Veterinary and Biological Informatics Lab Smith College Department of Computer Science

Research

Here is a list of publications associated with ongoing work in the VBIL.

All

2024

Missing history of a modern domesticate: Historical demographics and genetic diversity in farm-bred red fox populations
Missing history of a modern domesticate: Historical demographics and genetic diversity in farm-bred red fox populations
Halie M Rando, Emmarie P Alexander, Sophie Preckler-Quisquater, Cate B Quinn, Jeremy T Stutchman, ..., Anastasiya V Kharlamova, Lyudmila N Trut, Jonathan N Pauli, Benjamin N Sacks, Anna V Kukekova
Journal of Heredity   ·   16 Apr 2024   ·   doi:10.1093/jhered/esae022
domestication foxes wildlife
Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs
Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs
Halie M. Rando, Kiley Graim, Greg Hampikian, Casey S. Greene
Journal of the American Veterinary Medical Association   ·   27 Feb 2024   ·   doi:10.2460/javma.23.07.0372
reproducibility genetics dogs

2023

The Coming of Age of Nucleic Acid Vaccines during COVID-19
The Coming of Age of Nucleic Acid Vaccines during COVID-19
Halie M. Rando, Ronan Lordan, Likhitha Kolla, Elizabeth Sell, Alexandra J. Lee, ..., Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen
mSystems   ·   27 Apr 2023   ·   doi:10.1128/msystems.00928-22
manubot COVID-19
Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Halie M. Rando, Ronan Lordan, Alexandra J. Lee, Amruta Naik, Nils Wellhausen, ..., Yusha Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen
mSystems   ·   27 Apr 2023   ·   doi:10.1128/msystems.00927-22
manubot COVID-19

2022

Classifying animal breeds with the vertebrate breed ontology (VBO)
Classifying animal breeds with the vertebrate breed ontology (VBO)
Sabrina Toro, Nicolas Matentzoglu, Kathleen R. Mullen, Nicole Vasilevsky, Halie M. Rando, ..., Christopher J. Mungall, Zhi-Liang Hu, Gregoire Leroy, Imke Tammen, Frank W. Nicholas
Proceedings of the International Conference on Biomedical Ontology   ·   25 Sep 2022   ·   url:https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_1882.pdf
ontology animals domestication
Molecular and Serologic Diagnostic Technologies for SARS-CoV-2
Molecular and Serologic Diagnostic Technologies for SARS-CoV-2
Halie M. Rando, Christian Brueffer, Ronan Lordan, Anna Ada Dattoli, David Manheim, ..., David Mai, Nils Wellhausen, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene
arXiv   ·   01 Jan 2022   ·   doi:10.48550/ARXIV.2204.12598
manubot COVID-19

2021

Identification and Development of Therapeutics for COVID-19
Identification and Development of Therapeutics for COVID-19
Halie M. Rando, Nils Wellhausen, Soumita Ghosh, Alexandra J. Lee, Anna Ada Dattoli, ..., Rishi Raj Goel, YoSon Park, Simina M. Boca, Anthony Gitter, Casey S. Greene
mSystems   ·   21 Dec 2021   ·   doi:10.1128/mSystems.00233-21
manubot COVID-19
Characterizing Long COVID: Deep Phenotype of a Complex Condition
Characterizing Long COVID: Deep Phenotype of a Complex Condition
Rachel R Deer, Madeline A Rock, Nicole Vasilevsky, Leigh Carmody, Halie Rando, ..., Umit Topaloglu, George D. Vavougios, Liwei Wang, Melissa A Haendel, Peter N Robinson
eBioMedicine   ·   01 Dec 2021   ·   doi:10.1016/j.ebiom.2021.103722
ontology disease humans
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
Halie M. Rando, Adam L. MacLean, Alexandra J. Lee, Ronan Lordan, Sandipan Ray, ..., Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, Anthony Gitter, Casey S. Greene
mSystems   ·   26 Oct 2021   ·   doi:10.1128/msystems.00095-21
manubot COVID-19
An Open-Publishing Response to the COVID-19 Infodemic
An Open-Publishing Response to the COVID-19 Infodemic
Halie M. Rando, Simina M. Boca, Lucy D'Agostino McGowan, Daniel S. Himmelstein, Michael P. Robson, Vincent Rubinetti, Ryan Velazquez, Casey S. Greene, Anthony Gitter
Digital Infrastructures for Scholarly Content Objects 2021   ·   30 Sep 2021   ·   url:http://ceur-ws.org/Vol-2976/paper-2.pdf
manubot reproducibility documents
Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment
Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment
Ronan Lordan, Halie M. Rando, Casey S. Greene
mSystems   ·   29 Jun 2021   ·   doi:10.1128/mSystems.00122-21
manubot COVID-19
Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information
Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information
Halie M. Rando, Tellen D. Bennett, James Brian Byrd, Carolyn Bramante, Tiffany J. Callahan, ..., Joel H. Saltz, Anthony Solomonides, Anupam Sule, Umit Topaloglu, Melissa A. Haendel
Cold Spring Harbor Laboratory   ·   26 Mar 2021   ·   doi:10.1101/2021.03.20.21253896
ontology disease humans
Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography
Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography
Benjamin N. Sacks, Zachary T. Lounsberry, Halie M. Rando, Kristopher Kluepfel, Steven R. Fain, Sarah K. Brown, Anna V. Kukekova
Genes   ·   14 Jan 2021   ·   doi:10.3390/genes12010097
foxes genomes wildlife

2019

The Red Fox Y-Chromosome in Comparative Context
The Red Fox Y-Chromosome in Comparative Context
Halie M. Rando, William H. Wadlington, Jennifer L. Johnson, Jeremy T. Stutchman, Lyudmila N. Trut, Marta Farré, Anna V. Kukekova
Genes   ·   28 May 2019   ·   doi:10.3390/genes10060409
foxes genomes machine learning

2018

Four structural variants associated with human‐directed sociability in dogs are not found in tame red foxes (<i>Vulpes vulpes</i>)
Four structural variants associated with human‐directed sociability in dogs are not found in tame red foxes (Vulpes vulpes)
Estelle R. Bastounes, Halie M. Rando, Jennifer L. Johnson, Lyudmila N. Trut, Benjamin N. Sacks, Carlos A. Driscoll, Bridgett vonHoldt, Anna V. Kukekova
Animal Genetics   ·   10 Dec 2018   ·   doi:10.1111/age.12755
foxes genomes dogs behavior domestication
Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours
Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours
Anna V. Kukekova, Jennifer L. Johnson, Xueyan Xiang, Shaohong Feng, Shiping Liu, ..., Xu Wang, Andrew G. Clark, Gregory M. Acland, Lyudmila N. Trut, Guojie Zhang
Nature Ecology & Evolution   ·   06 Aug 2018   ·   doi:10.1038/s41559-018-0611-6
foxes genomes behavior domestication
Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly
Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly
Halie M. Rando, Marta Farré, Michael P. Robson, Naomi B. Won, Jennifer L. Johnson, ..., Jaebum Kim, Guojie Zhang, Lyudmila N. Trut, Denis M. Larkin, Anna V. Kukekova
Genes   ·   20 Jun 2018   ·   doi:10.3390/genes9060308
foxes genomes high-performance computing

2017

Development of a genotype‐by‐sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
Development of a genotype‐by‐sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
Michael E. Donaldson, Yessica Rico, Karsten Hueffer, Halie M. Rando, Anna V. Kukekova, Christopher J. Kyle
Ecology and Evolution   ·   02 Dec 2017   ·   doi:10.1002/ece3.3583
foxes genomes wildlife
Y-Chromosome Markers for the Red Fox
Y-Chromosome Markers for the Red Fox
Halie M Rando, Jeremy T Stutchman, Estelle R Bastounes, Jennifer L Johnson, Carlos A Driscoll, Christina S Barr, Lyudmila N Trut, Benjamin N Sacks, Anna V Kukekova
Journal of Heredity   ·   14 Aug 2017   ·   doi:10.1093/jhered/esx066
foxes genomes wildlife