Volume 35, Issue 1 | January 2025

Review
- - Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
    W.H. Adrian Tsui
    Spencer C. Ding
    Peiyong Jiang
    Y.M. Dennis Lo
    First Published January 22, 2025
Research
- - Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
    Shruthi Rengarajan
    Jason Derks
    Daniel W. Bellott
    Nikolai Slavov
    David C. Page
    First Published January 10, 2025
  - Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
    Yasine Malki
    Guannan Kang
    W.K. Jacky Lam
    Qing Zhou
    Suk Hang Cheng
    Peter P.H. Cheung Jinyue Bai Ming Lok Chan Chui Ting Lee Wenlei Peng Yiqiong Zhang Wanxia Gai Winsome W.S. Wong Mary-Jane L. Ma Wenshuo Li Xinzhou Xu Zhuoran Gao Irene O.L. Tse Huimin Shang
    ...[+14 authors]...,
    L.Y. Lois Choy
    Peiyong Jiang
    K.C. Allen Chan
    Y.M. Dennis Lo
    First Published November 27, 2024
  - The rate and spectrum of new mutations in mice inferred by long-read sequencing
    Eugenio López-Cortegano
    Jobran Chebib
    Anika Jonas
    Anastasia Vock
    Sven Künzel
    First Published December 2, 2024
  - Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
    Amy R. Vandiver
    Allen Herbst
    Paul Stothard
    Jonathan Wanagat
    First Published November 27, 2024
  - Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
    Fangyuan Yang
    Li-Jun Cao
    Petr Nguyen
    Zhong-Zheng Ma
    Jin-Cui Chen
    First Published January 6, 2025
  - Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
    Thomas D. Lewin
    Isabel Jiah-Yih Liao
    Mu-En Chen
    John D.D. Bishop
    Peter W.H. Holland
    First Published January 6, 2025
  - ISWI1 complex proteins facilitate developmental genome editing in Paramecium
    Aditi Singh
    Lilia Häußermann
    Christiane Emmerich
    Emily Nischwitz
    Brandon K.B. Seah
    First Published November 14, 2024
  - The chromatin landscape of the histone-possessing Bacteriovorax bacteria
    Georgi K. Marinov
    Benjamin Doughty
    Anshul Kundaje
    William J. Greenleaf
    First Published November 21, 2024
Methods
- - KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    Samuel H. Kim
    Georgi K. Marinov
    William J. Greenleaf
    First Published November 21, 2024
  - Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach
    Fabien Wehbe
    Levi Adams
    Jordan Babadoudou
    Samantha Yuen
    Yoon-Seong Kim
    First Published December 2, 2024
  - A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
    Shuai Guo
    Xiaoqian Liu
    Xuesen Cheng
    Yujie Jiang
    Shuangxi Ji
    Qingnan Liang Andrew Koval Yumei Li Leah A. Owen Ivana K. Kim Ana Aparicio Sanghoon Lee Anil K. Sood Scott Kopetz John Paul Shen
    ...[+10 authors]...,
    John N. Weinstein
    Margaret M. DeAngelis
    Rui Chen
    Wenyi Wang
    First Published November 25, 2024
  - Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
    Howard J. Womersley
    Daniel Muliaditan
    Ramanuj DasGupta
    Lih Feng Cheow
    First Published December 2, 2024
  - Modeling gene interactions in polygenic prediction via geometric deep learning
    Han Li
    Jianyang Zeng
    Michael P. Snyder
    Sai Zhang
    First Published November 19, 2024
Resources
- - High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
    Zihe Li
    Ziyu Xu
    Lei Zhu
    Tao Qin
    Jinrui Ma
    Zhanying Feng Huishan Yue Qing Guan Botong Zhou Ge Han Guokun Zhang Chunyi Li Shuaijun Jia
    ...[+8 authors]...,
    Qiang Qiu
    Dingjun Hao
    Yong Wang
    Wen Wang
    First Published November 14, 2024
  - Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
    Yujie Chen
    Yiran Hou
    Qinglin Zeng
    Irene Wang
    Meiru Shang
    Kwangdeok Shin Christopher Hemauer
    ...[+2 authors]...,
    Xiaoyun Xing
    Junsu Kang
    Guoyan Zhao
    Ting Wang
    First Published January 14, 2025

Table of Contents

Volume 35, Issue 1 | January 2025

Review

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics

Research

Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y

Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations

The rate and spectrum of new mutations in mice inferred by long-read sequencing

Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging

Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

ISWI1 complex proteins facilitate developmental genome editing in Paramecium

The chromatin landscape of the histone-possessing Bacteriovorax bacteria

Methods

KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome

Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach

A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression

Modeling gene interactions in polygenic prediction via geometric deep learning

Resources

High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration

Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution

Table of Contents

Volume 35, Issue 1 | January 2025

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Review

Research

Methods

Resources