Publications

Publications by categories in reversed chronological order.

2024

  1. 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

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, and 8 more authors
    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, and 3 more authors
    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, and 8 more authors
    Proceedings of the ACM on Human-Computer Interaction, 2021
  3. CoCoNet: an efficient deep learning tool for viral metagenome binning
    Cédric 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, and 8 more authors
    2021
  5. The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance
    Andrea J Jani, Jessie Bushell, Cédric G Arisdakessian, and 4 more authors
    The ISME Journal, 2021
  6. DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity
    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, and 8 more authors
    Journal of neuroendocrinology, 2020
  2. MetaFlow|mics: scalable and reproducible nextflow pipelines for the analysis of microbiome marker data
    Cédric 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, and 2 more authors
    Scientific reports, 2020

2019

  1. Usage Patterns of Wideband Display Environments In e-Science Research, Development and Training
    Jason Leigh, Dylan Kobayashi, Nurit Kirshenbaum, and 15 more authors
    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, and 8 more authors
    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, and 3 more authors
    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, and 8 more authors
    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, and 2 more authors
    Scientific reports, 2016
  4. Characterization of class II βchain major histocompatibility complex genes in a family of Hawaiian honeycreepers:‘amakihi (Hemignathus virens)
    Susan I Jarvi, Kiara R Bianchi, Margaret EM Farias, and 4 more authors
    Immunogenetics, 2016

2015

  1. Complete genome sequence of Burkholderia cepacia strain LO6
    Mahdi Belcaid, Yun Kang, Apichai Tuanyok, and 1 more author
    Genome Announcements, 2015
  2. Complete Genome Sequence of Pseudoalteromonas sp. Strain OCN003, Isolated from Kāne’ohe Bay, O’ahu, Hawaii
    Silvia Beurmann, Patrick Videau, Blake Ushijima, and 4 more authors
    Genome Announcements, 2015
  3. 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, and 4 more authors
    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, and 3 more authors
    MBio, 2014

2013

  1. Next-generation sequencing reveals cryptic mtDNA diversity of Plasmodium relictum in the Hawaiian Islands
    SI Jarvi, ME Farias, DA Lapointe, and 2 more authors
    Parasitology, 2013
  2. Are we missing half of the viruses in the ocean?
    Grieg F Steward, Alexander I Culley, Jaclyn A Mueller, and 3 more authors
    The ISME journal, 2013

2012

  1. Chimeric piggyBac transposases for genomic targeting in human cells
    Jesse B Owens, Johann Urschitz, Ilko Stoytchev, and 7 more authors
    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 1 more author
    PloS one, 2007

2006

  1. Wheat EST resources for functional genomics of abiotic stress
    Mario Houde, Mahdi Belcaid, François Ouellet, and 8 more authors
    BMC genomics, 2006