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Research Outputs from the SI High Performance Computing Cluster

Publications and other research outputs that have acknowledged the SI HPC by referencing or including the HPC's DOI somewhere in the output. If you find a mistake or omission on this page please notify si-rdm at

If you have used the SI HPC in your research please use to acknowledge or cite this shared resource.

citations below are listed by publication date (desc)


Valente, Jonathon J., Ruth E. Bennett, Camila Gómez, Nicholas J. Bayly, Robert A. Rice, Peter P. Marra, T. Brandt Ryder, and T. Scott Sillett. “Land-Sparing and Land-Sharing Provide Complementary Benefits for Conserving Avian Biodiversity in Coffee-Growing Landscapes.” Biological Conservation 270 (June 2022): 109568.

Choi, Jinkyul, Daven K. Henze, Hansen Cao, Caroline R. Nowlan, Gonzalo González Abad, Hyeong‐Ahn Kwon, Hyung‐Min Lee, et al. “An Inversion Framework for Optimizing Non‐Methane VOC Emissions Using Remote Sensing and Airborne Observations in Northeast Asia During the KORUS‐AQ Field Campaign.” Journal of Geophysical Research: Atmospheres 127, no. 7 (April 16, 2022).

Capo, Eric, Benjamin D. Peterson, Minjae Kim, Daniel S. Jones, Silvia G. Acinas, Marc Amyot, Stefan Bertilsson, et al. “A Consensus Protocol for the Recovery of Mercury Methylation Genes from Metagenomes.” Preprint. Microbiology, March 14, 2022.

Jasso-Martínez, Jovana M., Bernardo F. Santos, Alejandro Zaldívar-Riverón, Jose Fernandez-Triana, Barbara J. Sharanowski, Robin Richter, Jeremy R. Dettman, Bonnie B. Blaimer, Seán G. Brady, and Robert R. Kula. “Phylogenomics of Braconid Wasps (Hymenoptera, Braconidae) Sheds Light on Classification and the Evolution of Parasitoid Life History Traits.” Molecular Phylogenetics and Evolution, March 2022, 107452.

Segura-Trujillo, Cintya A, Sergio Ticul Álvarez-Castañeda, Susette Castañeda-Rico, and Jesús E Maldonado. “Taxonomic versus Ecological Prey Traits among Arthropodophagous Bats: Implications for Surveying Trophic Partitioning Patterns.” Edited by Ricardo Ojeda. Journal of Mammalogy, March 16, 2022, gyac027.

Sun, Kang, Mahdi Yousefi, Christopher Chan Miller, Kelly Chance, Gonzalo González Abad, Iouli E. Gordon, Xiong Liu, Ewan O’Sullivan, Christopher E. Sioris, and Steven C. Wofsy. “An Optimal Estimation-Based Retrieval of Upper Atmospheric Oxygen Airglow and Temperature from SCIAMACHY Limb Observations.” Preprint. Gases/Remote Sensing/Data Processing and Information Retrieval, March 15, 2022.

Liu, Bin‐Bin, Chen Ren, Myounghai Kwak, Richard G.J. Hodel, Chao Xu, Jian He, Wen‐Bin Zhou, et al. “Phylogenomic Conflict Analyses in the Apple Genus Malus s.l. Reveal Widespread Hybridization and Allopolyploidy Driving Diversification, with Insights into the Complex Biogeographic History in the Northern Hemisphere.” Journal of Integrative Plant Biology, March 11, 2022, jipb.13246.

Canty, Steven W. J., John Paul Kennedy, Graeme Fox, Kenan Matterson, Vanessa L. González, Mayra L. Núñez-Vallecillo, Richard F. Preziosi, and Jennifer K. Rowntree. “Mangrove Diversity Is More than Fringe Deep.” Scientific Reports 12, no. 1 (February 2022): 1695.

Finenko, Artem A., Bruno Bézard, Iouli E. Gordon, Daniil N. Chistikov, Sergei E. Lokshtanov, Sergey V. Petrov, and Andrey A. Vigasin. “Trajectory-Based Simulation of Far-Infrared Collision-Induced Absorption Profiles of CH 4 –N 2 for Modeling Titan’s Atmosphere.” The Astrophysical Journal Supplement Series 258, no. 2 (February 1, 2022): 33.

Shen, Chengcai, Bin Chen, Katharine K. Reeves, Sijie Yu, Vanessa Polito, and Xiaoyan Xie. “The Origin of Underdense Plasma Downflows Associated with Magnetic Reconnection in Solar Flares.” Nature Astronomy, January 27, 2022.

Edie, Stewart M., Safia C. Khouja, Katie S. Collins, Nicholas M. A. Crouch, and David Jablonski. “Evolutionary Modularity, Integration and Disparity in an Accretionary Skeleton: Analysis of Venerid Bivalvia.” Proceedings of the Royal Society B: Biological Sciences 289, no. 1967 (January 26, 2022): 20211199.

Hodel, Richard G. J., Elizabeth A. Zimmer, Bin-Bin Liu, and Jun Wen. “Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae—Gillenieae Clade.” Frontiers in Plant Science 12 (January 25, 2022): 820997.

Hanisch, Priscila Elena, Jeffrey Sosa-Calvo, and Ted R Schultz. “The Last Piece of the Puzzle? Phylogenetic Position and Natural History of the Monotypic Fungus-Farming Ant Genus Paramycetophylax (Formicidae: Attini).” Edited by Gabriela P Camacho. Insect Systematics and Diversity 6, no. 1 (January 1, 2022): 11.


Neves, Karen, Bernardo Santos, Ted Schultz, Dietrich Gotzek, Rodolfo C.R. Abreu, Giselda Durigan, and Heraldo L. Vasconcelos. “Woody Encroachment Affects Multiple Dimensions of Ant Diversity in a Neotropical Savanna.” Preprint. In Review, December 29, 2021.

Bossert, Silas, Thomas J. Wood, Sébastien Patiny, Denis Michez, Eduardo A. B. Almeida, Robert L. Minckley, Laurence Packer, et al. “Phylogeny, Biogeography and Diversification of the Mining Bee Family Andrenidae.” Systematic Entomology, December 21, 2021, syen.12530.

Johnson, Maggie D., Jarrod J. Scott, Matthieu Leray, Noelle Lucey, Lucia M. Rodriguez Bravo, William L. Wied, and Andrew H. Altieri. “Rapid Ecosystem-Scale Consequences of Acute Deoxygenation on a Caribbean Coral Reef.” Nature Communications 12, no. 1 (December 2021): 4522.

Myers, Edward A. “Genome-Wide Data Reveal Extensive Gene Flow during the Diversification of the Western Rattlesnakes (Viperidae: Crotalinae: Crotalus).” Molecular Phylogenetics and Evolution 165 (December 2021): 107313.

Shen, Chengcai, Bin Chen, Katharine K. Reeves, Sijie Yu, Vanessa Polito, and Xiaoyan Xie. “The Origin of Underdense Plasma Downflows Associated with Magnetic Reconnection in Solar Flares.” ArXiv:2111.11407 [Astro-Ph, Physics:Physics], November 22, 2021.

Mulder, Kevin.P., Lucía Alarcón-Ríos, Alfredo G. Nicieza, Robert C. Fleischer, Rayna C. Bell, and Guillermo Velo-Antón. “Independent Evolutionary Transitions to Pueriparity across Multiple Timescales in the Viviparous Genus Salamandra.” Molecular Phylogenetics and Evolution, November 2021, 107347.

Myers, Edward A, Daniel G Mulcahy, Bryan Falk, Kiyomi Johnson, Marina Carbi, and Kevin de Queiroz. “Interspecific Gene Flow and Mitochondrial Genome Capture During the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae).” Systematic Biology, November 4, 2021, syab089.

Liu, Bin-Bin, Chen Ren, Myounghai Kwak, Richard G.J. Hodel, Chao Xu, Jian He, Wen-Bin Zhou, et al. “Phylogenomic Analyses in the Apple Genus Malus s.l. Reveal Widespread Hybridization and Allopolyploidy Driving the Diversifications, with Insights into the Complex Biogeographic History in the Northern Hemisphere.” Preprint. Evolutionary Biology, October 14, 2021.

Arias, Carlos F, Rebecca B Dikow, W Owen McMillan, and Luis F De Leon. “De Novo Genome Assembly of the Electric Fish Brachyhypopomus Occidentalis (Hypopomidae, Gymnotiformes).” Edited by Bonnie Fraser. Genome Biology and Evolution, September 28, 2021, evab223.

Simon, Marcelo F., J. Moises F Mendoza, Hsiao‐Lei Liu, Márcio Lacerda Lopes Martins, Sergei V. Drovetski, Natalia A. S. Przelomska, Hope Loiselle, et al. “Phylogenomic Analysis Points to a South American Origin of Manihot and Illuminates the Primary Gene Pool of Cassava.” New Phytologist, September 19, 2021, nph.17743.

Barrera, Corina A., Jeffrey Sosa‐Calvo, Ted R. Schultz, Christian Rabeling, and Maurício Bacci. “Phylogenomic Reconstruction Reveals New Insights into the Evolution and Biogeography of Atta Leaf‐cutting Ants (Hymenoptera: Formicidae).” Systematic Entomology, September 3, 2021, syen.12513.

Gainett, Guilherme, Vanessa L. González, Jesús A. Ballesteros, Emily V. W. Setton, Caitlin M. Baker, Leonardo Barolo Gargiulo, Carlos E. Santibáñez-López, Jonathan A. Coddington, and Prashant P. Sharma. “The Genome of a Daddy-Long-Legs (Opiliones) Illuminates the Evolution of Arachnid Appendages.” Proceedings of the Royal Society B: Biological Sciences 288, no. 1956 (August 11, 2021): 20211168.

Casey, Jordan M., Emma Ransome, Allen G. Collins, Angka Mahardini, Eka M. Kurniasih, Andrianus Sembiring, Nina M. D. Schiettekatte, et al. “DNA Metabarcoding Marker Choice Skews Perception of Marine Eukaryotic Biodiversity.” Environmental DNA, August 10, 2021, edn3.245.

Baloković, M., S. E. Cabral, L. Brenneman, and C. M. Urry. “Properties of the Obscuring Torus in NGC 1052 from Multiepoch Broadband X-Ray Spectroscopy.” The Astrophysical Journal 916, no. 2 (August 1, 2021): 90.

Wang, Huiqun, and Gonzalo González Abad. “Cloud Masks Derived from the Mars Daily Global Maps and an Application to the Tropical Cloud Belt on Mars.” Geosciences 11, no. 8 (July 31, 2021): 324.

Kaganer, Alyssa W., Leah D. Nagel, Tess E. Youker‐Smith, Elizabeth M. Bunting, and Matthew P. Hare. “Environmental DNA‐derived Pathogen Gene Sequences Can Expand Surveillance When Pathogen Titers Are Decoupled in EDNA and Hosts.” Environmental DNA, July 22, 2021, edn3.240.

Vollmer, Nicole L., Patricia E. Rosel, Keith D. Mullin, Lori H. Schwacke, Lance P. Garrison, Brian C. Balmer, Kevin Barry, et al. “Assessing Common Bottlenose Dolphin ( Tursiops truncatus ) Population Structure in Mississippi Sound and Coastal Waters of the North Central Gulf of Mexico.” Aquatic Conservation: Marine and Freshwater Ecosystems, July 16, 2021, aqc.3668.

Pappalardo, Paula, Allen G Collins, Katrina M Pagenkopp Lohan, Kate M Hanson, Sarit B Truskey, William Jaeckle, Cheryl Lewis Ames, et al. “The Role of Taxonomic Expertise in Interpretation of Metabarcoding Studies.” Edited by William Grant. ICES Journal of Marine Science, May 17, 2021, fsab082.

O’Connell, Kyle A., Ivan Prates, Lauren A. Scheinberg, Kevin P. Mulder, and Rayna C. Bell. “Speciation and Secondary Contact in a Fossorial Island Endemic, the São Tomé Caecilian.” Molecular Ecology, May 10, 2021, mec.15928.

Santos, Bernardo F., David B. Wahl, Pascal Rousse, Andrew M. R. Bennett, Robert Kula, and Seán G. Brady. “Phylogenomics of Ichneumoninae (Hymenoptera, Ichneumonidae) Reveals Pervasive Morphological Convergence and the Shortcomings of Previous Classifications.” Systematic Entomology, April 24, 2021, syen.12484.

Bak, Juseon, Xiong Liu, Robert Spurr, Kai Yang, Caroline R. Nowlan, Christopher Chan Miller, Gonzalo Gonzalez Abad, and Kelly Chance. “Radiative Transfer Acceleration Based on the Principal Component Analysis and Lookup Table of Corrections: Optimization and Application to UV Ozone Profile Retrievals.” Atmospheric Measurement Techniques 14, no. 4 (April 7, 2021): 2659–72.

Videvall, Elin, Kristina L. Paxton, Michael G. Campana, Loren Cassin‐Sackett, Carter T. Atkinson, and Robert C. Fleischer. “Transcriptome Assembly and Differential Gene Expression of the Invasive Avian Malaria Parasite Plasmodium Relictum in Hawaiʻi.” Ecology and Evolution, March 27, 2021, ece3.7401.

Venkatraman, Madhvi, Robert C Fleischer, and Mirian T N Tsuchiya. “Comparative Analysis of Annotation Pipelines Using the First Japanese White-Eye ( Zosterops Japonicus ) Genome.” Edited by Bonnie Fraser. Genome Biology and Evolution, March 24, 2021, evab063.

Souri, Amir H., Kelly Chance, Juseon Bak, Caroline R. Nowlan, Gonzalo González Abad, Yeonjin Jung, David C. Wong, Jingqiu Mao, and Xiong Liu. “Unraveling Pathways of Elevated Ozone Induced by the 2020 Lockdown in Europe by an Observationally Constrained Regional Model: Non-Linear Joint Inversion of NOx and VOC Emissions Using TROPOMI.” Preprint. Gases/Atmospheric Modelling/Troposphere/Chemistry (chemical composition and reactions), March 12, 2021.

G. J. Hodel, Richard, Elizabeth Zimmer, and Jun Wen. “A Phylogenomic Approach Resolves the Backbone of Prunus (Rosaceae) and Identifies Signals of Hybridization and Allopolyploidy.” Molecular Phylogenetics and Evolution, February 2021, 107118.

Schott, Ryan K, Rayna C Bell, Ellis R Loew, Kate N Thomas, David J Gower, Jeffrey W Streicher, and Matthew K Fujita. “Genomic and Spectral Visual Adaptation in Southern Leopard Frogs during the Ontogenetic Transition from Aquatic to Terrestrial Light Environments.” Preprint. Genomics, February 20, 2021.

Gainett, Guilherme, Vanessa L. González, Jesús A. Ballesteros, Emily V. W. Setton, Caitlin M. Baker, Leonardo Barolo Gargiulo, Carlos E. Santibáñez-López, Jonathan A. Coddington, and Prashant P. Sharma. “The Genome of a Daddy-Long-Legs (Opiliones) Illuminates the Evolution of Arachnid Appendages and Chelicerate Genome Architecture.” Preprint. Developmental Biology, January 12, 2021.


Abreu Júnior, Edson Fiedler de. “Phylogenomics, Diversification, and Biogeography of Neotropical Squirrels (Sciurillinae and Sciurinae: Sciurini).” Doutorado em Ecologia Aplicada, Universidade de São Paulo, 2020.

Roa-Varón, Adela, Rebecca B Dikow, Giorgio Carnevale, Luke Tornabene, Carole C Baldwin, Chenhong Li, and Eric J Hilton. “Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes).” Systematic Biology, December 21, 2020,

Tsuchiya, Mirian T N, Rebecca B Dikow, Klaus-Peter Koepfli, Paul B Frandsen, Larry L Rockwood, and Jesús E Maldonado. “Whole Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou ( Potos Flavus ) and Northern Raccoon ( Procyon Lotor ).” Edited by Bonnie Fraser. Genome Biology and Evolution, December 17, 2020,

Fortuna-Perez, Ana Paula, Cristina Ribeiro Marinho, Mohammad Vatanparast, Wanderleia de Vargas, João Ricardo Vieira Iganci, Gwilym Peter Lewis, Elisa Silva Cândido, et al. “Secretory Structures of the Adesmia Clade (Leguminosae): Implications for Evolutionary Adaptation in Dry Environments.” Perspectives in Plant Ecology, Evolution and Systematics, December 2020,

Kistler, Logan, Heather B. Thakar, Amber M. VanDerwarker, Alejandra Domic, Anders Bergström, Richard J. George, Thomas K. Harper, Robin G. Allaby, Kenneth Hirth, and Douglas J. Kennett. “Archaeological Central American Maize Genomes Suggest Ancient Gene Flow from South America.” Proceedings of the National Academy of Sciences, December 14, 2020,

Harbach, Laura M., Sofia P. Moschou, Cecilia Garraffo, Jeremy J. Drake, Julián D. Alvarado-Gómez, Ofer Cohen, and Federico Fraschetti. “Stellar Winds Drive Strong Variations in Exoplanet Evaporative Outflows and Transit Absorption Signatures.” ArXiv:2012.05922 [Astro-Ph, Physics:Physics], December 10, 2020.

Olsen, Lindsey K., Jacqueline Heckenhauer, John S. Sproul, Rebecca B. Dikow, Vanessa L. Gonzalez, Matthew P. Kweskin, Adam M. Taylor, et al. “Draft Genome Assemblies and Annotations of Agrypnia Vestita Walker, and Hesperophylax Magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera).” Preprint. Genomics, November 17, 2020.

Cândido, Elisa Silva, Mohammad Vatanparast, Wanderleia de Vargas, Luísa M P A Bezerra, Gwilym P Lewis, Vidal F Mansano, André O Simões, et al. “Molecular Phylogenetic Insights into the Evolution of Eriosema (Fabaceae): A Recent Tropical Savanna-Adapted Genus.” Botanical Journal of the Linnean Society 194, no. 4 (November 12, 2020): 439–59.

McDonough, Molly M., Adam W. Ferguson, Robert C. Dowler, Matthew E. Gompper, and Jesús E. Maldonado. “Phylogenomic Systematics of the Spotted Skunks (Carnivora, Mephitidae, Spilogale ): Additional Species Diversity and Pleistocene Climate Change as a Major Driver of Diversification.” Preprint. Evolutionary Biology, October 25, 2020.

Conway, E. K., Gordon, I. E., Tennyson, J., Polyansky, O. L., Yurchenko, S. N., and Chance, K. 2020. “A semi-empirical potential energy surface and line list for H216O extending into the near-ultraviolet.” Atmospheric Chemistry and Physics, 20:10015–10027. doi:10.5194/acp-20-10015-2020.

Souri, A. H., Nowlan, C. R., González Abad, G., Zhu, L., Blake, D. R., Fried, A., … Chance, K. 2020. “An inversion of NOx and non-methane volatile organic compound (NMVOC) emissions using satellite observations during the KORUS-AQ campaign and implications for surface ozone over East Asia.” Atmospheric Chemistry and Physics, 20:9837–9854. doi:10.5194/acp-20-9837-2020.

Moraes, A. P., Vatanparast, M., Polido, C., Marques, A., Souza, G., Fortuna-Perez, A. P., and Forni-Martins, E. R. 2020. “Chromosome number evolution in dalbergioid legumes (Papilionoideae, Leguminosae).” Brazilian Journal of Botany.

Dommain, R., Andama, M., McDonough, M. M., Prado, N. A., Goldhammer, T., Potts, R., … Campana, M. G. 2020. “The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda.” Frontiers in Ecology and Evolution, 8:218. doi:10.3389/fevo.2020.00218.

Jacovich, T., Beniamini, P., and van der Horst, A. 2020. “Modeling Synchrotron Self-Compton and Klein-Nishina Effects in Gamma-Ray Burst Afterglows.” ArXiv:2007.04418 [Astro-Ph].

White, A. E., R. B. Dikow, M. Baugh, A. Jenkins, and P. B. Frandsen. 2020. Generating segmentation masks of herbarium specimens and a data set for training segmentation models using deep learning. Applications in Plant Sciences 8(6): e11352

de Abreu-Jr, E. F., Pavan, S. E., Tsuchiya, M. T., Wilson, D. E., Percequillo, A. R., and Maldonado, J. E. 2020. “Museomics of tree squirrels: A dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul.”

Menezes, R. S., Lloyd, M. W., and Brady, S. G. 2020. Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity. Proceedings of the Royal Society B, 287:20200480.

Torres, G., Melis, C., Kraus, A. L., Dupuy, T. J., Chilcote, J. K., and Crepp, J. R. 2020. Dynamical masses for the Pleiades binary system HII-2147. ArXiv Preprint ArXiv:2006.06670.

Tsuchiya, M. T., Dikow, R. B., and Cassin-Sackett, L. 2020. First genome sequence of the Gunnison’s prairie dog (Cynomys gunnisoni), a keystone species and player in the transmission of sylvatic plague. Genome Biology and Evolution, 12:618–625.



Tremblay, G. R., F. Combes, J. B. R. Oonk, H. R. Russell, M. A. McDonald, M. Gaspari, B. Husemann, et al. “A Galaxy-Scale Fountain of Cold Molecular Gas Pumped by a Black Hole.” The Astrophysical Journal 865, no. 1 (September 17, 2018): 13.

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