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Y Zhang
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Method
:
ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
Haotian Zhang
,
Yiming Zhang
,
Teng Gao
,
and
Yufeng Wu
Genome Res.
December 2025
35
:
2781
-
2791
;
Published in Advance
September 3, 2025
,
doi:
10.1101/gr.280542.125
Abstract
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Corrigendum
:
Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
Ran Li
,
Mian Gong
,
Xinmiao Zhang
,
Fei Wang
,
Zhenyu Liu
,
Lei Zhang
,
Qimeng Yang
,
Yuan Xu
,
Mengsi Xu
,
Huanhuan Zhang
,
Yunfeng Zhang
,
Xuelei Dai
,
Yuanpeng Gao
,
Zhuangbiao Zhang
,
Wenwen Fang
,
Yuta Yang
,
Weiwei Fu
,
Chunna Cao
,
Peng Yang
,
Zeinab Amiri Ghanatsaman
,
Niloufar Jafarpour Negari
,
Hojjat Asadollahpour Nanaei
,
Xiangpeng Yue
,
Yuxuan Song
,
Xianyong Lan
,
Weidong Deng
,
Xihong Wang
,
Chuanying Pan
,
Ruidong Xiang
,
Eveline M. Ibeagha-Awemu
,
Pat (J.S.) Heslop-Harrison
,
Benjamin D. Rosen
,
Johannes A. Lenstra
,
Shangquan Gan
,
and
Yu Jiang
Genome Res.
October 2025
35
:
2375
;
doi:
10.1101/gr.281340.125
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Method
:
A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
Meilin Zhang
,
Heng Du
,
Yu Zhang
,
Yue Zhuo
,
Zhen Liu
,
Yahui Xue
,
Lei Zhou
,
Sixuan Zhou
,
Wanying Li
,
and
Jian-Feng Liu
Genome Res.
August 2025
35
:
1875
-
1886
;
Published in Advance
July 15, 2025
,
doi:
10.1101/gr.280176.124
Abstract
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Research
:
Common
cis
-regulatory variation modifies the penetrance of pathogenic
SHROOM3
variants in craniofacial microsomia
Hao Zhu
,
Jiao Zhang
,
Soumya Rao
,
Matthew D. Durbin
,
Ying Li
,
Ruirui Lang
,
Jiqiang Liu
,
Baichuan Xiao
,
Hailin Shan
,
Ziqiu Meng
,
Jinmo Wang
,
Xiaokai Tang
,
Zhenni Shi
,
Liza L. Cox
,
Shouqin Zhao
,
Stephanie M. Ware
,
Tiong Y. Tan
,
Michelle de Silva
,
Lyndon Gallacher
,
Ting Liu
,
Jie Mi
,
Changqing Zeng
,
Hou-Feng Zheng
,
Qingguo Zhang
,
Stylianos E. Antonarakis
,
Timothy C. Cox
,
and
Yong-Biao Zhang
Genome Res.
May 2025
35
:
1065
-
1079
;
Published in Advance
April 15, 2025
,
doi:
10.1101/gr.280047.124
Abstract
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Method
:
Multisample motif discovery and visualization for tandem repeats
Yaran Zhang
,
Marc Hulsman
,
Alex Salazar
,
Niccolò Tesi
,
Lydian Knoop
,
Sven van der Lee
,
Sanduni Wijesekera
,
Jana Krizova
,
Erik-Jan Kamsteeg
,
and
Henne Holstege
Genome Res.
April 2025
35
:
850
-
862
;
Published in Advance
November 13, 2024
,
doi:
10.1101/gr.279278.124
Abstract
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Research
:
Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
Jian-Hai Chen
,
Patrick Landback
,
Deanna Arsala
,
Alexander Guzzetta
,
Shengqian Xia
,
Jared Atlas
,
Dylan Sosa
,
Yong E. Zhang
,
Jingqiu Cheng
,
Bairong Shen
,
and
Manyuan Long
Genome Res.
March 2025
35
:
379
-
392
;
Published in Advance
February 14, 2025
,
doi:
10.1101/gr.279498.124
Abstract
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Method
:
Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
Hang Zhang
,
Yi Zhang
,
Kai Ming Ting
,
Jie Zhang
,
and
Qiuran Zhao
Genome Res.
February 2025
35
:
355
-
367
;
Published in Advance
February 5, 2025
,
doi:
10.1101/gr.278983.124
Abstract
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Research
:
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
,
L.Y. Lois Choy
,
Peiyong Jiang
,
K.C. Allen Chan
,
and
Y.M. Dennis Lo
Genome Res.
January 2025
35
:
31
-
42
;
Published in Advance
November 27, 2024
,
doi:
10.1101/gr.279667.124
Abstract
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Research
:
Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
Song Zhang
,
Chao Wang
,
Shenghua Qin
,
Choulin Chen
,
Yongzhou Bao
,
Yuanyuan Zhang
,
Lingna Xu
,
Qingyou Liu
,
Yunxiang Zhao
,
Kui Li
,
Zhonglin Tang
,
and
Yuwen Liu
Genome Res.
December 2024
34
:
2190
-
2202
;
Published in Advance
October 21, 2024
,
doi:
10.1101/gr.278344.123
Abstract
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Method
:
Characterizing tandem repeat complexities across long-read sequencing platforms with TREAT and
otter
Niccoló Tesi
,
Alex Salazar
,
Yaran Zhang
,
Sven van der Lee
,
Marc Hulsman
,
Lydian Knoop
,
Sanduni Wijesekera
,
Jana Krizova
,
Anne-Fleur Schneider
,
Maartje Pennings
,
Kristel Sleegers
,
Erik-Jan Kamsteeg
,
Marcel Reinders
,
and
Henne Holstege
Genome Res.
November 2024
34
:
1942
-
1953
;
Published in Advance
October 15, 2024
,
doi:
10.1101/gr.279351.124
Abstract
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Single-cell gene signature scoring
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Short tandem repeat genotyping using long reads
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