Works by Xiaojian Shao

Results: 30

GenPipes: an open-source framework for distributed and scalable genomic analyses.

Published in:

GigaScience, 2019, v. 8, n. 6, p. 1, doi. 10.1093/gigascience/giz037

By:

Bourgey, Mathieu;
Dali, Rola;
Eveleigh, Robert;
Chen, Kuang Chung;
Letourneau, Louis;
Fillon, Joel;
Michaud, Marc;
Caron, Maxime;
Sandoval, Johanna;
Lefebvre, Francois;
Leveque, Gary;
Mercier, Eloi;
Bujold, David;
Marquis, Pascale;
Van, Patrick Tran;
Anderson de Lima Morais, David;
Tremblay, Julien;
Shao, Xiaojian;
Henrion, Edouard;
Gonzalez, Emmanuel

Publication type:

Article

Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types.

Published in:

Briefings in Functional Genomics, 2016, v. 15, n. 6, p. 399, doi. 10.1093/bfgp/elw013

By:

Xiaofei Yang;
Xiaojian Shao;
Lin Gao;
Shihua Zhang

Publication type:

Article

Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.

Published in:

2019

By:

Cheung, Warren A.;
Shao, Xiaojian;
Morin, Andréanne;
Siroux, Valérie;
Kwan, Tony;
Ge, Bing;
Aïssi, Dylan;
Chen, Lu;
Vasquez, Louella;
Allum, Fiona;
Guénard, Frédéric;
Bouzigon, Emmanuelle;
Simon, Marie-Michelle;
Boulier, Elodie;
Redensek, Adriana;
Watt, Stephen;
Datta, Avik;
Clarke, Laura;
Flicek, Paul;
Mead, Daniel

Publication type:

Correction Notice

Single-Cell Sequencing of Lung Macrophages and Monocytes Reveals Novel Therapeutic Targets in COPD.

Published in:

Cells (2073-4409), 2023, v. 12, n. 24, p. 2771, doi. 10.3390/cells12242771

By:

Hu, Yushan;
Shao, Xiaojian;
Xing, Li;
Li, Xuan;
Nonis, Geoffrey M.;
Koelwyn, Graeme J.;
Zhang, Xuekui;
Sin, Don D.

Publication type:

Article

Gene expression variations are predictive for stochastic noise.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 2, p. 403, doi. 10.1093/nar/gkq844

By:

Dong, Dong;
Shao, Xiaojian;
Deng, Naiyang;
Zhang, Zhaolei

Publication type:

Article

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1173-7

By:

Cheung, Warren A.;
Xiaojian Shao;
Morin, Andréanne;
Siroux, Valérie;
Kwan, Tony;
Bing Ge;
Aïssi, Dylan;
Lu Chen;
Vasquez, Louella;
Allum, Fiona;
Guénard, Frédéric;
Bouzigon, Emmanuelle;
Simon, Marie-Michelle;
Boulier, Elodie;
Redensek, Adriana;
Watt, Stephen;
Datta, Avik;
Clarke, Laura;
Flicek, Paul;
Mead, Daniel

Publication type:

Article

DNA Methylation at ABCG1 and Long-term Changes in Adiposity and Fat Distribution in Response to Dietary Interventions: The POUNDS Lost Trial.

Published in:

Diabetes Care, 2023, v. 46, n. 12, p. 2201, doi. 10.2337/dc23-0748

By:

Li, Xiang;
Shao, Xiaojian;
Kou, Minghao;
Wang, Xuan;
Ma, Hao;
Grundberg, Elin;
Bazzano, Lydia A.;
Smith, Steven R.;
Bray, George A.;
Sacks, Frank M.;
Qi, Lu

Publication type:

Article

Thousands of CpGs Show DNA Methylation Differences in ACPA-Positive Individuals.

Published in:

Genes, 2021, v. 12, n. 9, p. 1349, doi. 10.3390/genes12091349

By:

Zeng, Yixiao;
Zhao, Kaiqiong;
Oros Klein, Kathleen;
Shao, Xiaojian;
Fritzler, Marvin J.;
Hudson, Marie;
Colmegna, Inés;
Pastinen, Tomi;
Bernatsky, Sasha;
Greenwood, Celia M. T.

Publication type:

Article

Integrative COVID-19 biological network inference with probabilistic core decomposition.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab455

By:

Guo, Yang;
Esfahani, Fatemeh;
Shao, Xiaojian;
Srinivasan, Venkatesh;
Thomo, Alex;
Xing, Li;
Zhang, Xuekui

Publication type:

Article

NAD tagSeq for transcriptome-wide identification and characterization of NAD<sup>+</sup>-capped RNAs.

Published in:

Nature Protocols, 2020, v. 15, n. 9, p. 2813, doi. 10.1038/s41596-020-0363-z

By:

Shao, Xiaojian;
Zhang, Hailei;
Yang, Zhu;
Zhong, Huan;
Xia, Yiji;
Cai, Zongwei

Publication type:

Article

Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.

Published in:

Bioinformatics, 2017, v. 33, n. 4, p. 491, doi. 10.1093/bioinformatics/btw672

By:

Hocking, Toby Dylan;
Goerner-Potvin, Patricia;
Morin, Andreanne;
Xiaojian Shao;
Pastinen, Tomi;
Bourque, Guillaume

Publication type:

Article

DMEAS: DNA methylation entropy analysis software.

Published in:

Bioinformatics, 2013, v. 29, n. 16, p. 2044, doi. 10.1093/bioinformatics/btt332

By:

He, Jianlin;
Sun, Xinxi;
Shao, Xiaojian;
Liang, Liji;
Xie, Hehuang

Publication type:

Article

A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain–peptide interaction from primary sequence.

Published in:

Bioinformatics, 2011, v. 27, n. 3, p. 383, doi. 10.1093/bioinformatics/btq657

By:

Shao, Xiaojian;
Tan, Chris S. H.;
Voss, Courtney;
Li, Shawn S. C.;
Deng, Naiyang;
Bader, Gary D.

Publication type:

Article

Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective.

Published in:

Bioinformatics, 2011, v. 27, n. 2, p. 147, doi. 10.1093/bioinformatics/btq637

By:

Dong, Dong;
Shao, Xiaojian;
Zhang, Zhaolei

Publication type:

Article

Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming.

Published in:

BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-978

By:

Xiaojian Shao;
Cuiyun Zhang;
Ming-An Sun;
Xuemei Lu;
Hehuang Xie

Publication type:

Article

Erratum: Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants.

Published in:

Nature Communications, 2015, v. 6, n. 7, p. 8016, doi. 10.1038/ncomms9016

By:

Allum, Fiona;
Shao, Xiaojian;
Guénard, Frédéric;
Simon, Marie-Michelle;
Busche, Stephan;
Caron, Maxime;
Lambourne, John;
Lessard, Julie;
Tandre, Karolina;
Hedman, Åsa K;
Kwan, Tony;
Ge, Bing;
Rönnblom, Lars;
McCarthy, Mark I;
Deloukas, Panos;
Richmond, Todd;
Burgess, Daniel;
Spector, Timothy D;
Tchernof, André;
Marceau, Simon

Publication type:

Article

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants.

Published in:

Nature Communications, 2015, v. 6, n. 5, p. 7211, doi. 10.1038/ncomms8211

By:

Allum, Fiona;
Shao, Xiaojian;
Guénard, Frédéric;
Simon, Marie-Michelle;
Busche, Stephan;
Caron, Maxime;
Lambourne, John;
Lessard, Julie;
Tandre, Karolina;
Hedman, Åsa K.;
Kwan, Tony;
Ge, Bing;
Rönnblom, Lars;
McCarthy, Mark I.;
Deloukas, Panos;
Richmond, Todd;
Burgess, Daniel;
Spector, Timothy D.;
Tchernof, André;
Marceau, Simon

Publication type:

Article

Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature.

Published in:

Clinical Epigenetics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13148-022-01281-z

By:

Shao, Xiaojian;
Le Stunff, Catherine;
Cheung, Warren;
Kwan, Tony;
Lathrop, Mark;
Pastinen, Tomi;
Bougnères, Pierre

Publication type:

Article

The heterogeneity of plasma miRNA profiles in hepatocellular carcinoma patients and the exploration of diagnostic circulating miRNAs for hepatocellular carcinoma.

Published in:

PLoS ONE, 2019, v. 14, n. 2, p. 1, doi. 10.1371/journal.pone.0211581

By:

Bai, Xue;
Liu, Zhenzhen;
Shao, Xiaojian;
Wang, Di;
Dong, Encheng;
Wang, Yan;
Wu, Chung-I;
Yuan, Yunfei;
Lu, Xuemei;
Li, Chunyan

Publication type:

Article

The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men.

Published in:

Environmental Health Perspectives, 2024, v. 132, n. 1, p. 017008-1, doi. 10.1289/EHP12013

By:

Lismer, Ariane;
Xiaojian Shao;
Dumargne, Marie-Charlotte;
Lafleur, Christine;
Lambrot, Romain;
Chan, Donovan;
Toft, Gunnar;
Bonde, Jens Peter;
MacFarlane, Amanda J.;
Bornman, Riana;
Aneck-Hahn, Natalie;
Patrick, Sean;
Bailey, Janice M.;
de Jager, Christiaan;
Dumeaux, Vanessa;
Trasler, Jacquetta M.;
Kimmins, Sarah

Publication type:

Article

Customized MethylC-Capture Sequencing to Evaluate Variation in the Human Sperm DNA Methylome Representative of Altered Folate Metabolism.

Published in:

Environmental Health Perspectives, 2019, v. 127, n. 8, p. 1, doi. 10.1289/EHP4812

By:

Chan, Donovan;
Xiaojian Shao;
Dumargne, Marie-Charlotte;
Aarabi, Mahmoud;
Simon, Marie-Michelle;
Kwan, Tony;
Bailey, Janice L.;
Robaire, Bernard;
Kimmins, Sarah;
San Gabriel, Maria C.;
Zini, Armand;
Librach, Clifford;
Moskovtsev, Sergey;
Grundberg, Elin;
Bourque, Guillaume;
Pastinen, Tomi;
Trasler, Jacquetta M.

Publication type:

Article

Correction: Increased CpG methylation at the CDH1 locus in inflamed ileal mucosa of patients with Crohn disease.

Published in:

2024

By:

de Ponthaud, Charles;
Abdalla, Solafah;
Belot, Marie-Pierre;
Shao, Xiaojian;
Penna, Christophe;
Brouquet, Antoine;
Bougnères, Pierre

Publication type:

Correction Notice

Increased CpG methylation at the CDH1 locus in inflamed ileal mucosa of patients with Crohn disease.

Published in:

Clinical Epigenetics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13148-024-01631-z

By:

de Ponthaud, Charles;
Abdalla, Solafah;
Belot, Marie-Pierre;
Shao, Xiaojian;
Penna, Christophe;
Brouquet, Antoine;
Bougnères, Pierre

Publication type:

Article

Capturing sex-specific and hypofertility-linked effects of assisted reproductive technologies on the cord blood DNA methylome.

Published in:

Clinical Epigenetics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13148-023-01497-7

By:

Rahimi, Sophia;
Shao, Xiaojian;
Chan, Donovan;
Martel, Josée;
Bérard, Anick;
Fraser, William D.;
Simon, Marie-Michelle;
Kwan, Tony;
Bourque, Guillaume;
Trasler, Jacquetta

Publication type:

Article

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation.

Published in:

Genome Biology, 2015, v. 16, p. 1, doi. 10.1186/s13059-015-0856-1

By:

Busche, Stephan;
Xiaojian Shao;
Caron, Maxime;
Kwan, Tony;
Allum, Fiona;
Cheung, Warren A.;
Bing Ge;
Westfall, Susan;
Simon, Marie-Michelle;
Barrett, Amy;
Bell, Jordana T.;
McCarthy, Mark I.;
Deloukas, Panos;
Blanchette, Mathieu;
Bourque, Guillaume;
Spector, Timothy D.;
Lathrop, Mark;
Pastinen, Tomi;
Grundberg, Elin

Publication type:

Article

Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin.

Published in:

Human Molecular Genetics, 2015, v. 24, n. 15, p. 4374, doi. 10.1093/hmg/ddv172

By:

Xiaofei Yang;
Xiaojian Shao;
Lin Gao;
Shihua Zhang

Publication type:

Article

Dissecting features of epigenetic variants underlying cardiometabolic risk using full-resolution epigenome profiling in regulatory elements.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-09184-z

By:

Allum, Fiona;
Hedman, Åsa K.;
Shao, Xiaojian;
Cheung, Warren A.;
Vijay, Jinchu;
Guénard, Frédéric;
Kwan, Tony;
Simon, Marie-Michelle;
Ge, Bing;
Moura, Cristiano;
Boulier, Elodie;
Rönnblom, Lars;
Bernatsky, Sasha;
Lathrop, Mark;
McCarthy, Mark I.;
Deloukas, Panos;
Tchernof, André;
Pastinen, Tomi;
Vohl, Marie-Claude;
Grundberg, Elin

Publication type:

Article

High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations.

Published in:

Clinical Epigenetics, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13148-020-00988-1

By:

Cao, Mingju;
Shao, Xiaojian;
Chan, Peter;
Cheung, Warren;
Kwan, Tony;
Pastinen, Tomi;
Robaire, Bernard

Publication type:

Article

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing.

Published in:

Clinical Epigenetics, 2019, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13148-019-0699-9

By:

Shao, Xiaojian;
Hudson, Marie;
Colmegna, Ines;
Greenwood, Celia M. T.;
Fritzler, Marvin J.;
Awadalla, Philip;
Pastinen, Tomi;
Bernatsky, Sasha

Publication type:

Article

DNA Methylation Near CPT1A and Changes in Triglyceride-rich Lipoproteins in Response to Weight-loss Diet Interventions.

Published in:

Journal of Clinical Endocrinology & Metabolism, 2023, v. 108, n. 8, p. e542, doi. 10.1210/clinem/dgad086

By:

Xiang Li;
Xiaojian Shao;
Qiaochu Xue;
Minghao Kou;
Champagne, Catherine M.;
Koseva, Boryana S.;
Yoriko Heianza;
Grundberg, Elin;
Bazzano, Lydia A.;
Bray, George A.;
Sacks, Frank M.;
Lu Qi

Publication type:

Article