publications

Publications in reverse chronological order.

2026

  1. Benchmarking long-read RNA-seq across modalities, methods, and sequencing depth in iNeurons
    Gianfranco Botta*, David Wissel*, Samuel Higgins, and 14 more authors
    bioRxiv, Apr 2026
    DOI Zenodo Code Preprint
  2. Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation
    Atreya Choudhury, Tom Kitak, Ben Carrillo, and 9 more authors
    bioRxiv, May 2026
    DOI Zenodo Code Preprint
  3. A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification
    David Wissel*, Madison M. Mehlferber*, Khue M. Nguyen, and 4 more authors
    Genome Biology, Feb 2026
    DOI Zenodo Code Preprint

2025

  1. Inferring binding specificities of human transcription factors with the wisdom of crowds
    Nikita Gryzunov*, Dmitry Penzar*, Vasilii Kamenets, and 32 more authors
    bioRxiv, Nov 2025
    DOI Zenodo Code Preprint
  2. Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics
    David Wissel, Gloria M. Sheynkman, and Mark D. Robinson
    bioRxiv, Nov 2025
    DOI Zenodo Code Preprint
  3. SurvBoard: standardized benchmarking for multi-omics cancer survival models
    David Wissel*, Nikita Janakarajan*, Aayush Grover, and 3 more authors
    Briefings in Bioinformatics, Aug 2025
    DOI Zenodo Code Preprint

2024

  1. Ten simple rules for computational biologists collaborating with wet lab researchers
    Mark D. Robinson*, Peiying Cai*, Martin Emons*, and 10 more authors
    PLOS Computational Biology, Jun 2024
    DOI Preprint
  2. CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
    Alexander Theus*, Florian Barkmann*, David Wissel, and 1 more author
    bioRxiv, Nov 2024
    DOI Code Preprint
  3. sparsesurv: a Python package for fitting sparse survival models via knowledge distillation
    David Wissel, Nikita Janakarajan, Julius Schulte, and 3 more authors
    Bioinformatics, Aug 2024
    DOI Code

2023

  1. Systematic comparison of multi-omics survival models reveals a widespread lack of noise resistance
    David Wissel, Daniel Rowson, and Valentina Boeva
    Cell Reports Methods, Apr 2023
    DOI Zenodo Code

* indicates equal contribution; † indicates equal supervision.