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Hirotaka Iwaki, Hampton L Leonard, Mary B Makarious, Matt Bookman, Barry Landin, David Vismer, Bradford Casey, Raphael J Gibbs, Dena G Hernandez, Cornelis Blauwendraat, others

Accelerating Medicines Partnership: Parkinson’s Disease. Genetic Resource Journal Article

medRxiv, 2020.

Jacqueline M Tokarew, Daniel Nicolas El Kodsi, Nathalie A Lengacher, Travis K Fehr, Angela P Nguyen, Bojan Shutinoski, Brian O'Nuallain, Ming Jin, Jasmine Khan, Andy CH Ng, others

Age-Associated Insolubility of Parkin in Human Midbrain is Linked to Redox Balance and Sequestration of Reactive Dopamine Metabolites Journal Article

bioRxiv, 2020.

Carmen Domínguez-Baleón, Jue-Sheng Ong, Clemens R Scherzer, Miguel E Rentería, Xianjun Dong

Genetic evidence for protective effects of smoking and drinking behavior on Parkinson's disease: A Mendelian Randomization study Journal Article

medRxiv, 2020.

Adrian I Campos, Nathan Ingold, Yunru Huang, Pik Fang Kho, Xikun Han, Jue-Sheng Ong, Luis M Garcia-Marin, Matthew H Law, Nicholas G Martin, Xianjun Dong, others

Genome-wide analyses in 1,987,836 participants identify 39 genetic loci associated with sleep apnoea Journal Article

medRxiv, 2020.

Junko Tsuji, Travis Thomson, Elizabeth Chan, Christine K Brown, Julia Oppenheimer, Carol Bigelow, Xianjun Dong, William E Theurkauf, Zhiping Weng, Lawrence M Schwartz

High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death Journal Article

Physiological Genomics, 52 (10), pp. 492–511, 2020.

Zhenshen Bao, Yihua Zhu, Qinyu Ge, Wanjun Gu, Xianjun Dong, Yunfei Bai

Signaling Pathway Analysis Combined With the Strength Variations of Interactions Between Genes Under Different Conditions Journal Article

IEEE Access, 8 , pp. 138036–138045, 2020.


Zhenshen Bao, Yihua Zhu, Qinyu Ge, Wanjun Gu, Xianjun Dong, Yunfei Bai

gwSPIA: Improved Signaling Pathway Impact Analysis With Gene Weights Journal Article

IEEE Access, 7 , pp. 69172–69183, 2019.

Tao Wang, Junpeng Ruan, Quanwei Yin, Xianjun Dong, Yadong Wang

An automated quality control pipeline for eQTL analysis with RNA-seq data Inproceedings

2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 1780–1786, IEEE 2019.


Xianjun Dong, Zhixiang Liao, David Gritsch, Yavor Hadzhiev, Yunfei Bai, Joseph J Locascio, Boris Guennewig, Ganqiang Liu, Cornelis Blauwendraat, Tao Wang, others

Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease Journal Article

Nature neuroscience, 21 (10), pp. 1482–1492, 2018.


Shuchi Mittal, Kjetil Bjørnevik, Doo Soon Im, Adrian Flierl, Xianjun Dong, Joseph J Locascio, Kristine M Abo, Elizabeth Long, Ming Jin, Bing Xu, others

β2-Adrenoreceptor is a regulator of the α-synuclein gene driving risk of Parkinson’s disease Journal Article

Science, 357 (6354), pp. 891–898, 2017.

Ganqiang Liu, Brendon Boot, Joseph J Locascio, Zhixiang Liao, Daly Franco, Karen Duong, Kara Page, Iris Jansen, Tom Yi, Ana Trisini-Lipsanopoulos, others

Neuropathic Gaucher’s Mutations: Shifting Parkinson’s Into High Gear (S1. 002) Miscellaneous



Ganqiang Liu, Brendon Boot, Joseph J Locascio, Iris E Jansen, Sophie Winder-Rhodes, Shirley Eberly, Alexis Elbaz, Alexis Brice, Bernard Ravina, Jacobus J van Hilten, others

Specifically neuropathic Gaucher's mutations accelerate cognitive decline in Parkinson's Journal Article

Annals of neurology, 80 (5), pp. 674–685, 2016.


Joseph J Locascio, Shirley Eberly, Zhixiang Liao, Ganqiang Liu, Ashley N Hoesing, Karen Duong, Ana Trisini-Lipsanopoulos, Kaltra Dhima, Albert Y Hung, Alice W Flaherty, others

Association between α-synuclein blood transcripts and early, neuroimaging-supported Parkinson’s disease Journal Article

Brain, 138 (9), pp. 2659–2671, 2015.

Xianjun Dong, Junko Tsuji, Adam Labadorf, Panos Roussos, Jiang-Fan Chen, Richard H Myers, Schahram Akbarian, Zhiping Weng

The role of H3K4me3 in transcriptional regulation is altered in Huntington’s disease Journal Article

PloS one, 10 (12), pp. e0144398, 2015.


Guang Bai, Iris Cheung, Hennady P Shulha, Joana E Coelho, Ping Li, Xianjun Dong, Mira Jakovcevski, Yumei Wang, Anastasia Grigorenko, Yan Jiang, others

Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains Journal Article

Human molecular genetics, pp. ddu561, 2014.

Andrew G Hoss, Vinay K Kartha, Xianjun Dong, Jeanne C Latourelle, Alexandra Dumitriu, Tiffany C Hadzi, Marcy E MacDonald, James F Gusella, Schahram Akbarian, Jiang-Fan Chen, others

MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis Journal Article

PLoS Genet, 10 (2), pp. e1004188, 2014.

Vanja Haberle, Nan Li, Yavor Hadzhiev, Charles Plessy, Christopher Previti, Chirag Nepal, Jochen Gehrig, Xianjun Dong, Altuna Akalin, Ana Maria Suzuki, others

Two independent transcription initiation codes overlap on vertebrate core promoters Journal Article

Nature, 507 (7492), pp. 381–385, 2014.


Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin Lin, Troy W Whitfield, Melissa C Greven, Brian G Pierce, Xianjun Dong, Anshul Kundaje, Yong Cheng, others

77 Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors Journal Article

Journal of Biomolecular Structure and Dynamics, 31 (sup1), pp. 49–50, 2013.

Xin Zhiguo Li, Christian K Roy, Xianjun Dong, Ewelina Bolcun-Filas, Jie Wang, Bo W Han, Jia Xu, Melissa J Moore, John C Schimenti, Zhiping Weng, others

An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes Journal Article

Molecular cell, 50 (1), pp. 67–81, 2013.

Xianjun Dong, Zhiping Weng

The correlation between histone modifications and gene expression Journal Article

Epigenomics, 5 (2), pp. 113–116, 2013.


ENCODE Project Consortium, others

An integrated encyclopedia of DNA elements in the human genome Journal Article

Nature, 2012.

Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin-Ying Lin, Melissa C Greven, Bong-Hyun Kim, Jill Moore, Brian G Pierce, Xianjun Dong, Daniel Virgil, others

Factorbook. org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium Journal Article

Nucleic Acids Research, 2012.

Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, others

Modeling gene expression using chromatin features in various cellular contexts Journal Article

Genome biology, 13 (9), pp. 1, 2012.

Jie Wang, Jiali Zhuang, Sowmya Iyer, XinYing Lin, Troy W Whitfield, Melissa C Greven, Brian G Pierce, Xianjun Dong, Anshul Kundaje, Yong Cheng, others

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors Journal Article

Genome research, 22 (9), pp. 1798–1812, 2012.

Chao Cheng, Roger Alexander, Renqiang Min, Jing Leng, Kevin Y Yip, Joel Rozowsky, Koon-Kiu Yan, Xianjun Dong, Sarah Djebali, Yijun Ruan, others

Understanding transcriptional regulation by integrative analysis of transcription factor binding data Journal Article

Genome research, 22 (9), pp. 1658–1667, 2012.


ENCODE Project Consortium, others

A user’s guide to the encyclopedia of DNA elements (ENCODE) Journal Article

PLoS Biol, 9 (4), pp. e1001046, 2011.

Jie Wang, Jiali Zhuang, Sowmya Iyer, X Lin, Troy Whitfield, Melissa Greven, Shelley Force Aldred, Nathan Trinklein, Xianjun Dong, Anshul Kundaje, others

Genome-wide mapping of the binding sites of 119 human transcription factors Journal Article

Submitted, NCP010, 2011.

David Fredman, Xianjun Dong, Boris Lenhard

Making enhancers from spare parts of the genome Journal Article

Genome biology, 12 (12), pp. 1, 2011.

Ozlem Yildirim, Ruowang Li, Jui-Hung Hung, Poshen B Chen, Xianjun Dong, Ly-Sha Ee, Zhiping Weng, Oliver J Rando, Thomas G Fazzio

Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells Journal Article

Cell, 147 (7), pp. 1498–1510, 2011.


Xianjun Dong, Pavla Navratilova, David Fredman, Øyvind Drivenes, Thomas S Becker, Boris Lenhard

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons Journal Article

Nucleic acids research, 38 (4), pp. 1071–1085, 2010.

Xianjun Dong, Altuna Akalin, Yogita Sharma, Boris Lenhard

Translog, a web browser for studying the expression divergence of homologous genes Journal Article

BMC bioinformatics, 11 (1), pp. 1, 2010.


Xianjun Dong, David Fredman, Boris Lenhard

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes Journal Article

Genome biology, 10 (8), pp. 1, 2009.

Xianjun Dong

The brainstorm Journal Article

IEEE Potentials, 28 (1), pp. 8–9, 2009.

Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Christian Bryne, Harukazu Suzuki, Carsten O Daub, Yoshihide Hayashizaki, Boris Lenhard

Transcriptional features of genomic regulatory blocks Journal Article

Genome biology, 10 (4), pp. 1, 2009.


Sutada Mungpakdee, Hee-Chan Seo, Anna Rita Angotzi, Xianjun Dong, Altuna Akalin, Daniel Chourrout

Differential evolution of the 13 Atlantic salmon Hox clusters Journal Article

Molecular Biology and Evolution, 25 (7), pp. 1333–1343, 2008.

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