Table of Contents

Methods

• • Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model

    • Ahsan Sanaullah
    • Degui Zhi
    • Shaojie Zhang

    • First Published June 14, 2023

  • Fast inference of genetic recombination rates in biobank scale data

    • Ardalan Naseri
    • William Yue
    • Shaojie Zhang
    • Degui Zhi

    • First Published June 22, 2023

  • Ultrafast genome-wide inference of pairwise coalescence times

    • Regev Schweiger
    • Richard Durbin

    • First Published August 10, 2023

  • Leveraging family data to design Mendelian randomization that is provably robust to population stratification

    • Nathan LaPierre
    • Boyang Fu
    • Steven Turnbull
    • Eleazar Eskin
    • Sriram Sankararaman

    • First Published May 17, 2023

  • Improving quartet graph construction for scalable and accurate species tree estimation from gene trees

    • Yunheng Han
    • Erin K. Molloy

    • First Published May 17, 2023

  • A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings

    • Louxin Zhang
    • Niloufar Abhari
    • Caroline Colijn
    • Yufeng Wu

    • First Published May 22, 2023

  • Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash

    • Mahmudur Rahman Hera
    • N. Tessa Pierce-Ward
    • David Koslicki

    • First Published June 21, 2023

  • Efficient taxa identification using a pangenome index

    • Omar Ahmed
    • Massimiliano Rossi
    • Christina Boucher
    • Ben Langmead

    • First Published May 31, 2023

  • Modeling and predicting cancer clonal evolution with reinforcement learning

    • Stefan Ivanovic
    • Mohammed El-Kebir

    • First Published June 21, 2023

  • Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models

    • Yuelin Liu
    • Xuan Cindy Li
    • Farid Rashidi Mehrabadi
    • Alejandro A. Schäffer
    • Drew Pratt
    • David R. Crawford Salem Malikić Erin K. Molloy Vishaka Gopalan
    • ...[+4 authors]...,
    • Stephen M. Mount
    • Eytan Ruppin
    • Kenneth D. Aldape
    • S. Cenk Sahinalp

    • First Published June 14, 2023

  • Assessing transcriptomic reidentification risks using discriminative sequence models

    • Shuvom Sadhuka
    • Daniel Fridman
    • Bonnie Berger
    • Hyunghoon Cho

    • First Published August 4, 2023

  • Enabling tradeoffs in privacy and utility in genomic data Beacons and summary statistics

    • Rajagopal Venkatesaramani
    • Zhiyu Wan
    • Bradley A. Malin
    • Yevgeniy Vorobeychik

    • First Published May 22, 2023

  • Partial alignment of multislice spatially resolved transcriptomics data

    • Xinhao Liu
    • Ron Zeira
    • Benjamin J. Raphael

    • First Published August 8, 2023

  • Unsupervised contrastive peak caller for ATAC-seq

    • Ha T.H. Vu
    • Yudi Zhang
    • Geetu Tuteja
    • Karin S. Dorman

    • First Published May 22, 2023

  • Leveraging protein language models for accurate multiple sequence alignments

    • Claire D. McWhite
    • Isabel Armour-Garb
    • Mona Singh

    • First Published July 6, 2023

  • Efficient minimizer orders for large values of k using minimum decycling sets

    • David Pellow
    • Lianrong Pu
    • Bariş Ekim
    • Lior Kotlar
    • Bonnie Berger

    • First Published August 9, 2023

  • Entropy predicts sensitivity of pseudorandom seeds

    • Benjamin Dominik Maier
    • Kristoffer Sahlin

    • First Published May 22, 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

    • First Published March 29, 2023

  • Efficient mapping of accurate long reads in minimizer space with mapquik

    • Bariş Ekim
    • Kristoffer Sahlin
    • Paul Medvedev
    • Bonnie Berger
    • Rayan Chikhi

    • First Published June 30, 2023

  • Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT

    • Andrea Cracco
    • Alexandru I. Tomescu

    • First Published May 30, 2023

  • Aligning distant sequences to graphs using long seed sketches

    • Amir Joudaki
    • Alexandru Meterez
    • Harun Mustafa
    • Ragnar Groot Koerkamp
    • André Kahles

    • First Published April 18, 2023

  • Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2

    • Daniel N. Baker
    • Ben Langmead

    • First Published July 6, 2023