Jim Shaw

Published articles and preprints

My Google Scholar profile also contains a list of my publications/pre-prints. The list below is sorted in order of original pre-printing.

* indicates co-lead authors

  1. Jim Shaw, Yun William Yu. Fairy: fast approximate coverage for multi-sample metagenomic binning (2024). bioRxiv.
  2. Jim Shaw*, Jean-Sebastien Gounot*, Hanrong Chen, Niranjan Nagarajan, Yun William Yu. Floria: Fast and accurate strain haplotyping in metagenomes (2024). ISMB/Bioinformatics (accepted).
  3. Jim Shaw, Yun William Yu. Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph (2023). bioRxiv.
  4. Jim Shaw, Yun William Yu. Fast and robust metagenomic sequence comparison through sparse chaining with skani (2023). Nature Methods.
  5. Andrew Zheng, Jim Shaw, Yun William Yu. Mora: abundance aware metagenomic read re-assignment for disentangling similar strains (2024). BMC Bioinformatics.
  6. Jim Shaw, Yun William Yu. Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic (2023). Genome Research.
  7. Martin Frith, Jim Shaw, John Spouge. How to optimally sample a sequence for rapid analysis (2023). Bioinformatics.
  8. Jim Shaw, Yun William Yu. Theory of local k-mer selection with applications to long-read alignment (2022). Bioinformatics.
  9. Jim Shaw, Yun William Yu. Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing (2022). Journal of Computational Biology: RECOMB 2021 Issue.
  10. Tom Ouellette, Jim Shaw, Philip Awadalla. Using image-based haplotype alignments to map global adaptation of SARS-CoV-2 (2020). bioRxiv.
  11. Ryan Cotsakis*, Jim Shaw*, Julien Tierny, Joshua Levine. Implementing Persistence-Based Clustering of Point Clouds in the Topology ToolKit (2021). Topological Methods in Data Analysis and Visualization VI. Mathematics and Visualization.
  12. Simone Hu*, Oliver Schnetz*, Jim Shaw*, Karen Yeats*. Further investigations into the graph theory of phi^4-periods and the c2 invariant (2020). Annales de l’Institut Henri Poincare D.
  13. D. Bertrand, J. Shaw, M Narayan, H.Q.A. Ng, S. Kumar, C. Li, M. Dvornicic, J.P. Soldo, J.Y. Kho, O.T. Ng, T. Barkham, B. Young, K. Marimuthu, K.R. Chng, M. Sikic, N. Nagarajan. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes (2019). Nature Biotechnology.

Talks and presentations

  1. sylph talk. (2023). Genome Informatics 2023, Cold Spring Harbor Laboratory.
  2. skani talk. (2023). ISMB 2023, Lyon.
  3. Seed-chain-extend alignment rigorous average-case analysis talk. (2023). RECOMB 2023, Istanbul.