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Hongbo Liu, Ph.D.

Hongbo Liu, Ph.D.

Contact

Administrative (585) 273-1441

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About Me

Faculty Appointments

Assistant Professor - Department of Biomedical Genetics (SMD)

Credentials

Post-doctoral Training & Residency

Research Associate, University of Pennsylvania 2023 - 2024

Postdoc Fellow, University of Pennsylvania 2018 - 2023

Postdoc Fellow, Van Andel Institute 2016 - 2018

Education

PhD | Harbin Institute of Technology. 2015

MS | Harbin Medical University. 2010

BS | Qufu Normal University. 2007

Research

Our research is focused on aging genomics. Utilizing cutting-edge sequencing technologies and machine learning models, we are dedicated to uncovering genetic determinants of lifespan, epigenetic regulators of aging, disease-causing genes, key cell types involved, and viable therapeutic targets.
Our research is focused on aging genomics. Utilizing cutting-edge sequencing technologies and machine learning models, we are dedicated to uncovering genetic determinants of lifespan, epigenetic regulators of aging, disease-causing genes, key cell types involved, and viable therapeutic targets.

Publications

Journal Articles

Proteomics and Incident Kidney Failure in Individuals With CKD: The African American Study of Kidney Disease and Hypertension and the Boston Kidney Biopsy Cohort.

Chen TK, Surapaneni AL, Schmidt IM, Waikar SS, Coresh J, Liu H, Susztak K, Rhee EP, Liu C, Schlosser P, Grams ME

Kidney medicine.. 2024 December 6 (12):100921. Epub 10/16/2024.

Human genetics identify convergent signals in mitochondrial LACTB-mediated lipid metabolism in cardiovascular-kidney-metabolic syndrome.

Li S, Liu H, Hu H, Ha E, Prasad P, Jenkins BC, Das US, Mukherjee S, Shishikura K, Hu R, Rader DJ, Pei L, Baur JA, Matthews ML, FitzGerald GA, McReynolds MR, Susztak K

Cell metabolism.. 2024 November 14 Epub 11/14/2024.

TET2 germline variants promote kidney disease by impairing DNA repair and activating cytosolic nucleotide sensors.

Liang X, Liu H, Hu H, Ha E, Zhou J, Abedini A, Sanchez-Navarro A, Klötzer KA, Susztak K

Nature communications.. 2024 November 715 (1):9621. Epub 11/07/2024.

A genome-wide association analysis reveals new pathogenic pathways in gout.

Major TJ, Takei R, Matsuo H, Leask MP, Sumpter NA, Topless RK, Shirai Y, Wang W, Cadzow MJ, Phipps-Green AJ, Li Z, Ji A, Merriman ME, Morice E, Kelley EE, Wei WH, McCormick SPA, Bixley MJ, Reynolds RJ, Saag KG, Fadason T, Golovina E, O'Sullivan JM, Stamp LK, Dalbeth N, Abhishek A, Doherty M, Roddy E, Jacobsson LTH, Kapetanovic MC, Melander O, Andrés M, Pérez-Ruiz F, Torres RJ, Radstake T, Jansen TL, Janssen M, Joosten LAB, Liu R, Gaal OI, Cri?an TO, Rednic S, Kurreeman F, Huizinga TWJ, Toes R, Lioté F, Richette P, Bardin T, Ea HK, Pascart T, McCarthy GM, Helbert L, Stib?rková B, Tausche AK, Uhlig T, Vitart V, Boutin TS, Hayward C, Riches PL, Ralston SH, Campbell A, MacDonald TM, , Nakayama A, Takada T, Nakatochi M, Shimizu S, Kawamura Y, Toyoda Y, Nakaoka H, Yamamoto K, Matsuo K, Shinomiya N, Ichida K, , Lee C, , Bradbury LA, Brown MA, Robinson PC, Buchanan RRC, Hill CL, Lester S, Smith MD, Rischmueller M, Choi HK, Stahl EA, Miner JN, Solomon DH, Cui J, Giacomini KM, Brackman DJ, Jorgenson EM, , Liu H, Susztak K, , Shringarpure S, So A, Okada Y, Li C, Shi Y, Merriman TR

Nature genetics.. 2024 October 15 Epub 10/15/2024.

Genome-wide association study of hospitalized patients and acute kidney injury.

Siew ED, Hellwege JN, Hung AM, Birkelo BC, Vincz AJ, Parr SK, Denton J, Greevy RA, Robinson-Cohen C, Liu H, Susztak K, Matheny ME, Velez Edwards DR

Kidney international.. 2024 August 106 (2):291-301. Epub 05/24/2024.

Single-cell multi-omic and spatial profiling of human kidneys implicates the fibrotic microenvironment in kidney disease progression.

Abedini A, Levinsohn J, Klötzer KA, Dumoulin B, Ma Z, Frederick J, Dhillon P, Balzer MS, Shrestha R, Liu H, Vitale S, Bergeson AM, Devalaraja-Narashimha K, Grandi P, Bhattacharyya T, Hu E, Pullen SS, Boustany-Kari CM, Guarnieri P, Karihaloo A, Traum D, Yan H, Coleman K, Palmer M, Sarov-Blat L, Morton L, Hunter CA, Kaestner KH, Li M, Susztak K

Nature genetics.. 2024 August 56 (8):1712-1724. Epub 07/24/2024.

Association of Integrated Proteomic and Metabolomic Modules with Risk of Kidney Disease Progression.

Schlosser P, Surapaneni AL, Borisov O, Schmidt IM, Zhou L, Anderson A, Deo R, Dubin R, Ganz P, He J, Kimmel PL, Li H, Nelson RG, Porter AC, Rahman M, Rincon-Choles H, Shah V, Unruh ML, Vasan RS, Zheng Z, Feldman HI, Waikar SS, Köttgen A, Rhee EP, Coresh J, Grams ME,

Journal of the American Society of Nephrology : JASN.. 2024 July 135 (7):923-935. Epub 04/19/2024.

Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development.

Yan Y, Liu H, Abedini A, Sheng X, Palmer M, Li H, Susztak K

Nature communications.. 2024 January 2915 (1):873. Epub 01/29/2024.

Improve-RRBS: a novel tool to correct the 3' trimming of reduced representation sequencing reads.

Fóthi Á, Liu H, Susztak K, Aranyi T

Bioinformatics advances.. 2024 4 (1):vbae076. Epub 05/24/2024.

ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules.

Mukhi D, Li L, Liu H, Doke T, Kolligundla LP, Ha E, Kloetzer K, Abedini A, Mukherjee S, Wu J, Dhillon P, Hu H, Guan D, Funai K, Uehara K, Titchenell PM, Baur JA, Wellen KE, Susztak K

The Journal of clinical investigation.. 2023 December 5134 (4)Epub 12/05/2023.

Unified Mouse and Human Kidney Single-Cell Expression Atlas Reveal Commonalities and Differences in Disease States.

Zhou J, Abedini A, Balzer MS, Shrestha R, Dhillon P, Liu H, Hu H, Susztak K

Journal of the American Society of Nephrology : JASN.. 2023 November 134 (11):1843-1862. Epub 08/28/2023.

Deletion of protein tyrosine phosphatase SHP-1 restores SUMOylation of podocin and reverses the progression of diabetic kidney disease.

Lizotte F, Rousseau M, Denhez B, Lévesque D, Guay A, Liu H, Moreau J, Higgins S, Sabbagh R, Susztak K, Boisvert FM, Côté AM, Geraldes P

Kidney international.. 2023 October 104 (4):787-802. Epub 07/27/2023.

Unbiased Human Kidney Tissue Proteomics Identifies Matrix Metalloproteinase 7 as a Kidney Disease Biomarker.

Hirohama D, Abedini A, Moon S, Surapaneni A, Dillon ST, Vassalotti A, Liu H, Doke T, Martinez V, Md Dom Z, Karihaloo A, Palmer MB, Coresh J, Grams ME, Niewczas MA, Susztak K

Journal of the American Society of Nephrology : JASN.. 2023 July 134 (7):1279-1291. Epub 04/05/2023.

Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage.

Schlosser P, Zhang J, Liu H, Surapaneni AL, Rhee EP, Arking DE, Yu B, Boerwinkle E, Welling PA, Chatterjee N, Susztak K, Coresh J, Grams ME

Genome biology.. 2023 June 2624 (1):150. Epub 06/26/2023.

DNA methylation markers for kidney function and progression of diabetic kidney disease.

Li KY, Tam CHT, Liu H, Day S, Lim CKP, So WY, Huang C, Jiang G, Shi M, Lee HM, , Lan HY, Szeto CC, Hanson RL, Nelson RG, Susztak K, Chan JCN, Yip KY, Ma RCW

Nature communications.. 2023 May 1514 (1):2543. Epub 05/15/2023.

Tet2- and Tet3- Mediated Cytosine Hydroxymethylation in Six2 Progenitor Cells in Mice Is Critical for Nephron Progenitor Differentiation and Nephron Endowment.

Liang X, Aranyi T, Zhou J, Guan Y, Hu H, Liu H, Susztak K

Journal of the American Society of Nephrology : JASN.. 2023 April 134 (4):572-589. Epub 12/15/2022.

Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development.

Dhillon P, Mulholland KA, Hu H, Park J, Sheng X, Abedini A, Liu H, Vassalotti A, Wu J, Susztak K

Nature communications.. 2023 February 214 (1):559. Epub 02/02/2023.

Genome-wide meta-analysis and omics integration identifies novel genes associated with diabetic kidney disease.

Sandholm N, Cole JB, Nair V, Sheng X, Liu H, Ahlqvist E, van Zuydam N, Dahlström EH, Fermin D, Smyth LJ, Salem RM, Forsblom C, Valo E, Harjutsalo V, Brennan EP, McKay GJ, Andrews D, Doyle R, Looker HC, Nelson RG, Palmer C, McKnight AJ, Godson C, Maxwell AP, Groop L, McCarthy MI, Kretzler M, Susztak K, Hirschhorn JN, Florez JC, Groop PH,

Diabetologia.. 2022 September 65 (9):1495-1509. Epub 06/28/2022.

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease.

Liu H, Doke T, Guo D, Sheng X, Ma Z, Park J, Vy HMT, Nadkarni GN, Abedini A, Miao Z, Palmer M, Voight BF, Li H, Brown CD, Ritchie MD, Shu Y, Susztak K

Nature genetics.. 2022 July 54 (7):950-962. Epub 06/16/2022.

Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus.

Tin A, Schlosser P, Matias-Garcia PR, Thio CHL, Joehanes R, Liu H, Yu Z, Weihs A, Hoppmann A, Grundner-Culemann F, Min JL, Kuhns VLH, Adeyemo AA, Agyemang C, Ärnlöv J, Aziz NA, Baccarelli A, Bochud M, Brenner H, Bressler J, Breteler MMB, Carmeli C, Chaker L, Coresh J, Corre T, Correa A, Cox SR, Delgado GE, Eckardt KU, Ekici AB, Endlich K, Floyd JS, Fraszczyk E, Gao X, Gào X, Gelber AC, Ghanbari M, Ghasemi S, Gieger C, Greenland P, Grove ML, Harris SE, Hemani G, Henneman P, Herder C, Horvath S, Hou L, Hurme MA, Hwang SJ, Kardia SLR, Kasela S, Kleber ME, Koenig W, Kooner JS, Kronenberg F, Kühnel B, Ladd-Acosta C, Lehtimäki T, Lind L, Liu D, Lloyd-Jones DM, Lorkowski S, Lu AT, Marioni RE, März W, McCartney DL, Meeks KAC, Milani L, Mishra PP, Nauck M, Nowak C, Peters A, Prokisch H, Psaty BM, Raitakari OT, Ratliff SM, Reiner AP, Schöttker B, Schwartz J, Sedaghat S, Smith JA, Sotoodehnia N, Stocker HR, Stringhini S, Sundström J, Swenson BR, van Meurs JBJ, van Vliet-Ostaptchouk JV, Venema A, Völker U, Winkelmann J, Wolffenbuttel BHR, Zhao W, Zheng Y, , , Loh M, Snieder H, Waldenberger M, Levy D, Akilesh S, Woodward OM, Susztak K, Teumer A, Köttgen A

Nature communications.. 2021 December 912 (1):7173. Epub 12/09/2021.

Meta-analyses identify DNA methylation associated with kidney function and damage.

Schlosser P, Tin A, Matias-Garcia PR, Thio CHL, Joehanes R, Liu H, Weihs A, Yu Z, Hoppmann A, Grundner-Culemann F, Min JL, Adeyemo AA, Agyemang C, Ärnlöv J, Aziz NA, Baccarelli A, Bochud M, Brenner H, Breteler MMB, Carmeli C, Chaker L, Chambers JC, Cole SA, Coresh J, Corre T, Correa A, Cox SR, de Klein N, Delgado GE, Domingo-Relloso A, Eckardt KU, Ekici AB, Endlich K, Evans KL, Floyd JS, Fornage M, Franke L, Fraszczyk E, Gao X, Gào X, Ghanbari M, Ghasemi S, Gieger C, Greenland P, Grove ML, Harris SE, Hemani G, Henneman P, Herder C, Horvath S, Hou L, Hurme MA, Hwang SJ, Jarvelin MR, Kardia SLR, Kasela S, Kleber ME, Koenig W, Kooner JS, Kramer H, Kronenberg F, Kühnel B, Lehtimäki T, Lind L, Liu D, Liu Y, Lloyd-Jones DM, Lohman K, Lorkowski S, Lu AT, Marioni RE, März W, McCartney DL, Meeks KAC, Milani L, Mishra PP, Nauck M, Navas-Acien A, Nowak C, Peters A, Prokisch H, Psaty BM, Raitakari OT, Ratliff SM, Reiner AP, Rosas SE, Schöttker B, Schwartz J, Sedaghat S, Smith JA, Sotoodehnia N, Stocker HR, Stringhini S, Sundström J, Swenson BR, Tellez-Plaza M, van Meurs JBJ, van Vliet-Ostaptchouk JV, Venema A, Verweij N, Walker RM, Wielscher M, Winkelmann J, Wolffenbuttel BHR, Zhao W, Zheng Y, , , Loh M, Snieder H, Levy D, Waldenberger M, Susztak K, Köttgen A, Teumer A

Nature communications.. 2021 December 912 (1):7174. Epub 12/09/2021.

Genome-wide association studies identify the role of caspase-9 in kidney disease.

Doke T, Huang S, Qiu C, Sheng X, Seasock M, Liu H, Ma Z, Palmer M, Susztak K

Science advances.. 2021 November 57 (45):eabi8051. Epub 11/05/2021.

Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease.

Quinn GZ, Abedini A, Liu H, Ma Z, Cucchiara A, Havasi A, Hill J, Palmer MB, Susztak K

Journal of the American Society of Nephrology : JASN.. 2021 November 32 (11):2863-2876. Epub 08/04/2021.

Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments.

Sheng X, Guan Y, Ma Z, Wu J, Liu H, Qiu C, Vitale S, Miao Z, Seasock MJ, Palmer M, Shin MK, Duffin KL, Pullen SS, Edwards TL, Hellwege JN, Hung AM, Li M, Voight BF, Coffman TM, Brown CD, Susztak K

Nature genetics.. 2021 September 53 (9):1322-1333. Epub 08/12/2021.

A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis.

Guan Y, Liang X, Ma Z, Hu H, Liu H, Miao Z, Linkermann A, Hellwege JN, Voight BF, Susztak K

Nature communications.. 2021 August 2312 (1):5078. Epub 08/23/2021.

Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis.

Doke T, Huang S, Qiu C, Liu H, Guan Y, Hu H, Ma Z, Wu J, Miao Z, Sheng X, Zhou J, Cao A, Li J, Kaufman L, Hung A, Brown CD, Pestell R, Susztak K

The Journal of clinical investigation.. 2021 May 17131 (10)Epub 1900 01 01.

Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets.

Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K

Nature communications.. 2021 April 1512 (1):2277. Epub 04/15/2021.

Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney.

Abedini A, Zhu YO, Chatterjee S, Halasz G, Devalaraja-Narashimha K, Shrestha R, S Balzer M, Park J, Zhou T, Ma Z, Sullivan KM, Hu H, Sheng X, Liu H, Wei Y, Boustany-Kari CM, Patel U, Almaani S, Palmer M, Townsend R, Blady S, Hogan J, Morton L, Susztak K,

Journal of the American Society of Nephrology : JASN.. 2021 March 32 (3):614-627. Epub 02/02/2021.

The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation.

Dhillon P, Park J, Hurtado Del Pozo C, Li L, Doke T, Huang S, Zhao J, Kang HM, Shrestra R, Balzer MS, Chatterjee S, Prado P, Han SY, Liu H, Sheng X, Dierickx P, Batmanov K, Romero JP, Prósper F, Li M, Pei L, Kim J, Montserrat N, Susztak K

Cell metabolism.. 2021 February 233 (2):379-394.e8. Epub 12/09/2020.

Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease.

Sheng X, Qiu C, Liu H, Gluck C, Hsu JY, He J, Hsu CY, Sha D, Weir MR, Isakova T, Raj D, Rincon-Choles H, Feldman HI, Townsend R, Li H, Susztak K

Proceedings of the National Academy of Sciences of the United States of America.. 2020 November 17117 (46):29013-29024. Epub 11/03/2020.

and -Decommissioned Fetal Enhancers are Linked to Kidney Disease.

Guan Y, Liu H, Ma Z, Li SY, Park J, Sheng X, Susztak K

Journal of the American Society of Nephrology : JASN.. 2020 April 31 (4):765-782. Epub 03/03/2020.

The MS-lincRNA landscape reveals a novel lincRNA BCLIN25 that contributes to tumorigenesis by upregulating ERBB2 expression via epigenetic modification and RNA-RNA interactions in breast cancer.

Xu S, Liu H, Wan L, Zhang W, Wang Q, Zhang S, Shang S, Zhang Y, Pang D

Cell death & disease.. 2019 December 410 (12):920. Epub 12/04/2019.

Development of highly potent glucocorticoids for steroid-resistant severe asthma.

He Y, Shi J, Nguyen QT, You E, Liu H, Ren X, Wu Z, Li J, Qiu W, Khoo SK, Yang T, Yi W, Sun F, Xi Z, Huang X, Melcher K, Min B, Xu HE

Proceedings of the National Academy of Sciences of the United States of America.. 2019 April 2116 (14):6932-6937. Epub 03/20/2019.

Long-Range Chromatin Interactions in the Kidney.

Guan Y, Liu H, Susztak K

Journal of the American Society of Nephrology : JASN.. 2019 March 30 (3):367-369. Epub 02/13/2019.

Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns.

Zhang S, Wang Y, Gu Y, Zhu J, Ci C, Guo Z, Chen C, Wei Y, Lv W, Liu H, Zhang D, Zhang Y

Molecular oncology.. 2018 June 12 (7):1047-1060. Epub 05/21/2018.

The landscape of DNA methylation-mediated regulation of long non-coding RNAs in breast cancer.

Zhang C, Wang X, Li X, Zhao N, Wang Y, Han X, Ci C, Zhang J, Li M, Zhang Y

Oncotarget.. 2017 August 18 (31):51134-51150. Epub 05/08/2017.

Survival differences of CIMP subtypes integrated with CNA information in human breast cancer.

Wang H, Yan W, Zhang S, Gu Y, Wang Y, Wei Y, Liu H, Wang F, Wu Q, Zhang Y

Oncotarget.. 2017 July 258 (30):48807-48819. Epub 1900 01 01.

Cell subpopulation deconvolution reveals breast cancer heterogeneity based on DNA methylation signature.

Wen Y, Wei Y, Zhang S, Li S, Liu H, Wang F, Zhao Y, Zhang D, Zhang Y

Briefings in bioinformatics. 2017 May 118 (3):426-440. Epub 1900 01 01.

DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database.

Xiong Y, Wei Y, Gu Y, Zhang S, Lyu J, Zhang B, Chen C, Zhu J, Wang Y, Liu H, Zhang Y

Nucleic acids research.. 2017 January 445 (D1):D888-D895. Epub 11/29/2016.

Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development.

Li J, Gao Z, Wang X, Liu H, Zhang Y, Liu Z

Scientific reports.. 2016 December 66 :38333. Epub 12/06/2016.

Folic Acid Alters Methylation Profile of JAK-STAT and Long-Term Depression Signaling Pathways in Alzheimer's Disease Models.

Li W, Liu H, Yu M, Zhang X, Zhang Y, Liu H, Wilson JX, Huang G

Molecular neurobiology.. 2016 November 53 (9):6548-6556. Epub 12/01/2015.

DNA methylation dynamics: identification and functional annotation.

Liu H, Li S, Wang X, Zhu J, Wei Y, Wang Y, Wen Y, Wang L, Huang Y, Zhang B, Shang S, Zhang Y

Briefings in functional genomics.. 2016 November 15 (6):470-484. Epub 08/10/2016.

Computational identification of putative lincRNAs in mouse embryonic stem cell.

Liu H, Lyu J, Liu H, Gao Y, Guo J, He H, Han Z, Zhang Y, Wu Q

Scientific reports.. 2016 October 76 :34892. Epub 10/07/2016.

The identification of age-associated cancer markers by an integrative analysis of dynamic DNA methylation changes.

Wang Y, Zhang J, Xiao X, Liu H, Wang F, Li S, Wen Y, Wei Y, Su J, Zhang Y, Zhang Y

Scientific reports.. 2016 March 76 :22722. Epub 03/07/2016.

Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.

Liu H, Liu X, Zhang S, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q, Zhang Y

Nucleic acids research.. 2016 January 844 (1):75-94. Epub 12/03/2015.

SEA: a super-enhancer archive.

Wei Y, Zhang S, Shang S, Zhang B, Li S, Wang X, Wang F, Su J, Wu Q, Liu H, Zhang Y

Nucleic acids research.. 2016 January 444 (D1):D172-9. Epub 11/17/2015.

CellMethy: Identification of a focal concordantly methylated pattern of CpGs revealed wide differences between normal and cancer tissues.

Wang F, Zhang S, Liu H, Wei Y, Wang Y, Han X, Su J, Zhang D, Xie B, Zhang Y

Scientific reports.. 2015 December 105 :18037. Epub 12/10/2015.

Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development.

Lv J, Liu H, Yu S, Liu H, Cui W, Gao Y, Zheng T, Qin G, Guo J, Zeng T, Han Z, Zhang Y, Wu Q

Molecular genetics and genomics : MGG.. 2015 April 290 (2):685-97. Epub 11/27/2014.

Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types.

Yan H, Zhang D, Liu H, Wei Y, Lv J, Wang F, Zhang C, Wu Q, Su J, Zhang Y

Scientific reports.. 2015 February 125 :8410. Epub 02/12/2015.

The identification of specific methylation patterns across different cancers.

Zhang C, Zhao H, Li J, Liu H, Wang F, Wei Y, Su J, Zhang D, Liu T, Zhang Y

PloS one.. 2015 10 (3):e0120361. Epub 03/16/2015.

DNA Methylation Patterns Can Estimate Nonequivalent Outcomes of Breast Cancer with the Same Receptor Subtypes.

Zhang M, Zhang S, Wen Y, Wang Y, Wei Y, Liu H, Zhang D, Su J, Wang F, Zhang Y

PloS one.. 2015 10 (11):e0142279. Epub 11/09/2015.

Identification and characterization of long intergenic non-coding RNAs related to mouse liver development.

Lv J, Huang Z, Liu H, Liu H, Cui W, Li B, He H, Guo J, Liu Q, Zhang Y, Wu Q

Molecular genetics and genomics : MGG.. 2014 December 289 (6):1225-35. Epub 07/11/2014.

Revealing the architecture of genetic and epigenetic regulation: a maximum likelihood model.

Wang F, Zhang S, Wen Y, Wei Y, Yan H, Liu H, Su J, Zhang Y, Che J

Briefings in bioinformatics. 2014 November 15 (6):1028-43. Epub 10/30/2013.

MetaImprint: an information repository of mammalian imprinted genes.

Wei Y, Su J, Liu H, Lv J, Wang F, Yan H, Wen Y, Liu H, Wu Q, Zhang Y

Development.. 2014 June 141 (12):2516-23. Epub 05/21/2014.

DevMouse, the mouse developmental methylome database and analysis tools.

Liu H, Zhu R, Lv J, He H, Yang L, Huang Z, Su J, Zhang Y, Yu S, Wu Q

Database : the journal of biological databases and curation.. 2014 2014 :bat084. Epub 01/09/2014.

Detection of type 2 diabetes related modules and genes based on epigenetic networks.

Liu H, Wang T, Liu H, Wei Y, Zhao G, Su J, Wu Q, Qiao H, Zhang Y

BMC systems biology.. 2014 8 Suppl 1 (Suppl 1):S5. Epub 01/24/2014.

Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features.

Lv J, Liu H, Huang Z, Su J, He H, Xiu Y, Zhang Y, Wu Q

Nucleic acids research.. 2013 December 41 (22):10044-61. Epub 09/13/2013.

Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae.

Wu X, Liu H, Liu H, Su J, Lv J, Cui Y, Wang F, Zhang Y

Gene.. 2013 November 1530 (1):8-18. Epub 08/16/2013.

Rice protein exerts a hypocholesterolemic effect through regulating cholesterol metabolism-related gene expression and enzyme activity in adult rats fed a cholesterol-enriched diet.

Yang L, Han G, Liu QH, Wu Q, He HJ, Cheng CZ, Duan YJ

International journal of food sciences and nutrition.. 2013 November 64 (7):836-42. Epub 06/14/2013.

Genome-wide identification of Polycomb target genes in human embryonic stem cells.

Xiao X, Li Z, Liu H, Su J, Wang F, Wu X, Liu H, Wu Q, Zhang Y

Gene.. 2013 April 15518 (2):425-30. Epub 01/09/2013.

CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.

Su J, Yan H, Wei Y, Liu H, Liu H, Wang F, Lv J, Wu Q, Zhang Y

Nucleic acids research.. 2013 January 741 (1):e4. Epub 08/31/2012.

Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data.

Lv J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y, Zhang Y, Wu Q

PloS one.. 2013 8 (8):e71152. Epub 08/14/2013.

Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

Liu H, Chen Y, Lv J, Liu H, Zhu R, Su J, Liu X, Zhang Y, Wu Q

Scientific reports.. 2013 3 :2576. Epub 1900 01 01.

Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network.

Su J, Qi Y, Liu S, Wu X, Lv J, Liu H, Zhang R, Zhang Y

Molecular biology reports.. 2012 February 39 (2):1701-12. Epub 05/28/2011.

Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts.

Su J, Shao X, Liu H, Liu S, Wu Q, Zhang Y

Genomics.. 2012 January 99 (1):10-7. Epub 10/25/2011.

DiseaseMeth: a human disease methylation database.

Lv J, Liu H, Su J, Wu X, Liu H, Li B, Xiao X, Wang F, Wu Q, Zhang Y

Nucleic acids research.. 2012 January 40 (Database issue):D1030-5. Epub 12/01/2011.

Prioritizing cancer-related genes with aberrant methylation based on a weighted protein-protein interaction network.

Liu H, Su J, Li J, Liu H, Lv J, Li B, Qiao H, Zhang Y

BMC systems biology.. 2011 October 115 :158. Epub 10/11/2011.

QDMR: a quantitative method for identification of differentially methylated regions by entropy.

Zhang Y, Liu H, Lv J, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F, Cui Y

Nucleic acids research.. 2011 May 39 (9):e58. Epub 02/08/2011.

Rice protein extracted by different methods affects cholesterol metabolism in rats due to its lower digestibility.

Yang L, Chen J, Xu T, Qiu W, Zhang Y, Zhang L, Xu F, Liu H

International journal of molecular sciences.. 2011 12 (11):7594-608. Epub 11/07/2011.

Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure.

Lv J, Qiao H, Liu H, Wu X, Zhu J, Su J, Wang F, Cui Y, Zhang Y

PloS one.. 2010 December 35 (12):e14219. Epub 12/03/2010.

Detecting novel hypermethylated genes in breast cancer benefiting from feature selection.

Lv J, Su J, Wang F, Qi Y, Liu H, Zhang Y

Computers in biology and medicine.. 2010 February 40 (2):159-67. Epub 12/31/2009.

CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

Su J, Zhang Y, Lv J, Liu H, Tang X, Wang F, Qi Y, Feng Y, Li X

Nucleic acids research.. 2010 January 38 (1):e6. Epub 10/23/2009.

HHMD: the human histone modification database.

Zhang Y, Lv J, Liu H, Zhu J, Su J, Wu Q, Qi Y, Wang F, Li X

Nucleic acids research.. 2010 January 38 (Database issue):D149-54. Epub 11/05/2009.