skip to Main Content

2021

43.

Qingfu Zhu, Liming Cheng, Chunyu Deng, Liu Huang, Jiaoyuan Li, Yong Wang, Meng Li, Qinsi Yang, Xianjun Dong, Jianzhong Su, Luke P. Lee, Fei Liu

The genetic source tracking of human urinary exosomes Journal Article

In: Proceedings of the National Academy of Sciences, 118 (43), 2021, ISSN: 0027-8424.

Abstract | Links

42.

T Wang, Y Liu, J Ruan, X Dong, Y Wang, J Peng

A pipeline for RNA-seq based eQTL analysis with automated quality control procedures Journal Article

In: BMC Bioinformatics, 22 (Suppl 9), pp. 403, 2021, ISSN: 1471-2105.

Abstract | Links

41.

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

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

In: Nat Genet, 53 (6), pp. 787–793, 2021, ISSN: 1546-1718.

Abstract | Links

40.

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

In: Bioinformatics, 2021, (btab385).

Abstract | Links

39.

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

In: Movement Disorders, 2021.

Links

38.

X Dong, C Liu, M Dozmorov

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

In: Briefings of Functional Genomics, 2021.

Abstract | Links

37.

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

In: Movement Disorders, 2021.

Abstract | Links

36.

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

In: Acta Neuropathol., 2021.

Abstract | Links

35.

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

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

Abstract | Links

34.

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

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

Abstract | Links

2020

33.

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

In: medRxiv, Forthcoming.

32.

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

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

31.

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

In: medRxiv, Forthcoming.

30.

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

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

Abstract

2019

29.

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

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

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

Abstract | Links

28.

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

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

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

2018

27.

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

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

Abstract | Links

2017

26.

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.

25.

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

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

Abstract

2016

24.

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

In: 80 (5), pp. 674–685, 2016.

Abstract

2015

23.

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

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

Abstract

22.

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

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

Abstract

21.

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

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

Abstract

2014

20.

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

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

Abstract

19.

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

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

Abstract

2013

18.

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

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

17.

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

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

Abstract

16.

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

In: Mol Cell, 50 (1), pp. 67–81, 2013.

Abstract

15.

X Dong, Z Weng

The correlation between histone modifications and gene expression Journal Article

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

2012

14.

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

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

Abstract

13.

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

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

Abstract

12.

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

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

Abstract

11.

ENCODE Project Consortium, others

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

In: Nature, 2012.

Abstract

2011

10.

D Fredman, X Dong, B Lenhard

Making enhancers from spare parts of the genome Journal Article

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

Abstract

9.

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

In: Cell, 147 (7), pp. 1498–1510, 2011.

Abstract

8.

ENCODE Project Consortium, others

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

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

Abstract

7.

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

In: Submitted, NCP010, 2011.

2010

6.

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

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

Abstract | Links

5.

X Dong, A Akalin, Y Sharma, B Lenhard

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

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

Abstract | Links

2009

4.

X Dong

The brainstorm Journal Article

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

Links

3.

X Dong, D Fredman, B Lenhard

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

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

Abstract | Links

2.

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

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

Abstract | Links

2008

1.

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

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

Abstract | Links

Back To Top
X