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2021

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

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

Abstract

2020

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 Forthcoming

medRxiv, Forthcoming.

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 Forthcoming

bioRxiv, Forthcoming.

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

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.

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.

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

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

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.

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

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

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

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

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, 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

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

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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