Searching journal content for articles similar to Sussman 16 (3): 305.

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  1. Editorial: RECOMB 2025 Special Issue
    • Sriram Sankararaman and
    • Bonnie Berger
    Genome Res. December 2025 35: v-vi; doi:10.1101/gr.281664.125
    ...forum for cutting-edge theoretical advances in computational biology and their applications in molecular biology and medicine, emphasizing advancements in computational biology methodologies, including artificial intelligence (AI) and machine learning. Genome Research has been a leading journal...
  2. Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
    • Tianyu Liu,
    • Tinglin Huang,
    • Wengong Jin,
    • Tinyi Chu,
    • Rex Ying,
    • and Hongyu Zhao
    Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  3. Editorial: Innovations in computational biology: RECOMB 2024 Special Issue
    • Jian Ma and
    • Bonnie Berger
    Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124
    ..., mathematical, statistical, and biological sciences. It is held annually in the Spring and is paired with its typically adjoining satellite conferences. It provides a scientific forum for the cutting-edge theoretical advances in computational biology and their applications in molecular biology and medicine...
  4. Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
    • Enzo Battistella,
    • Anant Maheshwari,
    • Barış Ekim,
    • Bonnie Berger,
    • and Victoria Popic
    Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
    ..., Toulon, France. OpenReview.net. https://openreview.net/forum?id=SJU4ayYgl ↵Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, et al. 2023. Scalable nanopore sequencing of human s provides a comprehensive view of haplotype...
  5. Method: Accurate short-read alignment through r-index-based pangenome indexing
    • Rahul Varki,
    • Massimiliano Rossi,
    • Eddie Ferro,
    • Marco Oliva,
    • Erik Garrison,
    • Ben Langmead,
    • and Christina Boucher
    Genome Res. July 2025 35: 1609-1620; Published in Advance June 12, 2025, doi:10.1101/gr.279858.124
    OPEN ACCESS ARTICLE
  6. Method: Graph-based self-supervised learning for repeat detection in metagenomic assembly
    • Ali Azizpour,
    • Advait Balaji,
    • Todd J. Treangen,
    • and Santiago Segarra
    Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
    .... 2017. Semi-supervised classification with graph convolutional networks. In International Conference on Learning Representations (ICLR), Palais des Congrès Neptune, Toulon, France. Curran Associates, Inc. https://openreview.net/forum?id=SJU4ayYgl ↵Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M...
  7. Research: Genomic epidemiology of carbapenem-resistant Enterobacterales at a New York City hospital over a 10-year period reveals complex plasmid-clone dynamics and evidence for frequent horizontal transfer of blaKPC
    • Angela Gomez-Simmonds,
    • Medini K. Annavajhala,
    • Dwayne Seeram,
    • Todd W. Hokunson,
    • Heekuk Park,
    • and Anne-Catrin Uhlemann
    Genome Res. November 2024 34: 1895-1907; Published in Advance October 4, 2024, doi:10.1101/gr.279355.124
    ...–3903. doi:10.1128/AAC.02412-14 ↵Castanheira M, Deshpande LM, Mendes RE, Canton R, Sader HS, Jones RN. 2019. Variations in the occurrence of resistance phenotypes and carbapenemase genes among Enterobacteriaceae isolates in 20 years of the SENTRY antimicrobial surveillance program. Open Forum Infect Dis 6: S...
    OPEN ACCESS ARTICLE
  8. Method: Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
    • Joseph W. Foley,
    • Chunfang Zhu,
    • Philippe Jolivet,
    • Shirley X. Zhu,
    • Peipei Lu,
    • Michael J. Meaney,
    • and Robert B. West
    Genome Res. November 2019 29: 1816-1825; Published in Advance September 13, 2019, doi:10.1101/gr.234807.118
    ...://github.com/jwfoley/Smart-3SEQ_paper_scripts. Additional support for the Smart-3SEQ protocol is available in an online forum at https://groups.google.com/forum/#!forum/smart-3seq.AcknowledgmentsWe thank the laboratory of Carlos D. Bustamante and especially Shirley Sutton and Alexandra Sockell for use of the Tape...
    OPEN ACCESS ARTICLE
  9. Resource: PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations
    • Bo Wen,
    • Xiaojing Wang,
    • and Bing Zhang
    Genome Res. March 2019 29: 485-493; Published in Advance January 4, 2019, doi:10.1101/gr.235028.118
    ...via a Google users group (https://groups.google.com/forum/#!forum/pepquery) and a gitter channel (https://gitter.im/PepQuery/). This provides multiple venues for users to have their questions answered quickly and efficiently.Mass spectrometry data sets and analysisThe spiked-in data set from the i...
  10. Method: Debiased personalized gene coexpression networks for population-scale scRNA-seq data
    • Shan Lu and
    • Sunduz Keles
    Genome Res. June 9, 2023 gr.277363.122; Published in Advance June 9, 2023, doi:10.1101/gr.277363.122
    ACCEPTED MANUSCRIPT
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