Publications

Peer-reviewed research, conference papers, and preprints from SAIL and its collaborators.

2026

  1. Plant Litter Trait Variation Between Native and Invasive Species Across Steep Climate Gradients in the Hawaiian Islands
    Manichanh Satdichanh, Rebecca Ostertag, William Harrigan, Mahdi Belcaid, and Kasey E Barton
    Ecology and Evolution, 2026
  2. Building Collaborative Intelligence: The Translational Journey of the Smart Amplified Group Environment Across Research, Education, and Practice
    Jason Leigh, Luc Renambot, Ryan Theriot, Lance Long, Chris Lee, Jesse Harden, Nurit Kirshenbaum, Mahdi Belcaid, Chris North, Andrew Johnson, and Maxine Brown
    SN Computer Science, 2026
  3. Analyzing planning meetings using large language models
    Dan Milz, Jennifer A Kagan, Mahdi Belcaid, and Guy Levy
    Planning Practice & Research, 2026
  4. Extending Protein Language Models to a Viral Genomic Scale Using Biologically Induced Sparse Attention
    Thibaut Dejean, Barbra D Ferrell, Zachary D Schreiber, and 5 more authors
    GigaScience, 2026

2025

  1. Fine-Tuning Protein Language Models Unlocks the Potential of Underrepresented Viral Proteomes
    Rajan Sawhney, Barbra Ferrell, Thibaut Dejean, and 5 more authors
    PeerJ, 2025
  2. Harnessing Hierarchical Clustering in Salience-Driven Text Summarization
    Akib Sadmanee, Sukhwa Hong, Jason Leigh, and Mahdi Belcaid
    In Americas' Conference on Information Systems (AMCIS), 2025
  3. Machine Learning-Based Characterization of Bacillus anthracis Phenotypes from pXO1 Plasmid Proteins
    William Harrigan, Thi H A La, Prashant Dahal, Mahdi Belcaid, and Michael H Norris
    Pathogens, 2025
  4. Focusing Events and Public Participation: An Analysis of Public Deliberation Following the Maui Wildfires Using Large Language Models
    Dan Milz, Jennifer Kagan, and Mahdi Belcaid
    In 82nd Annual Midwest Political Science Association (MPSA) Conference, 2025

2024

  1. Space to Teach: Content-Rich Canvases for Visually-Intensive Education
    Jesse Harden, Nurit Kirshenbaum, Roderick Tabalba, and 8 more authors
    In 2024 IEEE VIS Workshop on Visualization Education, Literacy, and Activities (EduVIS), 2024
  2. Tracking sero-molecular trends of swine brucellosis in Hawaiʻi and the central Pacific
    Thi H A La, Ian A McMillan, Prashant Dahal, Andrew H Burger, Mahdi Belcaid, Darrin M Phelps, Samuel M Goldstein, Vienna R Brown, and Michael H Norris
    Frontiers in Public Health, 2024
  3. Improvements in viral gene annotation using large language models and soft alignments
    William L Harrigan, Barbra D Ferrell, K Eric Wommack, and 3 more authors
    BMC bioinformatics, 2024
  4. Analyzing Participatory Planning Meetings Using Large Language Models
    Dan Milz, Jennifer Kagan, and Mahdi Belcaid
    In Proceedings of the ACSP 2024 Annual Conference, 2024

2023

  1. Reflecting on the Scalable Adaptive Graphics Environment Team’s 20-Year Translational Research Endeavor in Digital Collaboration Tools
    Mahdi Belcaid, Jason Leigh, Ryan Theriot, and 8 more authors
    Computing in Science & Engineering, 2023
  2. "There is no reason anybody should be using 1D anymore": Design and Evaluation of 2D Jupyter Notebooks
    Jesse Harden, Elizabeth Christman, Nurit Kirshenbaum, and 3 more authors
    2023

2022

  1. Leveraging deep contrastive learning for semantic interaction
    Mahdi Belcaid, Alberto Gonzalez Martinez, and Jason Leigh
    PeerJ Computer Science, 2022
  2. A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes
    Anthony S Amend, Sean OI Swift, John L Darcy, Mahdi Belcaid, Craig E Nelson, Joshua Buchanan, Nicolas Cetraro, Kauaoa MS Fraiola, Kiana Frank, Kacie Kajihara, and others
    Proceedings of the National Academy of Sciences, 2022
  3. Taming DNA clustering in massive datasets with SLYMFAST
    Mahdi Belcaid, Cedric Arisdakessian, and Yuliia Kravchenko
    ACM SIGAPP Applied Computing Review, 2022
  4. The C-MĀIKI gateway: a modern science platform for analyzing microbiome data
    Sean Cleveland, Cedric Arisdakessian, Craig Nelson, Mahdi Belcaid, Kiana Frank, and Gwen Jacobs
    2022

2021

  1. Efficient DNA sequence partitioning using probabilistic subsets and hypergraphs
    Mahdi Belcaid, Cedric Arisdakessian, and Yuliia Kravchenko
    2021
  2. Traces of time through space: Advantages of creating complex canvases in collaborative meetings
    Nurit Kirshenbaum, Kylie Davidson, Jesse Harden, Chris North, Dylan Kobayashi, Ryan Theriot, Roderick S Tabalba Jr, Michael L Rogers, Mahdi Belcaid, Andrew T Burks, and others
    Proceedings of the ACM on Human-Computer Interaction, 2021
  3. CoCoNet: an efficient deep learning tool for viral metagenome binning
    C{\'e}dric G Arisdakessian, Olivia D Nigro, Grieg F Steward, and 2 more authors
    Bioinformatics, 2021
  4. Securing Collaborative Work in Wide-band Display Environments
    Krishna Bharadwaj, Andrew Burks, Andrew Johnson, Lance Long, Luc Renambot, Maxine Brown, Dylan Kobayashi, Mahdi Belcaid, Nurit Kirshenbaum, Roderick Tabalba, and others
    2021
  5. The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance
    Andrea J Jani, Jessie Bushell, C{\'e}dric G Arisdakessian, Mahdi Belcaid, Daniel M Boiano, Cathy Brown, and Roland A Knapp
    The ISME Journal, 2021
  6. DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
    Jordan M Casey, Emma Ransome, Allen G Collins, Angka Mahardini, Eka M Kurniasih, Andrianus Sembiring, Nina MD Schiettekatte, Ni Kadek Dita Cahyani, Aji Wahyu Anggoro, Mikaela Moore, Abby Uehling, Mahdi Belcaid, and others
    Environmental DNA, 2021

2020

  1. Transcriptional regulation of prolactin in a euryhaline teleost: Characterisation of gene promoters through in silico and transcriptome analyses
    Andre P Seale, Gardi Hewage Tharindu Malintha, Fritzie T Celino-Brady, Tony Head, Mahdi Belcaid, Yoko Yamaguchi, Darren T Lerner, David A Baltzegar, Russell J Borski, Zoia R Stoytcheva, and others
    Journal of neuroendocrinology, 2020
  2. MetaFlow|mics: scalable and reproducible nextflow pipelines for the analysis of microbiome marker data
    C{\'e}dric Arisdakessian, Sean B Cleveland, and Mahdi Belcaid
    2020
  3. Transcriptome profile of nicotinic receptor-linked sensitization of beta amyloid neurotoxicity
    Komal Arora, Mahdi Belcaid, Megan J Lantz, Ruth Taketa, and Robert A Nichols
    Scientific reports, 2020

2019

  1. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods
    Mahdi Belcaid, Giorgio Casaburi, Sarah J McAnulty, Hannah Schmidbaur, Andrea M Suria, Silvia Moriano-Gutierrez, M Sabrina Pankey, Todd H Oakley, Natacha Kremer, Eric J Koch, and Andrew J Collins
    Proceedings of the National Academy of Sciences, 2019
  2. Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression
    Silvia Moriano-Gutierrez, Eric J Koch, Hailey Bussan, Kymberleigh Romano, Mahdi Belcaid, Federico E Rey, Edward G Ruby, and Margaret J McFall-Ngai
    Proceedings of the National Academy of Sciences, 2019
  3. Usage Patterns of Wideband Display Environments In e-Science Research, Development and Training
    Jason Leigh, Dylan Kobayashi, Nurit Kirshenbaum, Troy Wooton, Alberto Gonzalez, Luc Renambot, Andrew Johnson, Maxine Brown, Andrew Burks, Krishna Bharadwaj, Arthur Nishimoto, Lance Long, Jason Haga, John Burns, Francis Cristobal, Jared McLean, Roberto Pelayo, and Mahdi Belcaid
    2019

2018

  1. Detecting anomalies in the Cytochrome C Oxidase I amplicon sequences using minimum scoring segments
    Mahdi Belcaid, and Guylaine Poisson
    2018

2017

  1. A profile-based probabilistic approach for the detection of anomalies in the cytochrome C oxidase I amplicon sequences
    Mahdi Belcaid, and Guylaine Poisson
    2017
  2. Ultra-deep sequencing analysis on HIV drug-resistance-associated mutations among HIV-infected individuals: first report from the Philippines
    Ivo N SahBandar, Genesis Samonte, Elizabeth Telan, Nalyn Siripong, Mahdi Belcaid, David Schanzenbach, Susan Leano, Haorile Chagan-Yasutan, Toshio Hattori, Cecilia M Shikuma, and others
    AIDS Research and Human Retroviruses, 2017
  3. Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. compressa
    ZH Forsman, ISS Knapp, K Tisthammer, DAR Eaton, M Belcaid, and RJ Toonen
    Molecular Phylogenetics and Evolution, 2017

2016

  1. Identification of host genes leading to West Nile virus encephalitis in mice brain using RNA-seq analysis. Sci Rep 6: 26350
    M Kumar, M Belcaid, and VR Nerurkar
    2016
  2. Comparative genomics explains the evolutionary success of reef-forming corals
    Debashish Bhattacharya, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L Drake, Douglas Erwin, Sylvian Foret, Ruth D Gates, David F Gruber, and others
    elife, 2016
  3. Identification and preliminary characterization of chemosensory perception-associated proteins in the melon fly Bactrocera cucurbitae using RNA-seq
    Samia Elfekih, Chien-Yu Chen, Ju-Chun Hsu, Mahdi Belcaid, and David Haymer
    Scientific reports, 2016
  4. Characterization of class II β chain major histocompatibility complex genes in a family of Hawaiian honeycreepers:‘amakihi (Hemignathus virens)
    Susan I Jarvi, Kiara R Bianchi, Margaret EM Farias, Ann Txakeeyang, Thomas McFarland, Mahdi Belcaid, and Ashley Asano
    Immunogenetics, 2016

2015

  1. Preclinical development of HIvax: human survivin highly immunogenic vaccines
    Peter R Hoffmann, Maddalena Panigada, Elisa Soprana, Frances Terry, Ivo S Bandar, Antonella Napolitano, Aaron H Rose, Fukun W Hoffmann, Lishomwa C Ndhlovu, Mahdi Belcaid, and Leonard Moise
    Human Vaccines & Immunotherapeutics, 2015
  2. Complete genome sequence of Burkholderia cepacia strain LO6
    Mahdi Belcaid, Yun Kang, Apichai Tuanyok, and Tung T Hoang
    Genome Announcements, 2015
  3. Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from Kāne’ohe Bay, O’ahu, Hawaii
    Silvia Beurmann, Patrick Videau, Blake Ushijima, Ashley M Smith, Greta S Aeby, Sean M Callahan, and Mahdi Belcaid
    Genome Announcements, 2015
  4. Demystifying computer science for molecular ecologists
    Mahdi Belcaid, and Robert J Toonen
    Molecular Ecology, 2015

2014

  1. Long-term changes in Symbiodinium communities in Orbicella annularis in St. John, US Virgin Islands
    Peter J Edmunds, Xavier Pochon, Don R Levitan, Denise M Yost, Mahdi Belcaid, Hollie M Putnam, and Ruth D Gates
    Marine Ecology Progress Series, 2014
  2. The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics
    Alexander I Culley, Jaclyn A Mueller, Madhi Belcaid, Elisha M Wood-Charlson, Guylaine Poisson, and Grieg F Steward
    MBio, 2014

2013

  1. Next-generation sequencing reveals cryptic mtDNA diversity of Plasmodium relictum in the Hawaiian Islands
    SI Jarvi, ME Farias, DA Lapointe, M Belcaid, and CT Atkinson
    Parasitology, 2013
  2. Are we missing half of the viruses in the ocean?
    Grieg F Steward, Alexander I Culley, Jaclyn A Mueller, Elisha M Wood-Charlson, Mahdi Belcaid, and Guylaine Poisson
    The ISME journal, 2013

2012

  1. Chimeric piggyBac transposases for genomic targeting in human cells
    Jesse B Owens, Johann Urschitz, Ilko Stoytchev, Nong C Dang, Zoia Stoytcheva, Mahdi Belcaid, Kommineni J Maragathavally, Craig J Coates, David J Segal, and Stefan Moisyadi
    Nucleic acids research, 2012

2011

  1. The evolution of the tape measure protein: units, duplications and losses
    Mahdi Belcaid, Anne Bergeron, and Guylaine Poisson
    2011

2010

  1. Mosaic graphs and comparative genomics in phage communities
    Mahdi Belcaid, Anne Bergeron, and Guylaine Poisson
    Journal of Computational Biology, 2010

2007

  1. Divide and conquer: enriching environmental sequencing data
    Anne Bergeron, Mahdi Belcaid, Grieg F Steward, and Guylaine Poisson
    PloS one, 2007

2006

  1. Wheat EST resources for functional genomics of abiotic stress
    Mario Houde, Mahdi Belcaid, Fran{\c{c}}ois Ouellet, Jean Danyluk, Antonio F Monroy, Ani Dryanova, Patrick Gulick, Anne Bergeron, Andr{\'e} Laroche, Matthew G Links, and others
    BMC genomics, 2006