Department of Biochemistry and Molecular Biology

Websitehttps://med.psu.edu/biochemistry

United States

Organization profile

The Department of Biochemistry and Molecular Biology at Penn State College of Medicine strives to marry the increasingly powerful tools of genomics and computational biology with the classic approaches of biochemistry and molecular biology to reveal fundamental processes of biology and to convert those discoveries into treatments that improve the well-being of patients.

Fingerprint The fingerprint is based on mining the text of the scientific documents related to the associated persons. Based on that an index of weighted terms is created, which defines the key subjects of research unit

Proteins Medicine & Life Sciences

Genes Medicine & Life Sciences

DNA Medicine & Life Sciences

Mutation Medicine & Life Sciences

Yeasts Medicine & Life Sciences

Chromatin Medicine & Life Sciences

Neoplasms Medicine & Life Sciences

Plasmodium falciparum Medicine & Life Sciences

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Profiles

Cesar Aliaga, MS

Department of Biochemistry and Molecular Biology - Senior Research Associate

Person: Academic

Maria Bewley, PhD

Department of Biochemistry and Molecular Biology - Associate Professor

Person: Academic

James Broach, PhD

Department of Biochemistry and Molecular Biology - Distinguished Professor and Chair
Institute for Personalized Medicine
Penn State Cancer Institute
Cancer Institute, Experimental Therapeutics

Person: Academic

Laura Carrel, MA, PhD

Department of Biochemistry and Molecular Biology - Associate Professor
Huck Institutes of the Life Sciences

Person: Academic

Kun-Ming Chen, PhD, MS

Department of Biochemistry and Molecular Biology - Associate Professor
Penn State Cancer Institute
Cancer Institute, Mechanisms of Carcinogenesis

Person: Academic

Keith Cheng, MD, PhD

Department of Pathology and Laboratory Medicine - Distinguished Professor
Division of Experimental Pathology
Department of Biochemistry and Molecular Biology - Distinguished Professor
Department of Pharmacology - Distinguished Professor
Penn State Cancer Institute
Huck Institutes of the Life Sciences
Cancer Institute, Experimental Therapeutics

Person: Academic

Gary Clawson, MS, PhD, MD

Person: Academic

Paula Dalessio, MS, PhD

Department of Biochemistry and Molecular Biology - Assistant Professor

Person: Academic

Arunangshu Das, MSc, PhD

Department of Biochemistry and Molecular Biology - Assistant Professor

Person: Academic

Nikolay Dokholyan, PhD, MS

Department of Pharmacology - G. Thomas Passananti Professor and Vice Chair for Research
Department of Biochemistry and Molecular Biology - G. Thomas Passananti Professor
Cancer Institute, Experimental Therapeutics
Penn State Cancer Institute

Person: Academic

Research Output 1969 2019

107213 Citations
139 h-Index
1979 Article
139 Review article
43 Comment/debate
31 Chapter
91 More

5 Citations (Scopus)

Allostery in Its Many Disguises: From Theory to Applications

Wodak, S. J., Paci, E., Dokholyan, N., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J. P., Bolhuis, P. G., Vreede, J., Faccioli, P. & 19 othersOrioli, S., Ravasio, R., Yan, L., Brito, C., Wyart, M., Gkeka, P., Rivalta, I., Palermo, G., McCammon, J. A., Panecka-Hofman, J., Wade, R. C., Di Pizio, A., Niv, M. Y., Nussinov, R., Tsai, C. J., Jang, H., Padhorny, D., Kozakov, D. & McLeish, T., Apr 2 2019, In : Structure. 27, 4, p. 566-578 13 p.

Research output: Contribution to journal › Review article

Allosteric Regulation

Biological Phenomena

Education

Drug Design

Signal Transduction

A single nucleotide polymorphism in dopamine beta hydroxylase (rs6271(C>T)) is over-represented in inflammatory bowel disease patients and reduces circulating enzyme

Gonzalez-Lopez, E., Kawasawa-Imamura, Y., Zhang, L., Huang, X., Koltun, W., Coates, M. & Vrana, K., Feb 1 2019, In : PloS one. 14, 2, e0210175.

Research output: Contribution to journal › Article

Open Access

dopamine beta-monooxygenase

Dopamine beta-Hydroxylase

inflammatory bowel disease

Polymorphism

Inflammatory Bowel Diseases

1 Citation (Scopus)

Association between DNA methylation in obesity-related genes and body mass index percentile in adolescents

He, F., Berg, A., Imamura, Y., Bixler, E., Fernandez-Mendoza, J., Whitsel, E. A. & Liao, D., Dec 1 2019, In : Scientific reports. 9, 1, 2079.

Research output: Contribution to journal › Article

DNA Methylation

Body Mass Index

Obesity

Genes

Pediatric Obesity

7 Citations (Scopus)

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

23andMe Research Team, HUNT All-In Psychiatry, Liu, M., Jiang, Y., Wedow, R., Li, Y., Brazel, D. M., Chen, F., Datta, G., Davila-Velderrain, J., McGuire, D., Tian, C., Zhan, X., Agee, M., Alipanahi, B., Auton, A., Bell, R. K., Bryc, K., Elson, S. L., Fontanillas, P. & 32 othersFurlotte, N. A., Hinds, D. A., Hromatka, B. S., Huber, K. E., Kleinman, A., Litterman, N. K., McIntyre, M. H., Mountain, J. L., Northover, C. A. M., Sathirapongsasuti, J. F., Sazonova, O. V., Shelton, J. F., Shringarpure, S., Tian, C., Tung, J. Y., Vacic, V., Wilson, C. H., Pitts, S. J., Mitchell, A., Skogholt, A. H., Winsvold, B. S., Sivertsen, B., Stordal, E., Morken, G., Kallestad, H., Heuch, I., Zwart, J. A., Fjukstad, K. K., Pedersen, L. M., Gabrielsen, M. E., Johnsen, M. B. & Liu, D., Feb 1 2019, In : Nature Genetics. 51, 2, p. 237-244 8 p.

Research output: Contribution to journal › Letter

Tobacco Use

Alcohols

Tobacco Use Cessation

Genetic Association Studies

Synaptic Transmission

Brexanolone, a neurosteroid antidepressant, vindicates the gabaergic deficit hypothesis of depression and may foster resilience [version 1; peer review: 4 approved]

Luscher, B. & Möhler, H., Jan 1 2019, In : F1000Research. 8, 751.

Research output: Contribution to journal › Review article

Open Access

Pregnanolone

Postpartum Depression

Peer Review

GABA Receptors

Major Depressive Disorder

Cardiomyopathy Mutations in Metavinculin Disrupt Regulation of Vinculin-Induced F-Actin Assemblies

Sarker, M., Lee, H. T., Mei, L., Krokhotin, A., de los Reyes, S. E., Yen, L., Costantini, L. M., Griffith, J., Dokholyan, N., Alushin, G. M. & Campbell, S. L., Apr 5 2019, In : Journal of Molecular Biology. 431, 8, p. 1604-1618 15 p.

Research output: Contribution to journal › Article

Vinculin

Cardiomyopathies

Actins

Mutation

Dimerization

Characterization of histone deacetylase expression within in vitro and in vivo bladder cancer model systems

Buckwalter, J. M., Chan, W., Shuman, L., Wildermuth, T., Ellis-Mohl, J., Walter, V., Warrick, J., Wu, X. R., Kaag, M. G., Raman, J. & Degraff, D., May 2 2019, In : International journal of molecular sciences. 20, 10, 2599.

Research output: Contribution to journal › Article

Open Access

Histone Deacetylases

bladder

Polymerase chain reaction

Urinary Bladder Neoplasms

cancer

Circulating microRNAs in plasma among men with low-grade and high-grade prostate cancer at prostate biopsy

McDonald, A., Vira, M., Walter, V., Shen, J., Raman, J., Sanda, M. G., Patil, D. & Taioli, E., Jun 15 2019, In : Prostate. 79, 9, p. 961-968 8 p.

Research output: Contribution to journal › Article

MicroRNAs

Prostatic Neoplasms

Biopsy

Neoplasm Grading

Prostate-Specific Antigen

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations

Brodie, N. I., Popov, K. I., Petrotchenko, E. V., Dokholyan, N. & Borchers, C. H., Mar 1 2019, In : PLoS computational biology. 15, 3, e1006859.

Research output: Contribution to journal › Article

Open Access

Synucleins

Discrete Dynamics

molecular dynamics

protein structure

Molecular Dynamics Simulation

1 Citation (Scopus)

Dietary sugar silences a colonization factor in a mammalian gut symbiont

Townsend, G. E., Han, W., Schwalm, N. D., Raghavan, V., Barry, N. A., Goodman, A. L. & Groisman, E. A., Jan 2 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 1, p. 233-238 6 p.

Research output: Contribution to journal › Article

Dietary Sucrose

Fructose

Glucose

Diet

Food

Projects 1981 2023

11 Active
47 Finished

Structural and Molecular Basis of Human ATG3 Activation and Regulation for LC3 Lipid Conjugation in Autophagy

Tian, F.

National Institutes of Health

1/15/19 → 12/31/22

Project: Research project

Autophagy

Lipids

Membranes

Heart Neoplasms

Structural Models

Targeting Rab6-km23-1-mediated compartmentalized trafficking as a novel therapeutic approach to Alzheimers Disease

Mulder, K. & Liotta, L. A.

National Institutes of Health

8/15/18 → 5/31/20

Project: Research project

Amyloid beta-Protein Precursor

Alzheimer Disease

Amyloid

Protein Transport

Therapeutics

Visualization, modeling and validation of chromatin interaction data

Yue, F.

National Institutes of Health

1/8/18 → 12/31/22

Project: Research project

Visualization

Genes

Throughput

Transcription factors

Computational methods

Impact of genetic variants on gene regulation and 3D genome organization in human diseases

Yue, F.

National Institutes of Health

9/1/17 → 7/31/22

Project: Research project

Genome

Genes

Chromatin

Single Nucleotide Polymorphism

Deoxyribonucleases

Penn State Biomedical Big Data to Knowledge (B2D2K) Training Program

Honavar, V. G., Ritchie, M. D., Li, R., Ritchie, M. D. & Broach, J.

National Institutes of Health

4/1/16 → 3/31/21

Project: Research project

Health

Bioinformatics

Statistics

Information science

Big data

Molecular Insights into Membrane Curvature Recognition

Tian, F.

National Institutes of Health

2/1/14 → 11/30/19

Project: Research project

Membranes

Lipids

Bacillus subtilis

Recognition (Psychology)

Capsid Proteins

Genotoxicity and Repair of Tobacco-Specific Nitrosamine DNA Adducts

Spratt, T.

National Institutes of Health

7/20/12 → 5/31/23

Project: Research project

Nitrosamines

DNA Adducts

Tobacco

Oligodeoxyribonucleotides

Smoke

Preparing for research careers related to diabetes, digestive &kidney diseases

Matters, G., Matters, G., Reeves, W. B. & Bond, J.

National Institutes of Health

6/1/07 → 2/28/22

Project: Research project

chronic illness

career

Disease

student

experience

Ras and Tor Signaling in Yeast

Broach, J.

National Institutes of Health

4/1/07 → 1/31/20

Project: Research project

Yeasts

Food

Transcription Factors

Metabolome

Growth

GENE REGULATION DURING CHLAMYDOMONAS ZYGOTE DEVELOPMENT

Matters, G.

National Institutes of Health

3/14/88 → …

Project: Research project

Activities 2017 2017

3 Oral presentation

Motivations and Potential for a 3D Image Informatics for Histopathology (Panel Discussion)

Keith Cheng (Speaker)

Nov 4 2017

Activity: Talk types › Oral presentation

From Morphology to Math: Using whole zebrafish to create the engineering and computational infrastructure for Microanatomic Phenomics

Keith Cheng (Speaker), Y Ding (Speaker), SR Katz (Speaker), AY Lin (Speaker), D van Rossum (Speaker), D Vanselow (Speaker)

Sep 27 2017

Activity: Talk types › Oral presentation

Morphometric phenomics and Cross-Atlas Registration of Virtual 3D soft tissue microCT images of Zebrafish

Keith Cheng (Speaker), Y Ding (Speaker), AY Lin (Speaker), M Yakovlev (Speaker), D Vanselow (Speaker), X Xin (Speaker), S Katz (Speaker), D Vanselow (Speaker), PJ La Riviere (Speaker)

Jul 5 2017

Activity: Talk types › Oral presentation