Works by Xi, Ruibin

Results: 29

High-resolution detection of copy number alterations in single cells with HiScanner.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60446-5

By:

Zhao, Yifan;
Luquette, Lovelace J.;
Veit, Alexander D.;
Wang, Xiaochen;
Xi, Ruibin;
Viswanadham, Vinayak V.;
Zhang, Yuwei;
Shao, Diane D.;
Walsh, Christopher A.;
Yang, Hong Wei;
Johnson, Mark D.;
Park, Peter J.

Publication type:

Article

Detecting structural variations in the human genome using next generation sequencing.

Published in:

Briefings in Functional Genomics, 2010, v. 9, n. 5/6, p. 405, doi. 10.1093/bfgp/elq025

By:

Ruibin Xi;
Tae-Min Kim;
Park, Peter J.

Publication type:

Article

Global impact of somatic structural variation on the DNA methylome of human cancers.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1818-9

By:

Zhang, Yiqun;
Yang, Lixing;
Kucherlapati, Melanie;
Hadjipanayis, Angela;
Pantazi, Angeliki;
Bristow, Christopher A.;
Lee, Eunjung Alice;
Mahadeshwar, Harshad S.;
Tang, Jiabin;
Zhang, Jianhua;
Seth, Sahil;
Lee, Semin;
Ren, Xiaojia;
Song, Xingzhi;
Sun, Huandong;
Seidman, Jonathan;
Luquette, Lovelace J.;
Xi, Ruibin;
Chin, Lynda;
Protopopov, Alexei

Publication type:

Article

Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 4, p. 1, doi. 10.1093/bioinformatics/btaf131

By:

Chen, Xuanwei;
Ran, Qinghua;
Tang, Junjie;
Chen, Zihao;
Huang, Siyuan;
Shi, Xingjie;
Xi, Ruibin

Publication type:

Article

Single-cell gene fusion detection by scFusion.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28661-6

By:

Jin, Zijie;
Huang, Wenjian;
Shen, Ning;
Li, Juan;
Wang, Xiaochen;
Dong, Jiqiao;
Park, Peter J.;
Xi, Ruibin

Publication type:

Article

Detecting virus integration sites based on multiple related sequencing data by VirTect.

Published in:

BMC Medical Genomics, 2019, v. 12, n. 1, p. 1, doi. 10.1186/s12920-018-0461-8

By:

Xia, Yuchao;
Liu, Yun;
Deng, Minghua;
Xi, Ruibin

Publication type:

Article

Evidence for dosage compensation between the X chromosome and autosomes in mammals.

Published in:

2011

By:

Kharchenko, Peter V;
Xi, Ruibin;
Park, Peter J

Publication type:

Letter

Evaluation of somatic copy number estimation tools for whole-exome sequencing data.

Published in:

Briefings in Bioinformatics, 2016, v. 17, n. 2, p. 185, doi. 10.1093/bib/bbv055

By:

Jae-Yong Nam;
Kim, Nayoung K. D.;
Sang Cheol Kim;
Je-Gun Joung;
Ruibin Xi;
Lee, Semin;
Park, Peter J.;
Woong-Yang Park

Publication type:

Article

De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data.

Published in:

Genome Medicine, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13073-023-01269-1

By:

Zhang, Tianyun;
Jia, Hanying;
Song, Tairan;
Lv, Lin;
Gulhan, Doga C.;
Wang, Haishuai;
Guo, Wei;
Xi, Ruibin;
Guo, Hongshan;
Shen, Ning

Publication type:

Article

Pysim-sv: a package for simulating structural variation data with GC-biases.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 23, doi. 10.1186/s12859-017-1464-8

By:

Yuchao Xia;
Yun Liu;
Minghua Deng;
Ruibin Xi

Publication type:

Article

Compression and aggregation of Bayesian estimates for data intensive computing.

Published in:

Knowledge & Information Systems, 2012, v. 33, n. 1, p. 191, doi. 10.1007/s10115-011-0459-4

By:

Xi, Ruibin;
Lin, Nan;
Chen, Yixin;
Kim, Youngjin

Publication type:

Article

CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3890, doi. 10.1093/bioinformatics/btaa208

By:

Wu, Linjie;
Wang, Han;
Xia, Yuchao;
Xi, Ruibin

Publication type:

Article

scRMD: imputation for single cell RNA-seq data via robust matrix decomposition.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3156, doi. 10.1093/bioinformatics/btaa139

By:

Chen, Chong;
Wu, Changjing;
Wu, Linjie;
Wang, Xiaochen;
Deng, Minghua;
Xi, Ruibin

Publication type:

Article

SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3348, doi. 10.1093/bioinformatics/btx455

By:

Yuchao Xia;
Yun Liu;
Minghua Deng;
Ruibin Xi

Publication type:

Article

TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41649-0

By:

Xia, Yuchao;
Jin, Zijie;
Zhang, Chengsheng;
Ouyang, Linkun;
Dong, Yuhao;
Li, Juan;
Guo, Lvze;
Jing, Biyang;
Shi, Yang;
Miao, Susheng;
Xi, Ruibin

Publication type:

Article

Evolutionary dependency of cancer mutations in gene pairs inferred by nonsynonymous-synonymous mutation ratios.

Published in:

Genome Medicine, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13073-024-01376-7

By:

Han, Dong-Jin;
Kim, Sunmin;
Lee, Seo-Young;
Moon, Youngbeen;
Kang, Su Jung;
Yoo, Jinseon;
Jeong, Hye Young;
Cho, Hae Jin;
Jeon, Jeong Yang;
Sim, Byeong Chang;
Kim, Jaehoon;
Lee, Seungho;
Xi, Ruibin;
Kim, Tae-Min

Publication type:

Article

Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations.

Published in:

Nature Communications, 2017, v. 8, n. 5, p. 15290, doi. 10.1038/ncomms15290

By:

Chang, Jiang;
Tan, Wenle;
Ling, Zhiqiang;
Xi, Ruibin;
Shao, Mingming;
Chen, Mengjie;
Luo, Yingying;
Zhao, Yanjie;
Liu, Yun;
Huang, Xiancong;
Xia, Yuchao;
Hu, Jinlin;
Parker, Joel S.;
Marron, David;
Cui, Qionghua;
Peng, Linna;
Chu, Jiahui;
Li, Hongmin;
Du, Zhongli;
Han, Yaling

Publication type:

Article

rSW-seq: Algorithm for detection of copy numberalterations in deep sequencing data.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 432, doi. 10.1186/1471-2105-11-432

By:

Tae-Min Kim;
Luquette, Lovelace J.;
Ruibin Xi;
Park, Peter J.

Publication type:

Article

Differential network analysis via lasso penalized D-trace loss.

Published in:

Biometrika, 2017, v. 104, n. 4, p. 755, doi. 10.1093/biomet/asx049

By:

HUILI YUAN;
RUIBIN XI;
CHONG CHEN;
MINGHUA DENG

Publication type:

Article

Multi-model analysis of gallbladder cancer reveals the role of OxLDL-absorbing neutrophils in promoting liver invasion.

Published in:

Experimental Hematology & Oncology, 2024, v. 13, n. 1, p. 1, doi. 10.1186/s40164-024-00521-7

By:

Rao, Dongning;
Li, Jiaxin;
Zhang, Mao;
Huang, Siyuan;
Meng, Lu;
Song, Guohe;
Ma, Jiaqiang;
Wu, Yingcheng;
Cheng, Yifei;
Ji, Shuyi;
Wu, Gaohua;
Chen, Lv;
Liu, Yuming;
Shi, Yang;
Zhou, Jian;
Jia, Fan;
Zhang, Xiaoming;
Xi, Ruibin;
Gao, Qiang

Publication type:

Article

Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 13, p. 6274, doi. 10.1093/nar/gkw491

By:

Ruibin Xi;
Semin Lee;
Yuchao Xia;
Tae-Min Kim;
Park, Peter J.

Publication type:

Article

Single‐cell gene regulatory network analysis for mixed cell populations.

Published in:

Quantitative Biology, 2024, v. 12, n. 4, p. 375, doi. 10.1002/qub2.64

By:

Tang, Junjie;
Wang, Changhu;
Xiao, Feiyi;
Xi, Ruibin

Publication type:

Article

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Published in:

Nature, 2011, v. 471, n. 7339, p. 480, doi. 10.1038/nature09725

By:

Kharchenko, Peter V.;
Alekseyenko, Artyom A.;
Schwartz, Yuri B.;
Minoda, Aki;
Riddle, Nicole C.;
Ernst, Jason;
Sabo, Peter J.;
Larschan, Erica;
Gorchakov, Andrey A.;
Gu, Tingting;
Linder-Basso, Daniela;
Plachetka, Annette;
Shanower, Gregory;
Tolstorukov, Michael Y.;
Luquette, Lovelace J.;
Xi, Ruibin;
Jung, Youngsook L.;
Park, Richard W.;
Bishop, Eric P.;
Canfield, Theresa K.

Publication type:

Article

Patient-derived tumor-like cell clusters for drug testing in cancer therapy.

Published in:

Science Translational Medicine, 2020, v. 12, n. 549, p. 1, doi. 10.1126/scitranslmed.aaz1723

By:

Yin, Shenyi;
Xi, Ruibin;
Wu, Aiwen;
Wang, Shu;
Li, Yingjie;
Wang, Chaobin;
Tang, Lei;
Xia, Yuchao;
Yang, Di;
Li, Juan;
Ye, Buqing;
Yu, Ying;
Wang, Junyi;
Zhang, Hanshuo;
Ren, Fei;
Zhang, Yuanyuan;
Shen, Danhua;
Wang, Lin;
Ying, Xiangji;
Li, Zhongwu

Publication type:

Article

Hallmarks of pluripotency.

Published in:

Nature, 2015, v. 525, n. 7570, p. 469, doi. 10.1038/nature15515

By:

De Los Angeles, Alejandro;
Ferrari, Francesco;
Xi, Ruibin;
Fujiwara, Yuko;
Benvenisty, Nissim;
Deng, Hongkui;
Hochedlinger, Konrad;
Jaenisch, Rudolf;
Lee, Soohyun;
Leitch, Harry G.;
Lensch, M. William;
Lujan, Ernesto;
Pei, Duanqing;
Rossant, Janet;
Wernig, Marius;
Park, Peter J.;
Daley, George Q.

Publication type:

Article

A microscopic landscape of the invasive breast cancer genome.

Published in:

Scientific Reports, 2016, p. 27545, doi. 10.1038/srep27545

By:

Ping, Zheng;
Xia, Yuchao;
Shen, Tiansheng;
Parekh, Vishwas;
Siegal, Gene P.;
Eltoum, Isam-Eldin;
He, Jianbo;
Chen, Dongquan;
Deng, Minghua;
Xi, Ruibin;
Shen, Dejun

Publication type:

Article

Genomic footprints of activated telomere maintenance mechanisms in cancer.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-13824-9

By:

Sieverling, Lina;
Hong, Chen;
Koser, Sandra D.;
Ginsbach, Philip;
Kleinheinz, Kortine;
Hutter, Barbara;
Braun, Delia M.;
Cortés-Ciriano, Isidro;
Xi, Ruibin;
Kabbe, Rolf;
Park, Peter J.;
Eils, Roland;
Schlesner, Matthias;
PCAWG-Structural Variation Working Group;
Akdemir, Kadir C.;
Alvarez, Eva G.;
Baez-Ortega, Adrian;
Beroukhim, Rameen;
Boutros, Paul C.;
Bowtell, David D. L.

Publication type:

Article

Comprehensive analysis of neoantigens derived from structural variation across whole genomes from 2528 tumors.

Published in:

Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03005-9

By:

Shi, Yang;
Jing, Biyang;
Xi, Ruibin

Publication type:

Article

Systematic identification of synergistic drug pairs targeting HIV.

Published in:

Nature Biotechnology, 2012, v. 30, n. 11, p. 1125, doi. 10.1038/nbt.2391

By:

Tan, Xu;
Hu, Long;
Luquette, Lovelace J;
Gao, Geng;
Liu, Yifang;
Qu, Hongjing;
Xi, Ruibin;
Lu, Zhi John;
Park, Peter J;
Elledge, Stephen J

Publication type:

Article