Volume 34, Issue 9 | September 2024

Editorial
- - Innovations in computational biology: RECOMB 2024 Special Issue
    Jian Ma
    Bonnie Berger
    First Published October 11, 2024
Methods
- - Haplotype-aware sequence alignment to pangenome graphs
    Ghanshyam Chandra
    Daniel Gibney
    Chirag Jain
    First Published July 16, 2024
  - Genetics-driven risk predictions leveraging the Mendelian randomization framework
    Daniel Sens
    Liubov Shilova
    Ludwig Gräf
    Maria Grebenshchikova
    Bjoern M. Eskofier
    First Published September 27, 2024
  - Scalable summary-statistics-based heritability estimation method with individual genotype level accuracy
    Moonseong Jeong
    Ali Pazokitoroudi
    Zhengtong Liu
    Sriram Sankararaman
    First Published July 22, 2024
  - A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits
    Boyang Fu
    Prateek Anand
    Aakarsh Anand
    Joel Mefford
    Sriram Sankararaman
    First Published August 29, 2024
  - Matrix sketching framework for linear mixed models in association studies
    Myson Burch
    Aritra Bose
    Gregory Dexter
    Laxmi Parida
    Petros Drineas
    First Published September 4, 2024
  - Secure discovery of genetic relatives across large-scale and distributed genomic data sets
    Matthew M. Hong
    David Froelicher
    Ricky Magner
    Victoria Popic
    Bonnie Berger
    First Published August 7, 2024
  - Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption
    Meir Goldenberg
    Loay Mualem
    Amit Shahar
    Sagi Snir
    Adi Akavia
    First Published September 5, 2024
  - Size-based expectation maximization for characterizing nucleosome positions and subtypes
    Jianyu Yang
    Kuangyu Yen
    Shaun Mahony
    First Published June 17, 2024
  - CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing
    Kaiyuan Zhu
    Matthew G. Jones
    Jens Luebeck
    Xinxin Bu
    Hyerim Yi
    King L. Hung Ivy Tsz-Lo Wong
    ...[+2 authors]...,
    Shu Zhang
    Paul S. Mischel
    Howard Y. Chang
    Vineet Bafna
    First Published July 9, 2024
  - Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil
    Mădălina Giurgiu
    Nadine Wittstruck
    Elias Rodriguez-Fos
    Rocío Chamorro González
    Lotte Brückner
    Annabell Krienelke-Szymansky Konstantin Helmsauer Anne Hartebrodt Philipp Euskirchen
    ...[+4 authors]...,
    Richard P. Koche
    Kerstin Haase
    Knut Reinert
    Anton G. Henssen
    First Published August 7, 2024
  - Accurate assembly of circular RNAs with TERRACE
    Tasfia Zahin
    Qian Shi
    Xiaofei Carl Zang
    Mingfu Shao
    First Published July 26, 2024
  - Spatial Cellular Networks from omics data with SpaCeNet
    Stefan Schrod
    Niklas Lück
    Robert Lohmayer
    Stefan Solbrig
    Dennis Völkl
    Tina Wipfler Katherine H. Shutta Marouen Ben Guebila Andreas Schäfer Tim Beißbarth
    ...[+5 authors]...,
    Helena U. Zacharias
    Peter J. Oefner
    John Quackenbush
    Michael Altenbuchinger
    First Published September 4, 2024
  - A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
    Cameron Park
    Shouvik Mani
    Nicolas Beltran-Velez
    Katie Maurer
    Teddy Huang
    Shuqiang Li Satyen Gohil
    ...[+2 authors]...,
    Kenneth J. Livak
    David A. Knowles
    Catherine J. Wu
    Elham Azizi
    First Published September 5, 2024
  - Bayesian inference of sample-specific coexpression networks
    Enakshi Saha
    Viola Fanfani
    Panagiotis Mandros
    Marouen Ben Guebila
    Jonas Fischer
    First Published August 12, 2024
  - Designing realistic regulatory DNA with autoregressive language models
    Avantika Lal
    David Garfield
    Tommaso Biancalani
    Gokcen Eraslan
    First Published September 25, 2024
  - A best-match approach for gene set analyses in embedding spaces
    Lechuan Li
    Ruth Dannenfelser
    Charlie Cruz
    Vicky Yao
    First Published September 4, 2024
  - Protein domain embeddings for fast and accurate similarity search
    Benjamin Giovanni Iovino
    Haixu Tang
    Yuzhen Ye
    First Published September 5, 2024
  - Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction
    Shuai Zeng
    Duolin Wang
    Lei Jiang
    Dong Xu
    First Published July 26, 2024
  - Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
    Ali Osman Berk Şapcı
    Siavash Mirarab
    First Published August 29, 2024
  - Graph-based self-supervised learning for repeat detection in metagenomic assembly
    Ali Azizpour
    Advait Balaji
    Todd J. Treangen
    Santiago Segarra
    First Published July 19, 2024

Table of Contents

Volume 34, Issue 9 | September 2024

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Editorial

Methods