Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data. - Joseph Schlecht; Matthew E. Kaplan; Kobus Barnard; Tatiana Karafet; Michael F. Hammer; Nirav C. Merchant (PLoS Comput. Biol., 2008)

Building an environment to facilitate discoveries for plant sciences. - Andrew Lenards; Nirav C. Merchant; Dan Stanzione (SC-GCE, 2011)

iPlant atmosphere: a gateway to cloud infrastructure for the plant sciences. - Edwin Skidmore; Seung Jin Kim; Sangeeta Kuchimanchi; Sriramu Singaram; Nirav C. Merchant; Dan Stanzione (SC-GCE, 2011)

Bisque: Advances in Bioimage Databases. - Kristian Kvilekval; Dmitry V. Fedorov; Utkarsh Gaur; Steve Goff; Nirav C. Merchant; B. S. Manjunath; Ambuj K. Singh (IEEE Data Eng. Bull., 2012)

Building an open Genome Wide Association Study (GWAS) platform. - Liya Wang; Doreen Ware; Nirav C. Merchant; Carol Lushbough (CLUSTER, 2013)

Jetstream: a self-provisioned, scalable science and engineering cloud environment. - Craig A. Stewart; Timothy M. Cockerill; Ian T. Foster; David Y. Hancock; Nirav C. Merchant; Edwin Skidmore; Daniel Stanzione; James Taylor 001; Steven Tuecke; George W. Turner; Matthew Vaughn; Niall I. Gaffney (XSEDE, 2015)

A genome-wide association study platform built on iPlant cyber-infrastructure. - Liya Wang; Doreen Ware; Carol Lushbough; Nirav C. Merchant; Lincoln Stein (Concurr. Comput. Pract. Exp., 2015)

Jetstream: performance, early experiences, and early results. - Craig A. Stewart; David Y. Hancock; Matthew Vaughn; Jeremy Fischer; Tim Cockerill; Liming Lee; Nirav C. Merchant; Therese Miller; John Michael Lowe; Daniel C. Stanzione Jr.; James Taylor 001; Edwin Skidmore (XSEDE, 2016)

Scaling GIS analysis tasks from the desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study of project-based learning and cyberinfrastructure concepts. - Tyson Lee Swetnam; J. D. Pelletier; Craig Rasmussen; N. R. Callahan; Nirav C. Merchant; Eric Lyons 002; Mats Rynge; Yan Liu 009; Viswanath Nandigam; Christopher J. Crosby (XSEDE, 2016)

PGen: large-scale genomic variations analysis workflow and browser in SoyKB. - Yang Liu; Saad M. Khan; Juexin Wang; Mats Rynge; Yuanxun Zhang; Shuai Zeng; Shiyuan Chen; João V. Maldonado dos Santos; Babu Valliyodan; Prasad Calyam; Nirav C. Merchant; Henry T. Nguyen; et al. (BMC Bioinform., 2016)

Bringing your tools to CyVerse Discovery Environment using Docker. - Upendra Kumar Devisetty; Kathleen Kennedy; Paul Sarando; Nirav C. Merchant; Eric Lyons 002 (F1000Research, 2016)

GRAM: global research activity map. - Randy Burd; Kimberly Andrews Espy; Md. Iqbal Hossain 001; Stephen G. Kobourov; Nirav C. Merchant; Helen C. Purchase (AVI, 2018)

MAKER as a Service: Moving HPC Applications to Jetstream Cloud. - Nicholas L. Hazekamp; Upendra Kumar Devisetty; Nirav C. Merchant; Douglas Thain (IC2E, 2018)

Human-Centric Programming in the Large - Command Languages to Scalable Cyber Training. - Prasun Dewan; Blake L. Joyce; Nirav C. Merchant (VL/HCC, 2018)

The principles of tomorrow's university. - Daniel S. Katz; Gabrielle Allen; Lorena A. Barba; Devin R. Berg; Holly Bik; Carl Boettiger; Christine L. Borgman; C. Titus Brown; Stuart Buck; Randy Burd; Anita de Waard; Martin Paul Eve; et al. (F1000Research, 2018)

Deep Learning Classification of Chest X-Ray Images. - Mohammad S. Majdi; Khalil N. Salman; Michael F. Morris; Nirav C. Merchant; Jeffrey J. Rodríguez (SSIAI, 2020)

Ten simple rules for organizing a data science workshop. - Alise J. Ponsero; Ryan Bartelme; Gustavo de Oliveira Almeida; Alex Bigelow; Reetu Tuteja; Holly Ellingson; Tyson Lee Swetnam; Nirav C. Merchant; Maliaca Oxnam; Eric Lyons 002 (PLoS Comput. Biol., 2020)

Jetstream2: Accelerating cloud computing via Jetstream. - David Y. Hancock; Jeremy Fischer; John Michael Lowe; Winona Snapp-Childs; Marlon E. Pierce; Suresh Marru; J. Eric Coulter; Matthew Vaughn; Brian W. Beck; Nirav C. Merchant; Edwin Skidmore; Gwen A. Jacobs (PEARC, 2021)

Ten simple rules to cultivate transdisciplinary collaboration in data science. - Faryad Sahneh; Meghan A. Balk; Marina Kisley; Chi-Kwan Chan; Mercury Fox; Brian Nord; Eric Lyons 002; Tyson Lee Swetnam; Daniela Huppenkothen; Will Sutherland; Ramona L. Walls; Daven P. Quinn; et al. (PLoS Comput. Biol., 2021)

AZCOVIDTXT: Winning the Battle Against COVID-19 One Text at a Time. - M. Sriram Iyengar; Stephen Rains; Kacey Ernst; Nirav C. Merchant; Tracy Crane; Paulina Colombo; Maliaca Oxnam (AMIA, 2022)

MegaStitch: Robust Large-Scale Image Stitching. - Ariyan Zarei; Emmanuel Gonzalez; Nirav C. Merchant; Duke Pauli; Eric Lyons 002; Kobus Barnard (IEEE Trans. Geosci. Remote. Sens., 2022)

Resilience Informatics for Public Health. - M. Sriram Iyengar; Nirav C. Merchant; Kacey Ernst; Stephen Rains; Mona Arora; Maiya G. Block Ngaybe; Myla Gonzalez (MedInfo, 2023)

Cloud Computing for Research and Education Gets a Sweet Upgrade with CACAO. - Edwin Skidmore; Michele Cosi; Tyson Lee Swetnam; Nirav C. Merchant; Zhouyun Xu; Illyoung Choi; Sean Davey; Jeremy Frady; Mariah Wall; Michelle Yung (PEARC, 2023)

Deep learning powered real-time identification of insects using citizen science data. - Shivani Chiranjeevi; Mojdeh Saadati; Zi K. Deng; Jayanth Koushik; Talukder Z. Jubery; Daren S. Mueller; Matthew E. O. Neal; Nirav C. Merchant; Aarti Singh; Asheesh K. Singh; Soumik Sarkar; Arti Singh; et al. (CoRR, 2023)

BioTrove: A Large Curated Image Dataset Enabling AI for Biodiversity. - Chih-Hsuan Yang; Benjamin Feuer; Talukder Zaki Jubery; Zi K. Deng; Andre Nakkab; Md. Zahid Hasan; Shivani Chiranjeevi; Kelly O. Marshall; Nirmal Baishnab; Asheesh Kumar Singh; Arti Singh; Soumik Sarkar; et al. (NeurIPS, 2024)

AIIRA: AI Institute for Resilient Agriculture. - Baskar Ganapathysubramanian; Jessica M. P. Bell; George Kantor; Nirav C. Merchant; Soumik Sarkar; Patrick S. Schnable; Michelle Segovia; Arti Singh; Asheesh K. Singh (AI Mag., 2024)

Arboretum: A Large Multimodal Dataset Enabling AI for Biodiversity. - Chih-Hsuan Yang; Benjamin Feuer; Zaki Jubery; Zi K. Deng; Andre Nakkab; Md. Zahid Hasan; Shivani Chiranjeevi; Kelly O. Marshall; Nirmal Baishnab; Asheesh K. Singh; Arti Singh; Soumik Sarkar; et al. (CoRR, 2024)

CyVerse: Cyberinfrastructure for open science. - Tyson L. Swetnam; Parker B. Antin; Ryan Bartelme; Alexander Bucksch; David Camhy; Greg Chism; Illyoung Choi; Amanda M. Cooksey; Michele Cosi; Cindy Cowen; Michael Culshaw-Maurer; Robert Davey; et al. (PLoS Comput. Biol., 2024)

AI-VERDE: A Gateway for Egalitarian Access to Large Language Model-Based Resources For Educational Institutions. - Paul Mithun; Enrique Noriega-Atala; Nirav C. Merchant; Edwin Skidmore (CoRR, 2025)

WeedNet: A Foundation Model-Based Global-to-Local AI Approach for Real-Time Weed Species Identification and Classification. - Yanben Shen; Timilehin Ayanlade; Venkata Naresh Boddepalli; Mojdeh Saadati; Ashlyn Rairdin; Zi K. Deng; Muhammad Arbab Arshad; Aditya Balu; Daren S. Mueller; Asheesh K. Singh; Wesley Everman; Nirav C. Merchant; et al. (CoRR, 2025)

TerraIncognita: A Dynamic Benchmark for Species Discovery Using Frontier Models. - Shivani Chiranjeevi; Hossein Zaremehrjerdi; Zi K. Deng; Talukder Z. Jubery; Ari Grele; Arti Singh; Asheesh Kumar Singh; Soumik Sarkar; Nirav C. Merchant; Harold F. Greeney; Baskar Ganapathysubramanian; Chinmay Hegde (CoRR, 2025)