• Publication image for Ribosome profiling reveals differences in global translational vs transcriptional gene expression changes during early Candida albicans biofilm formation
    Ribosome profiling reveals differences in global translational vs transcriptional gene expression changes during early Candida albicans biofilm formation
    Vasanthakrishna Mundodi*, Saket Choudhary*, Andrew D Smith, David Kadosh
    Microbiology Spectrum, 2025
  • Publication image for Multiplexed single-cell characterization of alternative polyadenylation regulators
    Multiplexed single-cell characterization of alternative polyadenylation regulators
    Madeline H Kowalski*, Hans-Hermann Wessels*, Johannes Linder*, Carol Dalgarno, Isabella Mascio, Saket Choudhary, Austin Hartman, Yuhan Hao, Anshul Kundaje, Rahul Satija
    Cell, 2024
  • Publication image for Genome-wide translational response of Candida albicans to fluconazole treatment
    Genome-wide translational response of Candida albicans to fluconazole treatment
    Saket Choudhary*, Vasanthakrishna Mundodi*, Andrew D Smith, David Kadosh
    Microbiology Spectrum, 2023
  • Publication image for Dictionary learning for integrative, multimodal and scalable single-cell analysis
    Dictionary learning for integrative, multimodal and scalable single-cell analysis
    Yuhan Hao, Tim Stuart, Madeline H Kowalski, Saket Choudhary, Paul Hoffman, Austin Hartman, Avi Srivastava, Gesmira Molla, Shaista Madad, Carlos Fernandez-Granda, others
    Nature Biotechnology, 2023
  • Publication image for Comparison and evaluation of statistical error models for scRNA-seq
    Comparison and evaluation of statistical error models for scRNA-seq
    Saket Choudhary, Rahul Satija
    Genome Biology, 2022
  • Publication image for Global translational landscape of the Candida albicans morphological transition
    Global translational landscape of the Candida albicans morphological transition
    Vasanthakrishna Mundodi*, Saket Choudhary*, Andrew D Smith, David Kadosh
    G3, 2021
  • Publication image for Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
    Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
    Saket Choudhary, Suzanne C Burns, Hoda Mirsafian, Wenzheng Li, Dat T Vo, Mei Qiao, Xiufen Lei, Andrew D Smith, Luiz O Penalva
    Scientific Reports, 2020
  • Publication image for Accurate detection of short and long active ORFs using Ribo-seq data
    Accurate detection of short and long active ORFs using Ribo-seq data
    Saket Choudhary*, Wenzheng Li*, Andrew D. Smith
    Bioinformatics, 2020
  • Publication image for Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin
    Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin
    Juhye M Lee, Rachel Eguia, Seth J Zost, Saket Choudhary, Patrick C Wilson, Trevor Bedford, Terry Stevens-Ayers, Michael Boeckh, Aeron Hurt, Seema S Lakdawala, others
    Elife, 2019
  • Publication image for pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
    pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
    Saket Choudhary
    F1000Research, 2019
  • Publication image for Bioconda: sustainable and comprehensive software distribution for the life sciences
    Bioconda: sustainable and comprehensive software distribution for the life sciences
    Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster, Bioconda Team
    Nature Methods, 2018
  • Publication image for Reaction Decoder Tool (RDT): extracting features from chemical reactions
    Reaction Decoder Tool (RDT): extracting features from chemical reactions
    Syed Asad Rahman, Gilliean Torrance, Lorenzo Baldacci, Sergio Martínez Cuesta, Franz Fenninger, Nimish Gopal, Saket Choudhary, John W May, Gemma L Holliday, Christoph Steinbeck, others
    Bioinformatics, 2016
  • Publication image for Autoantibody profiling of glioma serum samples to identify biomarkers using human proteome arrays
    Autoantibody profiling of glioma serum samples to identify biomarkers using human proteome arrays
    Parvez Syed, Shabarni Gupta, Saket Choudhary, Narendra Goud Pandala, Apurva Atak, Annie Richharia, Manubhai Kp, Heng Zhu, Sridhar Epari, Santosh B Noronha, others
    Scientific Reports, 2015