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2021

C Domínguez-Baleón, J Ong, C Scherzer, M Rentería, X Dong

Understanding the effect of smoking and drinking behavior on Parkinson's disease risk: a Mendelian randomization study Journal Article

Scientific Reports, 11 (1), pp. 13980, 2021, ISSN: 2045-2322.

Abstract | Links

Y Chen, Q Zhu, L Cheng, Y Wang, M Li, Q Yang, L Hu, D Lou, J Li, X Dong, L P Lee, F Liu

Exosome detection via the ultrafast-isolation system: EXODUS Journal Article

Nature Methods, 18 (2), pp. 212–218, 2021.

Abstract | Links

J Tokarew, D Kodsi, N Lengacher, T Fehr, A Nguyen, B Shutinoski, B O'Nuallain, M Jin, J Khan, A Ng, J Li, Q Jiang, M Zhang, L Wang, R Sengupta, K Barber, A Tran, S Zandee, X Dong, C Scherzer, A Prat, E Tsai, M Takanashi, N Hattori, J Chan, L Zecca, A West, A Holmgren, L Puente, G Shaw, G Toth, J Woulfe, P Taylor, J Tomlinson, M Schlossmacher

Age-associated insolubility of parkin in human midbrain is linked to redox balance and sequestration of reactive dopamine metabolites Journal Article

Acta Neuropathol., 2021.

Abstract | Links

C Li, R Ou, Y Chen, X Gu, Q Wei, B Cao, L Zhang, Y Hou, K Liu, X Chen, W Song, B Zhao, Y Wu, T Li, X Dong, H Shang

Genetic Modifiers of Age at Onset for Parkinson's Disease in Asians: A Genome-Wide Association Study Journal Article

Movement Disorders, 2021.

Abstract | Links

X Dong, C Liu, M Dozmorov

Review of multi-omics data resources and integrative analysis for human brain disorders Journal Article

Briefings of Functional Genomics, 2021.

Abstract | Links

Liu G, Peng J, Liao Z, Locascio JJ, Corvol JC, Zhu F, Dong X, Maple-Grødem J, Campbell MC, Elbaz A, Lesage S, Brice A, Mangone G, Growdon JH, Hung AY, Schwarzschild MA, Hayes MT, Wills AM, Herrington TM, Ravina B, Shoulson I, Taba P, Kõks S, Beach TG, Cormier-Dequaire F, Alves G, Tysnes OB, Perlmutter JS, Heutink P, Amr SS, van Hilten JJ, Kasten M, Mollenhauer B, Trenkwalder C, Klein C, Barker RA, Williams-Gray CH, Marinus J; International Genetics of Parkinson Disease Progression (IGPP) Consortium, Scherzer CR.

Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson's disease Journal Article

Nature Genetics, 2021.

Abstract | Links

H Iwaki, H Leonard, M Makarious, M Bookman, B Landin, D Vismer, B Casey, R Gibbs, D Hernandez, C Blauwendraat, D Vitale, Y Song, D Kumar, C Dalgard, M Sadeghi, X Dong, L Misquitta, S Scholz, C Scherzer, M Nalls, S Biswas, A Singleton, Uniformed Services University of the Health Sciences Associates, AMP PD Whole Genome Sequencing Working Group, AMP PD consortium

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

Movement Disorders, 2021.

Links

X Dong, X Li, TW Chang, CR Scherzer, ST Weiss, W Qiu

powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis Journal Article

Bioinformatics, 2021, (btab385).

Abstract | Links

2020

C Domínguez-Baleón, J Ong, C Scherzer, M Rentería, X Dong

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

medRxiv, Forthcoming.

A Campos, N Ingold, Y Huang, P Kho, X Han, J Ong, L Garcia-Marin, M Law, N Martin, X Dong, G Cuellar-Partida, S MacGregor, S Aslibekyan, M Rentería

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

medRxiv, Forthcoming.

J Tsuji, T Thomson, E Chan, C K Brown, J Oppenheimer, C Bigelow, X Dong, W E Theurkauf, Z Weng, L M Schwartz

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

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

Abstract

Z Bao, Y Zhu, Q Ge, W Gu, X Dong, Y 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.

2019

T Wang, J Ruan, Q Yin, X Dong, Y 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.

Z Bao, Y Zhu, Q Ge, W Gu, X Dong, Y Bai

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

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

2018

X Dong, Z Liao, D Gritsch, Y Hadzhiev, Y Bai, J J Locascio, B Guennewig, G Liu, C Blauwendraat, T Wang, C H Adler, J C Hedreen, R L M Faull, M P Frosch, P T Nelson, P Rizzu, A A Cooper, P Heutink, T G Beach, J S Mattick, F Müller, C R Scherzer

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

Nat Neurosci, 21 (10), pp. 1482–1492, 2018.

Abstract

2017

G Liu, B Boot, J Locascio, Z Liao, D Franco, K Duong, K Page, I Jansen, T Yi, A Trisini-Lipsanopoulos, X Dong, S Hutten, S Winder-Rhodes, S Amr, C Tanner, A Lang, M Nalls, S Eberly, H, CamPaIGN, PICNICS, PROPARK, PSG, DIGPD, L Sudarsky, A Elbaz, A Brice, B Ravina, I Shoulson, J Hilten, F Cormier-Dequaire, J Corvol, R Barker, P Heutink, J Marinus, C Williams-Gray, C Scherzer, International Genetics of Parkinson Disease Progression (IGPP) Consortium

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

2017.

S Mittal, K Bjornevik, D S Im, A Flierl, X Dong, J J Locascio, K M Abo, E Long, M Jin, B Xu, Y K Xiang, J C Rochet, A Engeland, P Rizzu, P Heutink, T Bartels, D J Selkoe, B J Caldarone, M A Glicksman, V Khurana, B Schule, D S Park, T Riise, C R Scherzer

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.

Abstract

2016

G Liu, B Boot, J J Locascio, I E Jansen, S Winder-Rhodes, S Eberly, A Elbaz, A Brice, B Ravina, J J van Hilten, F Cormier-Dequaire, J C Corvol, R A Barker, P Heutink, J Marinus, C H Williams-Gray, C R Scherzer, C Scherzer, B T Hyman, A J Ivinson, A Trisini-Lipsanopoulos, D Franco, K Burke, L R Sudarsky, M T Hayes, C C Umeh, J H Growdon, M A Schwarzschild, A Y Hung, A W Flaherty, A M Wills, N I Mejia, S N Gomperts, V Khurana, D J Selkoe, T Yi, K Page, Z Liao, R Barker, T Foltynie, C H Williams-Gray, S Mason, S Winder-Rhodes, R Barker, C H Williams-Gray, D Breen, G Cummins, J Evans, S Winder-Rhodes, J C Corvol, A Brice, A Elbaz, A Mallet, M Vidailhet, A M Bonnet, C Bonnet, D Grabli, A Hartmann, S Klebe, L Lacomblez, G Mangone, F Bourdain, J P Brandel, P Derkinderen, F Durif, V Mesnage, F Pico, O Rascol, S Forlani, S Lesage, K Tahiri, J J van Hilten, J Marinus, Z Liao, K Page, D Franco, K Duong, T Yi, A Trisini-Lipsanopoulos, X Dong, L R Sudarsky, S J Hutten, S S Amr, I Shoulson, C M Tanner, A E Lang, M A Nalls

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

80 (5), pp. 674–685, 2016.

Abstract

2015

X Dong, J Tsuji, A Labadorf, P Roussos, J F Chen, R H Myers, S Akbarian, Z Weng

The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease Journal Article

PLoS One, 10 (12), pp. e0144398, 2015.

Abstract

G Bai, I Cheung, H P Shulha, J E Coelho, P Li, X Dong, M Jakovcevski, Y Wang, A Grigorenko, Y Jiang, A Hoss, K Patel, M Zheng, E Rogaev, R H Myers, Z Weng, S Akbarian, J F Chen

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

Hum Mol Genet, 24 (5), pp. 1441–1456, 2015.

Abstract

J J Locascio, S Eberly, Z Liao, G Liu, A N Hoesing, K Duong, A Trisini-Lipsanopoulos, K Dhima, A Y Hung, A W Flaherty, M A Schwarzschild, M T Hayes, A M Wills, U Shivraj Sohur, N I Mejia, D J Selkoe, D Oakes, I Shoulson, X Dong, K Marek, B Zheng, A Ivinson, B T Hyman, J H Growdon, L R Sudarsky, M G Schlossmacher, B Ravina, C R Scherzer

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

Brain, 138 (Pt 9), pp. 2659–2671, 2015.

Abstract

2014

A G Hoss, V K Kartha, X Dong, J C Latourelle, A Dumitriu, T C Hadzi, M E Macdonald, J F Gusella, S Akbarian, J F Chen, Z Weng, R H Myers

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

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

Abstract

V Haberle, N Li, Y Hadzhiev, C Plessy, C Previti, C Nepal, J Gehrig, X Dong, A Akalin, A M Suzuki, W F J van IJcken, O Armant, M Ferg, U Strähle, P Carninci, F Müller, B Lenhard

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

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

Abstract

2013

J Wang, J Zhuang, S Iyer, X Lin, T Whitfield, M Greven, B Pierce, X Dong, A Kundaje, Y Cheng, O Rando, E Birney, R Myers, W Noble, M Snyder, Z Weng

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.

X Z Li, C K Roy, X Dong, E Bolcun-Filas, J Wang, B W Han, J Xu, M J Moore, J C Schimenti, Z Weng, P D Zamore

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

Mol Cell, 50 (1), pp. 67–81, 2013.

Abstract

J Wang, J Zhuang, S Iyer, X Y Lin, M C Greven, B H Kim, J Moore, B G Pierce, X Dong, D Virgil, E Birney, J H Hung, Z Weng

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

Nucleic Acids Res, 41 (Database issue), pp. D171–176, 2013.

Abstract

X Dong, Z Weng

The correlation between histone modifications and gene expression Journal Article

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

2012

ENCODE Project Consortium, others

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

Nature, 2012.

Abstract

X Dong, M C Greven, A Kundaje, S Djebali, J B Brown, C Cheng, T R Gingeras, M Gerstein, R Guigó, E Birney, Z Weng

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

Genome Biol, 13 (9), pp. R53, 2012.

Abstract

J Wang, J Zhuang, S Iyer, X Lin, T W Whitfield, M C Greven, B G Pierce, X Dong, A Kundaje, Y Cheng, O J Rando, E Birney, R M Myers, W S Noble, M Snyder, Z Weng

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

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

Abstract

C Cheng, R Alexander, R Min, J Leng, K Y Yip, J Rozowsky, K K Yan, X Dong, S Djebali, Y Ruan, C A Davis, P Carninci, T Lassman, T R Gingeras, R Guigó, E Birney, Z Weng, M Snyder, M Gerstein

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

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

Abstract

2011

ENCODE Project Consortium, others

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

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

Abstract

J Wang, J Zhuang, S Iyer, X Lin, T Whitfield, M Greven, S Aldred, N Trinklein, X Dong, A Kundaje, Y Cheng, O Rando, E Birney, R Myers, W Noble, M Snyder, Z Weng

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

Submitted, NCP010, 2011.

D Fredman, X Dong, B Lenhard

Making enhancers from spare parts of the genome Journal Article

Genome Biol, 12 (12), pp. 138, 2011.

Abstract

O Yildirim, R Li, J H Hung, P B Chen, X Dong, L S Ee, Z Weng, O J Rando, T 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.

Abstract

2010

X Dong, A Akalin, Y Sharma, B Lenhard

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

BMC Bioinformatics, 11 Suppl 1 , pp. S59, 2010.

Abstract

X Dong, P Navratilova, D Fredman, Ø Drivenes, T S Becker, B Lenhard

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

Nucleic Acids Res, 38 (4), pp. 1071–1085, 2010.

Abstract

2009

X Dong, D Fredman, B Lenhard

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

Genome Biol, 10 (8), pp. R86, 2009.

Abstract

X Dong

The brainstorm Journal Article

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

A Akalin, D Fredman , E Arner, X Dong , JC Bryne, H Suzuki , CO Daub ,Y Hayashizaki, B Lenhard

Transcriptional features of genomic regulatory blocks Journal Article

Genome Biol, 10 (4), pp. R38, 2009.

Abstract

2008

S Mungpakdee, H C Seo, A R Angotzi, X Dong, A Akalin, D Chourrout

Differential evolution of the 13 Atlantic salmon Hox clusters Journal Article

Mol Biol Evol, 25 (7), pp. 1333–1343, 2008.

Abstract

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