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Table of Contents
February 2024; 34 (2)
Review
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The structure, function, and evolution of plant centromeres
Matthew Naish
and
Ian R. Henderson
Genome Res.
February 2024
34
:
161
-
178
;
Published in Advance
March 14, 2024
,
doi:
10.1101/gr.278409.123
Abstract
Full Text
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Research
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Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments
John T. Chamberlin
,
Younghee Lee
,
Gabor T. Marth
,
and
Aaron R. Quinlan
Genome Res.
February 2024
34
:
179
-
188
;
Published in Advance
February 14, 2024
,
doi:
10.1101/gr.278253.123
Abstract
Full Text
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Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
Huiwen Che
,
Peiyong Jiang
,
L.Y. Lois Choy
,
Suk Hang Cheng
,
Wenlei Peng
,
Rebecca W.Y. Chan
,
Jing Liu
,
Qing Zhou
,
W.K. Jacky Lam
,
Stephanie C.Y. Yu
,
So Ling Lau
,
Tak Y. Leung
,
John Wong
,
Vincent Wai-Sun Wong
,
Grace L.H. Wong
,
Stephen L. Chan
,
K.C. Allen Chan
,
and
Y.M. Dennis Lo
Genome Res.
February 2024
34
:
189
-
200
;
Published in Advance
February 26, 2024
,
doi:
10.1101/gr.278556.123
Abstract
Full Text
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Supplemental Material
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Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
Kamal Ajit
,
Adele Alagia
,
Kaspar Burger
,
and
Monika Gullerova
Genome Res.
February 2024
34
:
201
-
216
;
Published in Advance
March 11, 2024
,
doi:
10.1101/gr.278644.123
Abstract
Full Text
Full Text (PDF)
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Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
Uditi Bhatt
,
Anne Cucchiarini
,
Yu Luo
,
Cameron W. Evans
,
Jean-Louis Mergny
,
K. Swaminathan Iyer
,
and
Nicole M. Smith
Genome Res.
February 2024
34
:
217
-
230
;
Published in Advance
February 14, 2024
,
doi:
10.1101/gr.278236.123
Abstract
Full Text
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RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
Brigitta Szabo
,
Therese C. Mandl
,
Bernhard Woldrich
,
Gregor Diensthuber
,
David Martin
,
Michael F. Jantsch
,
and
Konstantin Licht
Genome Res.
February 2024
34
:
231
-
242
;
Published in Advance
March 12, 2024
,
doi:
10.1101/gr.277686.123
Abstract
Full Text
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Pathogenic variants in
CRX
have distinct
cis
-regulatory effects on enhancers and silencers in photoreceptors
James L. Shepherdson
,
Ryan Z. Friedman
,
Yiqiao Zheng
,
Chi Sun
,
Inez Y. Oh
,
David M. Granas
,
Barak A. Cohen
,
Shiming Chen
,
and
Michael A. White
Genome Res.
February 2024
34
:
243
-
255
;
Published in Advance
February 14, 2024
,
doi:
10.1101/gr.278133.123
Abstract
Full Text
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Supplemental Material
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Dynamic DNA
N
6
-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote
Pseudocohnilembus persalinus
Yongqiang Liu
,
Junhua Niu
,
Fei Ye
,
Therese Solberg
,
Borong Lu
,
Chundi Wang
,
Mariusz Nowacki
,
and
Shan Gao
Genome Res.
February 2024
34
:
256
-
271
;
Published in Advance
March 12, 2024
,
doi:
10.1101/gr.278796.123
Abstract
Full Text
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Modeling alternative translation initiation sites in plants reveals evolutionarily conserved
cis
-regulatory codes in eukaryotes
Ting-Ying Wu
,
Ya-Ru Li
,
Kai-Jyun Chang
,
Jhen-Cheng Fang
,
Daisuke Urano
,
and
Ming-Jung Liu
Genome Res.
February 2024
34
:
272
-
285
;
Published in Advance
March 13, 2024
,
doi:
10.1101/gr.278100.123
Abstract
Full Text
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Major impacts of widespread structural variation on sorghum
Zhihai Zhang
,
Joao Paulo Gomes Viana
,
Bosen Zhang
,
Kimberly K.O. Walden
,
Hans Müller Paul
,
Stephen P. Moose
,
Geoffrey P. Morris
,
Chris Daum
,
Kerrie W. Barry
,
Nadia Shakoor
,
and
Matthew E. Hudson
Genome Res.
February 2024
34
:
286
-
299
;
Published in Advance
March 13, 2024
,
doi:
10.1101/gr.278396.123
Abstract
Full Text
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Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle
Alexander S. Leonard
,
Xena M. Mapel
,
and
Hubert Pausch
Genome Res.
February 2024
34
:
300
-
309
;
Published in Advance
February 14, 2024
,
doi:
10.1101/gr.278267.123
Abstract
Full Text
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Haplotype-resolved 3D chromatin architecture of the hybrid pig
Yu Lin
,
Jing Li
,
Yiren Gu
,
Long Jin
,
Jingyi Bai
,
Jiaman Zhang
,
Yujie Wang
,
Pengliang Liu
,
Keren Long
,
Mengnan He
,
Diyan Li
,
Can Liu
,
Ziyin Han
,
Yu Zhang
,
Xiaokai Li
,
Bo Zeng
,
Lu Lu
,
Fanli Kong
,
Ying Sun
,
Yongliang Fan
,
Xun Wang
,
Tao Wang
,
An'an Jiang
,
Jideng Ma
,
Linyuan Shen
,
Li Zhu
,
Yanzhi Jiang
,
Guoqing Tang
,
Xiaolan Fan
,
Qingyou Liu
,
Hua Li
,
Jinyong Wang
,
Li Chen
,
Liangpeng Ge
,
Xuewei Li
,
Qianzi Tang
,
and
Mingzhou Li
Genome Res.
February 2024
34
:
310
-
325
;
Published in Advance
March 13, 2024
,
doi:
10.1101/gr.278101.123
Abstract
Full Text
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OPEN ACCESS ARTICLE
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Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
Wenjuan Yu
,
Haohui Luo
,
Jinbao Yang
,
Shengchen Zhang
,
Heling Jiang
,
Xianjia Zhao
,
Xingqi Hui
,
Da Sun
,
Liang Li
,
Xiu-qing Wei
,
Stefano Lonardi
,
and
Weihua Pan
Genome Res.
February 2024
34
:
326
-
340
;
Published in Advance
March 1, 2024
,
doi:
10.1101/gr.278232.123
Abstract
Full Text
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February 2024;
34
(2)
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February 2024, 34 (2)
From the Cover
Long cell-free DNA in human plasma
Sampling biases in single-cell/nucleus RNA-seq
Transcriptional repression in response to DNA damage
Z-RNA over intercalated motifs in lncRNA
Plant genomics
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