Publications

Jim's Google Scholar profile also lists a complete set of publications and preprints. In computational biology, conferences (e.g., RECOMB) have associated journals (e.g., Genome Research). An asterisk (*) indicates co-lead authors.

Selected works

2026

High-resolution metagenome assembly for modern long reads with myloasm

Jim Shaw, Maximillian G. Marin, Heng Li — Nature Biotechnology

Paper Docs
2024

Rapid species-level metagenome profiling and containment estimation with sylph

Jim Shaw, Yun William Yu — Nature Biotechnology

Paper Code
2023

Fast and robust metagenomic sequence comparison through sparse chaining with skani

Jim Shaw, Yun William Yu — Nature Methods

Paper Code
2023

Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

Jim Shaw, Yun William Yu — Genome Research / RECOMB 2023

Paper

All publications

2026

Sensitive long-read amplicon sequence variant recovery with savont

Jim Shaw, Marie Riisgaard-Jensen, Kasper Skytte Andersen, Rasmus Kirkegaard, Morten Kam Dahl Dueholm, Heng Li — bioRxiv

Preprint Code
2026

High-resolution metagenome assembly for modern long reads with myloasm

Jim Shaw, Maximillian G. Marin, Heng Li — Nature Biotechnology

Paper Docs
2025

A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions

Antonio Pedro Camargo, Fotis A. Baltoumas, Eric Olo Ndela, Mateus B. Fiamenghi, Bryan D. Merrill, Matthew M. Carter, Yishay Pinto, Meenakshi Chakraborty, Antonina Andreeva, Gabriele Ghiotto, Jim Shaw, Amy D. Proal, Justin L. Sonnenburg, Ami S. Bhatt, Simon Roux, Georgios A. Pavlopoulos, Stephen Nayfach, Nikos C. Kyrpides — bioRxiv

Preprint
2025

devider: long-read reconstruction of many diverse haplotypes

Jim Shaw, Christina Boucher, Yun William Yu, Noelle Noyes, Heng Li — Genome Research / RECOMB 2025

Paper Code
2024

Rapid species-level metagenome profiling and containment estimation with sylph

Jim Shaw, Yun William Yu — Nature Biotechnology

Paper Code
2024

Floria: Fast and accurate strain haplotyping in metagenomes

Jim Shaw*, Jean-Sebastien Gounot*, Hanrong Chen, Niranjan Nagarajan, Yun William Yu — ISMB / Bioinformatics

Paper Code
2024

Fairy: fast approximate coverage for multi-sample metagenomic binning

Jim Shaw, Yun William Yu — Microbiome

Paper Code
2024

skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements

Brian Zhang, Grace Oualline, Jim Shaw, Yun William Yu — ECCB / Bioinformatics

Paper
2024

Mora: abundance aware metagenomic read re-assignment for disentangling similar strains

Andrew Zheng, Jim Shaw, Yun William Yu — BMC Bioinformatics

Paper Code
2023

Fast and robust metagenomic sequence comparison through sparse chaining with skani

Jim Shaw, Yun William Yu — Nature Methods

Paper Code
2023

Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

Jim Shaw, Yun William Yu — Genome Research / RECOMB 2023

Paper
2023

How to optimally sample a sequence for rapid analysis

Martin Frith, Jim Shaw, John Spouge — Bioinformatics

Paper
2022

Theory of local k-mer selection with applications to long-read alignment

Jim Shaw, Yun William Yu — Bioinformatics

Paper
2022

Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing

Jim Shaw, Yun William Yu — Journal of Computational Biology (RECOMB 2021 Issue)

Paper Code
2021

Implementing Persistence-Based Clustering of Point Clouds in the Topology ToolKit

Ryan Cotsakis*, Jim Shaw*, Julien Tierny, Joshua Levine — Topological Methods in Data Analysis and Visualization VI, Mathematics and Visualization

Paper
2020

Using image-based haplotype alignments to map global adaptation of SARS-CoV-2

Tom Ouellette, Jim Shaw, Philip Awadalla — bioRxiv

Preprint
2020

Further investigations into the graph theory of phi^4-periods and the c2 invariant

Simone Hu*, Oliver Schnetz*, Jim Shaw*, Karen Yeats* — Annales de l'Institut Henri Poincare D

Paper
2019

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

D. Bertrand, Jim 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 — Nature Biotechnology

Paper Code