Department of Biochemistry and Molecular Biology

  • United States

Research Output 1969 2019

Filter
Review article
2019
8 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 others, Orioli, 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 journalReview article

Allosteric Regulation
Biological Phenomena
Education
Drug Design
Signal Transduction
Open Access
Pregnanolone
Peer Review
Antidepressive Agents
Neurotransmitter Agents
Depression
5 Citations (Scopus)

Mechanisms of DNA damage tolerance: post-translational regulation of PCNA

Leung, W., Baxley, R. M., Moldovan, G-L. & Bielinsky, A. K., Jan 1 2019, In : Genes. 10, 1, 10.

Research output: Contribution to journalReview article

Proliferating Cell Nuclear Antigen
DNA Damage
Post Translational Protein Processing
Ubiquitin
Genetic Recombination
1 Citation (Scopus)

TRPM2 in Cancer

Miller, B., Jun 1 2019, In : Cell Calcium. 80, p. 8-17 10 p.

Research output: Contribution to journalReview article

Cell Survival
Neoplasms
Neuroblastoma
Autophagy
Breast Neoplasms
2 Citations (Scopus)

Unraveling the multiplex folding of nucleosome chains in higher order chromatin

Grigoryev, S. & Schubert, M., Jan 1 2019, In : Essays in biochemistry. 63, 1, p. 109-121 13 p.

Research output: Contribution to journalReview article

Nucleosomes
Chromatin
Chromosomes
Epigenomics
DNA
2018
4 Citations (Scopus)

A network-based cancer drug discovery: From integrated multi-omics approaches to precision medicine

Turanli, B., Karagoz, K., Gulfidan, G., Sinha, R., Mardinoglu, A. & Arga, K. Y., Jan 1 2018, In : Current Pharmaceutical Design. 24, 32, p. 3778-3790 13 p.

Research output: Contribution to journalReview article

Precision Medicine
Drug Discovery
Drug Delivery Systems
Neoplasms
Biological Phenomena
3 Citations (Scopus)

Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles

Grigoryev, S., May 22 2018, In : Biophysical journal. 114, 10, p. 2290-2297 8 p.

Research output: Contribution to journalReview article

Nucleosomes
Chromatin
DNA
Eukaryotic Cells
Cell Nucleus
1 Citation (Scopus)
oncogenes
DNA-Directed DNA Polymerase
DNA Replication
Oncogenes
DNA
5 Citations (Scopus)

Disease prevention and delayed aging by dietary sulfur amino acid restriction: Translational implications

Dong, Z., Sinha, R. & Richie, J., Jan 1 2018, In : Annals of the New York Academy of Sciences. 1418, 1, p. 44-55 12 p.

Research output: Contribution to journalReview article

Sulfur Amino Acids
Aging of materials
Insulin
Oxidative stress
Sulfur
8 Citations (Scopus)

Effectiveness of Practices to Support Appropriate Laboratory Test Utilization

Rubinstein, M., Hirsch, R., Bandyopadhyay, K., Madison, B., Taylor, T., Ranne, A., Linville, M., Donaldson, K., Lacbawan, F. & Cornish, N., Feb 17 2018, In : American journal of clinical pathology. 149, 3, p. 197-221 25 p.

Research output: Contribution to journalReview article

Medical Order Entry Systems
Reflex
Length of Stay
Clinical Decision Support Systems
Education
1 Citation (Scopus)

Epidemiology, drug resistance, and pathophysiology of plasmodium vivax malaria

Dayananda, K. K., Achur, R. N. & Gowda, C., Mar 1 2018, In : Journal of Vector Borne Diseases. 55, 1, p. 1-8 8 p.

Research output: Contribution to journalReview article

Vivax Malaria
Drug Resistance
Plasmodium vivax
Malaria
Epidemiology

Genetically modified labeling policies: Moving forward or backward?

Borges, B. J. P., Arantes, O. M. N., Fernandes, A. A. R., Broach, J. & Fernandes, P. M. B., Nov 27 2018, In : Frontiers in Bioengineering and Biotechnology. 6, NOV, 181.

Research output: Contribution to journalReview article

Genetically Modified Food
Food Labeling
Genetically Modified Organisms
Labeling
Food Supply

Parasite Recognition and Signaling Mechanisms in Innate Immune Responses to Malaria

Gowda, C. & Wu, X., Jan 1 2018, In : Frontiers in immunology. 9, 1 p.

Research output: Contribution to journalReview article

Innate Immunity
Malaria
Parasites
Immunity
Infection
1 Citation (Scopus)

Pathophysiology of diverticular disease

Schieffer, K. M., Kline, B. P., Yochum, G. & Koltun, W., Jul 3 2018, In : Expert Review of Gastroenterology and Hepatology. 12, 7, p. 683-692 10 p.

Research output: Contribution to journalReview article

Diverticulitis
Microbiota
Diverticulum
Genetic Predisposition to Disease
PubMed
2 Citations (Scopus)

Utilizing peptide ligand GPCRs to image and treat pancreatic cancer

Matters, G. & Harms, J. F., Jun 1 2018, In : Biomedicines. 6, 2, 65.

Research output: Contribution to journalReview article

G-Protein-Coupled Receptors
Pancreatic Neoplasms
Tumors
Ligands
Peptides
2017
10 Citations (Scopus)

Carcinogenesis of the oral cavity: Environmental causes and potential prevention by black raspberry

El-Bayoumy, K., Chen, K-M., Zhang, S. M., Sun, Y-W., Amin, S., Stoner, G. & Guttenplan, J. B., Jan 1 2017, In : Chemical Research in Toxicology. 30, 1, p. 126-144 19 p.

Research output: Contribution to journalReview article

Mouth Neoplasms
Mouth
Environmental Carcinogens
Carcinogenesis
Animal Models
11 Citations (Scopus)

Casein Kinase II (CK2), Glycogen Synthase Kinase-3 (GSK-3) and Ikaros mediated regulation of leukemia

Gowda, C., Soliman, M., Kapadia, M., Ding, Y., Payne, K. & Dovat, S., Aug 1 2017, In : Advances in Biological Regulation. 65, p. 16-25 10 p.

Research output: Contribution to journalReview article

Phosphatidylinositol 3-Kinase
Glycogen Synthase Kinase 3
Casein Kinase II
Leukemia
Phosphorylation
7 Citations (Scopus)

Casein kinase II (CK2) as a therapeutic target for hematological malignancies

Gowda, C., Sachdev, M., Muthusami, S., Kapadia, M., Petrovic-Dovat, L., Hartman, M., Ding, Y., Song, C., Payne, J. L., Tan, B. & Dovat, S., Jan 1 2017, In : Current Pharmaceutical Design. 23, 1, p. 95-107 13 p.

Research output: Contribution to journalReview article

Casein Kinase II
Hematologic Neoplasms
Leukemia
Neoplasms
Therapeutics
50 Citations (Scopus)

Forging Ahead through Darkness: PCNA, Still the Principal Conductor at the Replication Fork

Choe, K. N. & Moldovan, G-L., Feb 2 2017, In : Molecular cell. 65, 3, p. 380-392 13 p.

Research output: Contribution to journalReview article

Darkness
Proliferating Cell Nuclear Antigen
DNA-Directed DNA Polymerase
Post Translational Protein Processing
Molecular Structure
15 Citations (Scopus)
DNA-Directed DNA Polymerase
Maintenance
Genome
Genomic Instability
Recombinational DNA Repair
4 Citations (Scopus)

Pitfalls of exome sequencing: A case study of the attribution of HABP2 rs7080536 in familial non-medullary thyroid cancer

Gerhard, G. S., Bann, D. V., Broach, J. & Goldenberg, D., Dec 1 2017, In : npj Genomic Medicine. 2, 1, 8.

Research output: Contribution to journalReview article

Exome
Neoplasm Genes
Gene Frequency
Population
Guidelines
16 Citations (Scopus)

Regulation of cellular proliferation in acute lymphoblastic leukemia by Casein Kinase II (CK2) and Ikaros

Gowda, C., Song, C., Kapadia, M., Payne, J. L., Hu, T., Ding, Y. & Dovat, S., Jan 1 2017, In : Advances in Biological Regulation. 63, p. 71-80 10 p.

Research output: Contribution to journalReview article

Casein Kinase II
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Leukemia
Cell Proliferation
Ikaros Transcription Factor
3 Citations (Scopus)

The use of nanoparticulates to treat breast cancer

Tang, X., Loc, W. S., Dong, C., Matters, G., Butler, P. J., Kester, M., Meyers, C., Jiang, Y. & Adair, J. H., Oct 1 2017, In : Nanomedicine. 12, 19, p. 2367-2388 22 p.

Research output: Contribution to journalReview article

Tumors
Breast Neoplasms
Oncology
Hemodynamics
Blood Circulation Time
1 Citation (Scopus)

Transient Receptor Potential-Melastatin Channel Family Member 2: Friend or Foe

Cheung, J. Y. & Miller, B., Jan 1 2017, In : Transactions of the American Clinical and Climatological Association. 128, p. 308-329 22 p.

Research output: Contribution to journalReview article

Transient Receptor Potential Channels
Reactive Oxygen Species
Cell Respiration
Monovalent Cations
Neoplasms
12 Citations (Scopus)

When the lyon(Ized chromosome) roars: Ongoing expression from an inactive X chromosome

Carrel, L. & Brown, C. J., Nov 5 2017, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 372, 1733, 20160355.

Research output: Contribution to journalReview article

X Chromosome Inactivation
X Chromosome
X chromosome
Chromosomes
inactivation
2016
21 Citations (Scopus)

Applications of Discrete Molecular Dynamics in biology and medicine

Proctor, E. A. & Dokholyan, N., Apr 1 2016, In : Current Opinion in Structural Biology. 37, p. 9-13 5 p.

Research output: Contribution to journalReview article

Molecular Dynamics Simulation
Medicine
Microcomputers
Proteostasis Deficiencies
Petroleum Pollution
47 Citations (Scopus)

Controlling Allosteric Networks in Proteins

Dokholyan, N., Jun 8 2016, In : Chemical Reviews. 116, 11, p. 6463-6487 25 p.

Research output: Contribution to journalReview article

Proteins
Ligands
Cystic Fibrosis Transmembrane Conductance Regulator
Biological systems
Binding Sites
26 Citations (Scopus)

DNA methylation, early life environment, and health outcomes

Mitchell, C., Schneper, L. & Notterman, D. A., Jan 1 2016, In : Pediatric Research. 79, 1-2, p. 212-219 8 p.

Research output: Contribution to journalReview article

DNA Methylation
Epigenomics
Health
Genome
Pediatrics
21 Citations (Scopus)

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications

Allen, S. E., Dokholyan, N. & Bowers, A. A., Jan 15 2016, In : ACS Chemical Biology. 11, 1, p. 10-24 15 p.

Research output: Contribution to journalReview article

Biological Products
Scaffolds
Pharmaceutical Chemistry
Point contacts
Proteins
5 Citations (Scopus)

Perioperative circulating tumor cell detection: Current perspectives

Kaifi, J. T., Li, G., Clawson, G., Kimchi, E. T. & Staveley-O'Carroll, K. F., Aug 2 2016, In : Cancer Biology and Therapy. 17, 8, p. 859-869 11 p.

Research output: Contribution to journalReview article

Circulating Neoplastic Cells
Neoplasms
Metastasectomy
Bone Marrow
Recurrence
35 Citations (Scopus)

Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases

Convertino, M., Das, J. & Dokholyan, N., Jun 17 2016, In : ACS Chemical Biology. 11, 6, p. 1471-1489 19 p.

Research output: Contribution to journalReview article

Pharmacology
Protein folding
Poisons
Protein Folding
Bioactivity
10 Citations (Scopus)

Review article: the pathogenesis of pouchitis

Schieffer, K. M., Williams, E., Yochum, G. & Koltun, W., Oct 1 2016, In : Alimentary Pharmacology and Therapeutics. 44, 8, p. 817-835 19 p.

Research output: Contribution to journalReview article

Pouchitis
Colonic Pouches
Ulcerative Colitis
Adenomatous Polyposis Coli
Microbiota
2015
83 Citations (Scopus)

Gangliosides: Glycosphingolipids essential for normal neural development and function

Schengrund, C-L., Jan 1 2015, In : Trends in Biochemical Sciences. 40, 7, p. 397-406 10 p.

Research output: Contribution to journalReview article

Glycosphingolipids
Gangliosides
Brain
Cell signaling
Lipids
2014
14 Citations (Scopus)

Computational approaches to understanding protein aggregation in neurodegeneration

Redler, R. L., Shirvanyants, D., Dagliyan, O., Ding, F., Kim, D. N., Kota, P., Proctor, E. A., Ramachandran, S., Tandon, A. & Dokholyan, N., Jan 1 2014, In : Journal of Molecular Cell Biology. 6, 2, p. 104-115 12 p.

Research output: Contribution to journalReview article

Proteins
Poisons
Amyotrophic Lateral Sclerosis
Information Systems
Neurodegenerative Diseases
12 Citations (Scopus)

Coordinated post-transcriptional regulation of the chemokine system: Messages from CCL2

Panganiban, R. P., Vonakis, B. M., Ishmael, F. & Stellato, C., Apr 1 2014, In : Journal of Interferon and Cytokine Research. 34, 4, p. 255-266 12 p.

Research output: Contribution to journalReview article

Chemokines
Lung Diseases
Chronic Obstructive Pulmonary Disease
Asthma
RNA-Binding Proteins
22 Citations (Scopus)

HFE gene variants, iron, and lipids: A novel connection in Alzheimer's disease

Ali-Rahmani, F., Schengrund, C-L. & Connor, J., Jan 1 2014, In : Frontiers in Pharmacology. 5 JUL, 165.

Research output: Contribution to journalReview article

Lipid A
Neurodegenerative Diseases
Alzheimer Disease
Iron
Genes
60 Citations (Scopus)

Interplay between DNA repair and inflammation, and the link to cancer

Kidane, D., Chae, W. J., Czochor, J., Eckert, K., Glazer, P. M., Bothwell, A. L. M. & Sweasy, J. B., Jan 1 2014, In : Critical Reviews in Biochemistry and Molecular Biology. 49, 2, p. 116-139 24 p.

Research output: Contribution to journalReview article

DNA Repair
DNA Damage
Repair
Inflammation
DNA
9 Citations (Scopus)

Novel strategies for managing pancreatic cancer

Loc, W. S., Smith, J. P., Matters, G., Kester, M. & Adair, J. H., Oct 28 2014, In : World journal of gastroenterology. 20, 40, p. 14717-14725 9 p.

Research output: Contribution to journalReview article

Pancreatic Neoplasms
Nanomedicine
Neoplasms
Drug Resistance
Early Diagnosis
6 Citations (Scopus)

Pathogenesis and regulation of cellular proliferation in acute lymphoblastic leukemia - The role of Ikaros

Wang, H., Ouyang, H., Lai, L., Petrovic-Dovat, L., Stankov, K., Bogdanovic, G. & Dovat, S., Jan 1 2014, In : Journal of B.U.ON.. 19, 1, p. 22-28 7 p.

Research output: Contribution to journalReview article

Precursor Cell Lymphoblastic Leukemia-Lymphoma
Cell Proliferation
Leukemia
Chromatin Assembly and Disassembly
Sequence Deletion
5 Citations (Scopus)

Splenic infarction caused by a rare coinfection of epstein-barr virus, cytomegalovirus, and mycoplasma pneumoniae

Li, Y., Pattan, V., Syed, B., Islam, M. & Yousif, A., Jan 1 2014, In : Pediatric Emergency Care. 30, 9, p. 636-637 2 p.

Research output: Contribution to journalReview article

Splenic Infarction
Mycoplasma pneumoniae
Cytomegalovirus
Human Herpesvirus 4
Coinfection
2013
150 Citations (Scopus)

A dynamic and intricate regulatory network determines Pseudomonas aeruginosa virulence

Balasubramanian, D., Schneper, L., Kumari, H. & Mathee, K., Jan 1 2013, In : Nucleic acids research. 41, 1, p. 1-20 20 p.

Research output: Contribution to journalReview article

Pseudomonas aeruginosa
Virulence
Virulence Factors
Biofilms
Microbial Drug Resistance
2 Citations (Scopus)

Ikaros: The enhancer makes the difference

Dovat, S., Oct 31 2013, In : Blood. 122, 18, p. 3091-3092 2 p.

Research output: Contribution to journalReview article

Hematopoiesis
Blood
34 Citations (Scopus)

Intersection of Hippo/YAP and Wnt/β-catenin signaling pathways

Konsavage, W. M. & Yochum, G., Jan 1 2013, In : Acta Biochimica et Biophysica Sinica. 45, 2, p. 71-79 9 p.

Research output: Contribution to journalReview article

Catenins
Wnt Signaling Pathway
Carcinogenesis
Homeostasis
Repair
18 Citations (Scopus)

Tumor-specific microsatellite instability: Do distinct mechanisms underlie the MSI-L and EMAST phenotypes?

Hile, S. E., Shabashev, S. & Eckert, K., Mar 1 2013, In : Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 743-744, p. 67-77 11 p.

Research output: Contribution to journalReview article

Microsatellite Instability
Phenotype
Neoplasms
Microsatellite Repeats
N-methylsuccinimide
2012
17 Citations (Scopus)

Cholesterol, GM1, and autism

Schengrund, C-L., Ali-Rahmani, F. & Ramer, J., Jun 1 2012, In : Neurochemical Research. 37, 6, p. 1201-1207 7 p.

Research output: Contribution to journalReview article

Autistic Disorder
Blood
Cholesterol
Cell membranes
Erythrocytes
85 Citations (Scopus)

Chromatin organization - The 30nm fiber

Grigoryev, S. & Woodcock, C. L., Jul 15 2012, In : Experimental Cell Research. 318, 12, p. 1448-1455 8 p.

Research output: Contribution to journalReview article

Chromatin
Nucleosomes
69 Citations (Scopus)

Merlin: A tumour suppressor with functions at the cell cortex and in the nucleus

Li, W., Cooper, J., Karajannis, M. A. & Giancotti, F. G., Jan 1 2012, In : EMBO Reports. 13, 3, p. 204-215 12 p.

Research output: Contribution to journalReview article

Neurofibromin 2
Tumors
Neoplasms
Contact Inhibition
Catenins
257 Citations (Scopus)

Nutritional control of growth and development in yeast

Broach, J., Sep 1 2012, In : Genetics. 192, 1, p. 73-105 33 p.

Research output: Contribution to journalReview article

Growth and Development
Yeasts
Nitrogen Compounds
Sugar Acids
ras Proteins

Ribonomic approaches to identify protein-mRNA and microRNA-mRNA interactions: Implications for drug design

Dziublenski, M., Roff, A. N. & Ishmael, F., Nov 1 2012, In : Drug Development Research. 73, 7, p. 406-413 8 p.

Research output: Contribution to journalReview article

Drug Design
MicroRNAs
RNA-Binding Proteins
RNA
Proteins
92 Citations (Scopus)

The interface of protein structure, protein biophysics, and molecular evolution

Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L. J., De Koning, A. P. J., Dokholyan, N., Echave, J., Elofsson, A., Gerloff, D. L., Goldstein, R. A., Grahnen, J. A., Holder, M. T., Lakner, C., Lartillot, N., Lovell, S. C., Naylor, G., Perica, T. & 13 others, Pollock, D. D., Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjølander, K., Sunyaev, S., Teufel, A. I., Thorne, J. L., Thornton, J. W., Weinreich, D. M. & Whelan, S., Jun 1 2012, In : Protein Science. 21, 6, p. 769-785 17 p.

Research output: Contribution to journalReview article

Biophysics
Molecular Evolution
Proteins
Biochemistry
Intrinsically Disordered Proteins