Bioinformatics

  1. Cellpose-SAM: superhuman generalization for cellular segmentation

    1. Marius Pachitariu
    2. Michael Rariden
    3. Carsen Stringer

    Reviewed by Arcadia Science

    7 evaluationsAppears in 1 listLatest version Latest activity

  2. Translational buffering tunes gene expression in mice and humans

    1. Shilpa Rao
    2. Aden Y Le
    3. Logan Persyn
    4. Can Cenik

    Reviewed by Review Commons

    3 evaluationsAppears in 1 listLatest version Latest activity

  3. MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics

    1. Naomi Martin
    2. Paul Olsen
    3. Jacob Quon
    4. Jazmin Campos
    5. Nasmil Valera Cuevas
    6. Josh Nagra
    7. Marshall VanNess
    8. Zoe Maltzer
    9. Emily C Gelfand
    10. Alana Oyama
    11. Amanda Gary
    12. Yimin Wang
    13. Angela Alaya
    14. Augustin Ruiz
    15. Cade Reynoldson
    16. Cameron Bielstein
    17. Christina Alice Pom
    18. Cindy Huang
    19. Cliff Slaughterbeck
    20. Elizabeth Liang
    21. Jason Alexander
    22. Jeanelle Ariza
    23. Jocelin Malone
    24. Jose Melchor
    25. Kaity Colbert
    26. Krissy Brouner
    27. Lyudmila Shulga
    28. Melissa Reding
    29. Patrick Latimer
    30. Raymond Sanchez
    31. Stuard Barta
    32. Tom Egdorf
    33. Zachary Madigan
    34. Chelsea M Pagan
    35. Jennie L Close
    36. Brian Long
    37. Michael Kunst
    38. Ed S Lein
    39. Hongkui Zeng
    40. Delissa McMillen
    41. Jack Waters

    • Curated by eLife

      eLife Assessment

      This study provides a valuable contribution to spatial transcriptomics by introducing MerQuaCo, a computational tool for standardizing quality control in image-based spatial transcriptomics datasets. The tool addresses the lack of consensus in the field and provides robust metrics to identify and quantify common imperfections in datasets. The work is supported by an impressive dataset and compelling analyses, and will be of significant interest to researchers focused on data reproducibility and downstream analysis reliability in spatial transcriptomics.

    Reviewed by eLife

    8 evaluationsAppears in 1 listLatest version Latest activity

  4. From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models

    1. Etowah Adams
    2. Liam Bai
    3. Minji Lee
    4. Yiyang Yu
    5. Mohammed AlQuraishi

    Reviewed by Arcadia Science

    3 evaluationsAppears in 1 listLatest version Latest activity

  5. The Implications of Alternative Splicing Regulation for Maximum Lifespan

    1. Wei Jiang
    2. Sika Zheng
    3. Liang Chen

    Reviewed by Arcadia Science

    2 evaluationsAppears in 1 listLatest version Latest activity

  6. Unsupervised Representation Learning of C. elegans Poses and Behavior Sequences From Microscope Video Recordings

    1. Maurice Deserno
    2. Katarzyna Bozek

    • Curated by eLife

      eLife Assessment

      This valuable study introduces a self-supervised machine learning method to classify C. elegans postures and behaviors directly from video data, offering an alternative to the skeleton-based approaches that rely on often error-prone tracking. This novel approach holds promise for advancing ethology research. That said, the strength of evidence is currently incomplete, as key aspects - including measuring head-tail orientation, increased behavioral interpretability, and quantitative comparisons to established methods - are underdeveloped and would benefit from further validation.

    Reviewed by Arcadia Science, eLife

    7 evaluationsAppears in 2 listsLatest version Latest activity

  7. Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing

    1. Jessie J -Y Chang
    2. Xuan Yang
    3. Haotian Teng
    4. Jianshu Zhang
    5. Benjamin Reames
    6. Shuxin Zhang
    7. Vincent Corbin
    8. Lachlan J M Coin

    Reviewed by GigaScience

    2 evaluationsAppears in 1 listLatest version Latest activity

  8. Nanopore- and AI-empowered microbial viability inference

    1. Harika Ürel
    2. Sabrina Benassou
    3. Hanna Marti
    4. Tim Reska
    5. Ela Sauerborn
    6. Yuri Pinheiro Alves De Souza
    7. Albert Perlas
    8. Enrique Rayo
    9. Michael Biggel
    10. Stefan Kesselheim
    11. Nicole Borel
    12. Edward J Martin
    13. Constanza B Venegas
    14. Michael Schloter
    15. Kathrin Schröder
    16. Jana Mittelstrass
    17. Simone Prospero
    18. James M Ferguson
    19. Lara Urban

    Reviewed by GigaScience

    2 evaluationsAppears in 1 listLatest version Latest activity

  9. WaveSeekerNet: Accurate Prediction of Influenza A Virus Subtypes and Host Source Using Attention-Based Deep Learning

    1. Hoang-Hai Nguyen
    2. Josip Rudar
    3. Nathaniel Lesperance
    4. Oksana Vernygora
    5. Graham W. Taylor
    6. Chad Laing
    7. David Lapen
    8. Carson K. Leung
    9. Oliver Lung

    Reviewed by GigaScience

    6 evaluationsAppears in 1 listLatest version Latest activity

  10. SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis

    1. Xiao Li
    2. Ximo Pechuan-Jorge
    3. Tyler Risom
    4. Conrad Foo
    5. Alexander Prilipko
    6. Artem Zubkov
    7. Caleb Chan
    8. Patrick Chang
    9. Frank Peale
    10. James Ziai
    11. Sandra Rost
    12. Derrek Hibar
    13. Lisa McGinnis
    14. Evgeniy Tabatsky
    15. Xin Ye
    16. Hector Corrada Bravo
    17. Zhen Shi
    18. Malgorzata Nowicka
    19. Jon Scherdin
    20. James Cowan
    21. Jennifer Giltnane
    22. Darya Orlova
    23. Rajiv Jesudason

    Reviewed by GigaScience

    3 evaluationsAppears in 1 listLatest version Latest activity
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