Bioinformatics

  1. 3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

    1. Mihaly Varadi
    2. Sreenath Nair
    3. Ian Sillitoe
    4. Gerardo Tauriello
    5. Stephen Anyango
    6. Stefan Bienert
    7. Clemente Borges
    8. Mandar Deshpande
    9. Tim Green
    10. Demis Hassabis
    11. Andras Hatos
    12. Tamas Hegedus
    13. Maarten L Hekkelman
    14. Robbie Joosten
    15. John Jumper
    16. Agata Laydon
    17. Dmitry Molodenskiy
    18. Damiano Piovesan
    19. Edoardo Salladini
    20. Steven L. Salzberg
    21. Markus J Sommer
    22. Martin Steinegger
    23. Erzsebet Suhajda
    24. Dmitri Svergun
    25. Luiggi Tenorio-Ku
    26. Silvio Tosatto
    27. Kathryn Tunyasuvunakool
    28. Andrew Mark Waterhouse
    29. Augustin Žídek
    30. Torsten Schwede
    31. Christine Orengo
    32. Sameer Velankar

    Reviewed by GigaScience

    1 evaluationAppears in 1 listLatest version Latest activity

  2. Making Common Fund data more findable: catalyzing a data ecosystem

    1. Amanda L Charbonneau
    2. Arthur Brady
    3. Karl Czajkowski
    4. Jain Aluvathingal
    5. Saranya Canchi
    6. Robert Carter
    7. Kyle Chard
    8. Daniel J B Clarke
    9. Jonathan Crabtree
    10. Heather H Creasy
    11. Mike D'Arcy
    12. Victor Felix
    13. Michelle Giglio
    14. Alicia Gingrich
    15. Rayna M Harris
    16. Theresa K Hodges
    17. Olukemi Ifeonu
    18. Minji Jeon
    19. Eryk Kropiwnicki
    20. Marisa C W Lim
    21. R Lee Liming
    22. Jessica Lumian
    23. Anup A Mahurkar
    24. Meisha Mandal
    25. James B Munro
    26. Suvarna Nadendla
    27. Rudyard Richter
    28. Cia Romano
    29. Philippe Rocca-Serra
    30. Michael Schor
    31. Robert E Schuler
    32. Hongsuda Tangmunarunkit
    33. Alex Waldrop
    34. Cris Williams
    35. Karen Word
    36. Susanna-Assunta Sansone
    37. Avi Ma'ayan
    38. Rick Wagner
    39. Ian Foster
    40. Carl Kesselman
    41. C Titus Brown
    42. Owen White

    Reviewed by GigaScience

    1 evaluationAppears in 1 listLatest version Latest activity

  3. Utilizing artificial intelligence system to build the digital structural proteome of reef-building corals

    1. Yunchi Zhu
    2. Xin Liao
    3. Tingyu Han
    4. J.-Y. Chen
    5. Chunpeng He
    6. Zuhong Lu

    Reviewed by GigaScience

    1 evaluationAppears in 1 listLatest version Latest activity

  4. What the Phage: a scalable workflow for the identification and analysis of phage sequences

    1. Mike Marquet
    2. Martin Hölzer
    3. Mathias W Pletz
    4. Adrian Viehweger
    5. Oliwia Makarewicz
    6. Ralf Ehricht
    7. Christian Brandt

    Reviewed by GigaScience

    1 evaluationAppears in 1 listLatest version Latest activity

  5. Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE

    1. Matthew Roberts
    2. Julia Ogden
    3. AS Mukarram Hossain
    4. Anshuman Chaturvedi
    5. Alastair RW Kerr
    6. Caroline Dive
    7. Jennifer Ellen Beane
    8. Carlos Lopez-Garcia

    • Curated by eLife

      eLife assessment

      The authors have developed a useful and user-friendly software to analyse gene expression data from four datasets representing premalignant lung lesions. This software would be of interest to those working in lung cancer and specifically the pre-malignant space. The major strength is the ease of use while the major limitation is the inability for the user to integrate other datasets.

    Reviewed by eLife

    4 evaluationsAppears in 1 listLatest version Latest activity

  6. TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles

    1. Varuni Sarwal
    2. Jaqueline Brito
    3. Serghei Mangul
    4. David Koslicki

    Reviewed by GigaScience

    3 evaluationsAppears in 1 listLatest version Latest activity

  7. Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data

    1. Tommaso Lanciano
    2. Aurora Savino
    3. Francesca Porcu
    4. Davide Cittaro
    5. Francesco Bonchi
    6. Paolo Provero

    Reviewed by GigaScience

    5 evaluationsAppears in 1 listLatest version Latest activity

  8. scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data

    1. Malindrie Dharmaratne
    2. Ameya S Kulkarni
    3. Atefeh Taherian Fard
    4. Jessica C Mar

    Reviewed by GigaScience

    1 evaluationAppears in 1 listLatest version Latest activity

  9. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments

    1. Jesse Farek
    2. Daniel Hughes
    3. William Salerno
    4. Yiming Zhu
    5. Aishwarya Pisupati
    6. Adam Mansfield
    7. Olga Krasheninina
    8. Adam C English
    9. Ginger Metcalf
    10. Eric Boerwinkle
    11. Donna M Muzny
    12. Richard Gibbs
    13. Ziad Khan
    14. Fritz J Sedlazeck

    Reviewed by GigaScience

    1 evaluationAppears in 1 listLatest version Latest activity

  10. Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation

    1. Jorge Avila Cartes
    2. Santosh Anand
    3. Simone Ciccolella
    4. Paola Bonizzoni
    5. Gianluca Della Vedova

    Reviewed by GigaScience

    1 evaluationAppears in 1 listLatest version Latest activity
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