.” BioHackrXiv. Preprint, 2021.

2020

Hokin, Samuel, Alan Cleary, and Joann Mudge. “Disease association with frequented regions of genotype graphs.” medRxiv. Preprint, 2020.

Pasha, Asher, Shabari Subramaniam, Alan Cleary, Xingguo Chen, Tanya Z Berardini, Andrew Farmer, Chris Town and Nicholas J. Provart. “Araport Lives: An Updated Framework for Arabidopsis Bioinformatics.” The Plant Cell. American Society of Plant Biologists, 2020. (The Plant Cell article of the week)

Huang, Wei, Joel Berendzen, Anne V. Brown, Connor T. Cameron, Jacqueline D. Campbell, Ethalinda Cannon, Alan Cleary, Sudhansu Dash, Samuel A. Hokin, Sven Gato Redsun, Scott R. Kalberer, Nathan Weeks, Andrew Wilkey, Andrew Farmer and Steven B. Cannon. “Legumeinfo.org: Online Resources Facilitate Basic Research and Crop Improvement for Legumes.” Plant and Animal Genome XXVIII Conference. Plant and Animal Genome, 2020.

2019

Bauchet, Guillaume, Kirstin Bett, Connor Cameron, Jacqueline Campbell, Ethalinda Cannon, Steven Cannon, Joseph Carlson, Agnes Chan, Alan Cleary, Timothy Close, Douglas Cook, Amanda Cooksey, Clarice Coyne, Sudhansu Dash, Rebecca Dickstein, Andrew Farmer, David Fernández‐Baca, Samuel Hokin, Elizabeth Jones, Yun Kang, Maria Monteros, María Muñoz‐Amatriaín, Kirankumar Mysore, Catalina Pislariu, Chris Richards, Ainong Shi, Christopher Town, Michael Udvardi, Eric Bishop von Wettberg, Nevin Young and Patrick Zhao. “The future of legume genetic data resources: Challenges, opportunities, and priorities.” Legume Science. 2019.

Llamas, Bastien, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten and Ben Busby. “A strategy for building and using a human reference pangenome.” F1000Research. 2019.

Manuweera, Buwani, Joann Mudge, Indika Kahanda, Brendan Mumey, Thiruvarangan Ramaraj and Alan Cleary. “Pangenome-Wide Association Studies with Frequented Regions.” 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM-BCB, 2019.

Hokin, Samuel and Alan Cleary. “Disease Classification with Pan-Genome Frequented Regions and Machine Learning.” Gordon Research Conference on Human Genetics and Genomics. GRS, 2019.

Campbell, Jacqueline D., Joel Berendzen, Connor T. Cameron, Ethalinda Cannon, Alan Cleary, Sudhansu Dash, David Grant, Sam Hokin, Wei Huang, Scott R. Kalberer, Nathan T. Weeks, Andrew Farmer, and Steven Cannon. “legumeinfo.org: A Resource to Facilitate Basic Research and Crop Improvement in Legumes.” Plant and Animal Genome XXVII Conference. Plant and Animal Genome, 2019.

Campbell, Jacqueline D, Joel Berendzen, Connor T. Cameron, Ethalinda Cannon, Steven Cannon, Agnes P. Chan, Yongwook Choi, Alan Cleary, Amanda M. Cooksey, Sudhansu Dash, Andrew Farmer, David Grant, Sam Hokin, Wei Huang, Christopher D. Town, Akshay Yadav, Nathan T. Weeks, Andrew Wilkey, and David Fernandez-Baca. “legumefederation.org: A Federation of Legume Data Providers Promoting Data Standards and Providing Software Solutions for Cross-Platform Comparative Legume Research.” Plant and Animal Genome XXVII Conference. Plant and Animal Genome, 2019.

2018

Cleary, Alan. “Computational pan-genomics: algorithms and applications.” Montana State University-Bozeman, College of Engineering. 2018. (dissertation)

Cleary, Alan, Thiruvarangan Ramaraj, Indika Kahanda, Joann Mudge, and Brendan Mumey. “Exploring Frequented Regions in Pan-Genomic Graphs.” IEEE/ACM transactions on computational biology and bioinformatics. TCBB, 2018.

Mudge, Joann, Alan Cleary, Indika Kahanda, Brendan Mumey, and Thiruvarangan Ramaraj. “Enabling Biological Insights through Eukaryotic Pangenomics.” 13th Annual Sequencing, Finishing, and Analysis in the Future Meeting. LANL SFAF, 2018.

Farmer, Andrew, Jacqueline Campbell, Sudhansu Dash, Wei Huang, Malachy O’Connell, Andrew Wilkey, Akshay Yadav, Nathan T. Weeks, Joel Berendzen, Alan Cleary, Sam Hokin, Connor Cameron, Vivek Krishnakumar, Amanda Cooksey, Agnes Chan, Ethalinda Cannon, Eric Lyons, Christopher Town, Steven Cannon, and David Fernandez-Baca. “The Federated Plant Database Initiative for thee Legumes.” Plant and Animal Genome XXVI Conference. Plant and Animal Genome, 2018.

Cannon, Steven, Jacqueline Campbell, Sam Hokin, Joel Berendzen, Ethalinda Cannon, Alan Cleary, Sudhansu Dash, Connor T. Cameron, Wei Huang, Scott R. Kalberer, Amanda Cooksey, Nathan Weeks, and Andrew Farmer. “legumeinfo.org: Legume Research and Trait Data that is Findable, Accessible, Interoperable and Re-Usable.” Plant and Animal Genome XXVI Conference. Plant and Animal Genome, 2018.

2017

Cleary, Alan Cleary, Thiruvarangan Ramaraj, Indika Kahanda, Joann Mudge, Shubhang Kulkarni, and Brendan Mumey. “Exploring Frequented Regions in Pan-Genomic Graphs.” 15th Annual Rocky Mountain Bioinformatics Conference. ROCKY, 2017.

Cleary, Alan, and Andrew Farmer. “Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny.” Bioinformatics. 1:3, 2017.

Cleary, Alan, Thiruvarangan Ramaraj, Indika Kahanda, Joann Mudge, and Brendan Mumey. “Exploring Frequented Regions in Pan-Genomic Graphs.” 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM-BCB, 2017. (best student paper)

Cleary, Alan, Joann Mudge, Thiruvarangan Ramaraj, and Brendan Mumey. “Mining Frequented Regions for Pan-Genome Analysis.” 12th Annual Sequencing, Finishing, and Analysis in the Future Meeting. LANL SFAF, 2017.

Cleary, Alan M., Thiruvarangan Ramaraj, Joann Mudge, and Brendan Mumey. “Approximate Frequent Subpath Mining Applied to Pangenomics.” 9th International Conference on Bioinformatics and Computational Biology. BICOB, 2017.

Cleary, Alan M., Thiruvarangan Ramaraj, Joann Mudge, and Brendan Mumey. “Investigating Frequented Regions (FRs) in a Yeast Pan-Genome.” Plant and Animal Genome XXV Conference. Plant and Animal Genome, 2017.

Huang, Wei, Sudhansu Dash, Alan M. Cleary, Alex G. Rice, Sam Hokin, Jacqueline D. Campbell, Joel Berendzen, Maria Hadres, Pooja E. Umale, Nathan T. Weeks, Andrew Wilkey, Andrew Farmer, Steven B. Cannon, and Ethalinda Cannon. “PeanutBase.org: A Genomic and Genetic Data Resource to Support Crop Improvement in Peanut.” Plant and Animal Genome XXV Conference. Plant and Animal Genome, 2017.

Berendzen, Joel, Ethalinda Cannon, Alan M. Cleary, Sudhansu Dash, Sam Hokin, Wei Huang, Alex G. Rice, Pooja E. Umale, Nathan T. Weeks, Andrew Wilkey, Andrew Farmer, Steven B. Cannon, and Maria Hadres. “LegumeInfo.org: Legume Research and Trait Data That is Findable, Accessible, Interoperable and Re-Usable.” Plant and Animal Genome XXV Conference. Plant and Animal Genome, 2017.

Farmer, Andrew, Alan Cleary, Sudhansu Dash, Alex G. Rice, Joel Berendzen, Sam Hokin, Maria Hadres, Pooja E. Umale, Jacqueline D. Campbell, Wei Huang, Nathan T. Weeks, Akshay Yadav, Andrew Wilkey, David Grant, Rex Nelson, Kevin H. Feeley, Victoria Carollo Blake, Ethalinda Cannon, Vivek Krishnakumar, Steven B. Cannon, Agnes P. Chan, Eric Lyons, Christopher D. Town, and David Fernandez-Baca. “The Legume Information System (http://legumeinfo.org) and The Legume Federation (http://legumefederation.org): Comparative Genomics and Genetics through Cooperative Resource Development.” Plant and Animal Genome XXV Conference. Plant and Animal Genome, 2017.

Farmer, Andrew, and Alan Cleary. “Genome Context Viewer: A User-Friendly Web Application for Visualizing and Mining Shared Gene Content Among Multiple Genomes.” Plant and Animal Genome XXV Conference. Plant and Animal Genome, 2017.

Dash, Sudhansu, Joel Berendzen, Jacqueline D. Campbell, Ethalinda Cannon, Steven B. Cannon, Alan Cleary, Andrew Farmer, Maria Hadres, Sam Hokin, Wei Huang, Alex G. Rice, Pooja E. Umale, Nathan T. Weeks, and Andrew Wilkey. “Customizing Tripal Sites with Non-Tripal Components at the Legume Information System and Peanutbase.” Plant and Animal Genome XXV Conference. Plant and Animal Genome, 2017.

2016

Cleary, Alan, Thiruvarangan Ramaraj, Joann Mudge, and Brendan Mumey. “Mining Frequent Subpaths in Pan-Genomes.” 11th Annual Sequencing, Finishing, and Analysis in the Future Meeting. LANL SFAF, 2016.

Cleary, Alan, Thiruvarangan Ramaraj, Joann Mudge, and Brendan Mumey. “Pangenomics: Persistent Homology for Pan-Genome Analysis.” 11th Annual Sequencing, Finishing, and Analysis in the Future Meeting. LANL SFAF, 2016.

Campbell, Jacqueline D., Sudhansu Dash, Ethalinda Cannon, Alan M. Cleary, Wei Huang, Scott R. Kalberer, Alex G. Rice, Jugpreet Singh, Pooja E. Umale, Nathan T. Weeks, Andrew Wilkey, Christopher D. Town, Jeremy D. DeBarry, David Fernandez-Baca, Andrew D. Farmer, and Steven B. Cannon. “What’s New in the Legume Information System and the Federated Legume Database Initiative.” Plant and Animal Genome XXIV Conference. Plant and Animal Genome, 2016.

Farmer, Andrew D., Alan Cleary, Alex G. Rice, Pooja E. Umale, Sam Hokin, Sudhansu Dash, Jacqueline D. Campbell, Wei Huang, Nathan T. Weeks, Andrew Wilkey, David Grant, Rex Nelson, Kevin H. Feeley, Vivek Krishnakumar, Akshay Yadav, Jeremy D. DeBarry, David Fernandez-Baca, Ethalinda Cannon, Christopher D. Town, and Steven B. Cannon. “The Legume Information System and The Legume Federation: Working Together for the Legume-Fed World.” Plant and Animal Genome XXIV Conference. Plant and Animal Genome, 2016.

Dash, Sudhansu, Wei Huang, Jacqueline D. Campbell, Jugpreet Singh, Alex G. Rice, Pooja E. Umale, Alan Cleary, Scott R. Kalberer, Nathan T. Weeks, Vijay Karingula, Prateek Gupta, Shivan Gunda, Ethalinda Cannon, Andrew D. Farmer, and Steven B. Cannon. “LIS (Legume Information System): A Clade Based Web Resource for Legumes.” Plant and Animal Genome XXIV Conference. Plant and Animal Genome, 2016.

2015

Dash, Sudhansu, Jacqueline D. Campbell, Ethalinda KS Cannon, Alan M. Cleary, Wei Huang, Scott R. Kalberer, Vijay Karingula, Alex G. Rice, Jugpreet Singh, Pooja E. Umale, Nathan T. Weeks, Andrew P. Wilkey, Andrew D. Farmer, and Steven B. Cannon. “Legume information system (LegumeInfo. org): a key component of a set of federated data resources for the legume family.” Nucleic Acids Research (2015): gkv1159.

Cleary, Alan, Lucas Vandenbergh, and John Peterson. “Reactive Game Engine Programming for STEM Outreach.” Proceedings of the 46th ACM Technical Symposium on Computer Science Education. ACM, 2015.

Cleary, Alan, Longhui Ren, Steven B. Cannon, and Andrew D. Farmer. “Tools for Phylogenomic Exploration within and Among Clade-Oriented Databases.” Plant and Animal Genome XXIII Conference. Plant and Animal Genome, 2015.

Cannon, Steven B, Andrew D. Farmer, Pooja E. Umale, Hrishikesh Lokhande, Alan Cleary, Nathan T. Weeks, Scott R. Kalberer, Ethalinda Cannon, Sudhansu Dash, Deepak Bitragunta, and Jugpreet Singh. “The Legume Information System (LegumeInfo. org) 2015.” Plant and Animal Genome XXIII Conference. Plant and Animal Genome, 2015.

Farmer, Andrew D, Steven B. Cannon, Scott R. Kalberer, Jugpreet Singh, Ethalinda Cannon, Pooja E. Umale, Hrishikesh Lokhande, Alan Cleary, Nathan T. Weeks, Vijay Karingula, and Sudhansu Dash. “Methods for Collecting, Integrating, and Displaying Complex Genetic Data, Using the Legume Information System and PeanutBase.” Plant and Animal Genome XXIII Conference. Plant and Animal Genome, 2015.

Peterson, John, Alan Cleary, and Ken Roe. “PyFRP: Function Reactive Programming in Python.” ACM SIGPLAN conference on Systems, Programming, Languages, and Applications: Software for Humanity - Education Symposium. SPLASH-E, 2015.

2013

Peterson, John and Alan Cleary. “Functional Reactive Programming in K12 Education.” 2nd International Workshop on Trends in Functional Programming in Education. TFPIE, 2013.

2012

Cleary, Alan. “A Mathematical Approach to Artificial Intelligence: Deriving and Implementing an Artificial Neural Network Model.” Western State College, Math and Computer Information Science Department. 2012. (senior capstone)

2011

Just, Seth, Alan Cleary, Brandon Shirley, and Christian Hammer. “Information flow analysis for javascript.” Proceedings of the 1st ACM SIGPLAN international workshop on Programming language and systems technologies for internet clients. ACM, 2011.

2010

Nelson, Jeremy, and Alan Cleary. “FRBRizing an E-Library: Migrating from Dublin Core to FRBR and MODS.” Code4Lib Journal 12 (2010).

2009

Cleary, Alan, Kendric Evans, Michael Reed, John Peterson. “Automated vision tracking with OpenCV.” 19th International Joint Conference on Artificial Intelligence. IJCAI, 2009.