Department of Biochemistry and Molecular Biology

  • United States

Research Output 1969 2019

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Chapter
2018
1 Citation (Scopus)

Spherical nanoparticle supported lipid bilayers: A tool for modeling protein interactions with curved membranes

Tyndall, E. R. & Tian, F., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 99-109 11 p. (Methods in Molecular Biology; vol. 1688).

Research output: Chapter in Book/Report/Conference proceedingChapter

Lipid Bilayers
Nanoparticles
Membranes
Silicon Dioxide
Membrane Proteins
2017
5 Citations (Scopus)

Computational protein design through grafting and stabilization

Zhu, C., Mowrey, D. D. & Dokholyan, N., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., p. 227-241 15 p. (Methods in Molecular Biology; vol. 1529).

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutation
Proteins
Protein Stability
Software
Databases
2016
1 Citation (Scopus)

Computational modeling of small molecule ligand binding interactions and affinities

Convertino, M. & Dokholyan, N., May 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 23-32 10 p. (Methods in Molecular Biology; vol. 1414).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ligands
Biological Phenomena
Preclinical Drug Evaluations
Propranolol
Adrenergic Receptors
3 Citations (Scopus)

Electron cryotomography

Oikonomou, C. M., Swulius, M. T., Briegel, A., Beeby, M., Yao, Q. & Jensen, G. J., Jan 1 2016, Imaging Bacterial Molecules, Structures and Cells, 2016. Jensen, G. J. & Harwood, C. (eds.). Academic Press Inc., p. 115-139 25 p. (Methods in Microbiology; vol. 43).

Research output: Chapter in Book/Report/Conference proceedingChapter

Electrons
Macromolecular Substances
Bacterial Structures
Microbiology
5 Citations (Scopus)

Whole-Organism Cellular Pathology: A Systems Approach to Phenomics

Cheng, K., Katz, S. R., Lin, A. Y., Xin, X. & Ding, Y., Jan 1 2016, Genetics, Genomics and Fish Phenomics, 2016. Foulkes, N. S. & Foulkes, N. S. (eds.). Academic Press Inc., p. 89-115 27 p. (Advances in Genetics; vol. 95).

Research output: Chapter in Book/Report/Conference proceedingChapter

Systems Analysis
Pathology
Phenotype
Histology
Zebrafish
2015
5 Citations (Scopus)

Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models

Krokhotin, A. & Dokholyan, N., Jan 1 2015, Methods in Enzymology. Academic Press Inc., p. 65-89 25 p. (Methods in Enzymology; vol. 553).

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational methods
RNA
Atoms
Nucleotides
Guide RNA
5 Citations (Scopus)

Forms of selenium in cancer prevention

El-Bayoumy, K., Sinha, R. & Richie, J., Jan 1 2015, Diversity of Selenium Functions in Health and Disease. CRC Press, p. 137-172 36 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Selenoproteins
Selenium
Selenium Compounds
Selenocysteine
Neoplasms
30 Citations (Scopus)

GABAergic control of depression-related brain states

Luscher, B. & Fuchs, T., Jan 1 2015, Advances in Pharmacology. Academic Press Inc., p. 97-144 48 p. (Advances in Pharmacology; vol. 73).

Research output: Chapter in Book/Report/Conference proceedingChapter

Major Depressive Disorder
Depression
Brain
Antidepressive Agents
Aminobutyrates

Post-transcriptional regulation of glucocorticoid function

Ishmael, F. & Stellato, C., Jan 1 2015, Post-Transcriptional Mechanisms in Endocrine Regulation. Springer International Publishing, p. 277-313 37 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Glucocorticoids
Anti-Inflammatory Agents
Immune System Diseases
Glucocorticoid Receptors
RNA Stability
1 Citation (Scopus)

Replicating sequencing-based association studies of rare variants

Liu, D. & Leal, S. M., Jan 1 2015, Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies. Springer New York, p. 201-213 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Exome
Genes
Chromosome Mapping
Genetic Models
Population Genetics
2014

Mass spectrometry and protein array for environment

Spera, R., Belmonte, L., Festa, F., Pechkova, E., Chong, S., Labaer, J. & Nicolinia, C., Jan 1 2014, Nanobiotechnology in Energy, Environment and Electronics: Methods and Applications. Pan Stanford Publishing Pte. Ltd., p. 243-278 36 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Electronics engineering
Protein Array Analysis
Electronics industry
Energy management
Energy resources
2013

Hematopoietin Receptors

Miller, B., Feb 15 2013, Encyclopedia of Biological Chemistry: Second Edition. Elsevier Inc., p. 526-531 6 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Hematopoietic Cell Growth Factors
Transducers
Chemical activation
MAP Kinase Kinase 3
Erythropoietin Receptors

Identification of Recurrent DNA Copy Number Aberrations in Tumors

Walter, V., Nobel, A. B., Hayes, D. N. & Wright, F. A., Apr 8 2013, Statistical Diagnostics for Cancer: Analyzing High-Dimensional Data. Wiley-VCH, Vol. 3. p. 239-260 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Aberrations
Tumors
DNA
Neoplasms
Genes
4 Citations (Scopus)

Impact of genetic targets on prostate cancer therapy

Sheikh, H., Abdulghani, J., Ali, S., Sinha, R. & Lipton, A., Feb 15 2013, Impact of Genetic Targets on Cancer Therapy. El-Deiry, W. (ed.). p. 359-383 25 p. (Advances in Experimental Medicine and Biology; vol. 779).

Research output: Chapter in Book/Report/Conference proceedingChapter

Prostatic Neoplasms
Pharmaceutical Preparations
Therapeutics
Inborn Genetic Diseases
Survival

RNA three-dimensional structure determination using experimental constraints

Ding, F. & Dokholyan, N., Jan 1 2013, RNA Nanotechnology and Therapeutics. CRC Press, p. 159-175 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA
Riboswitch
Drug Design
Proteins
Bacterial RNA
2012

GABAA and GABAC receptors: Regulation of assembly, localization, clustering and turnover

Luscher, B., Mar 22 2012, Receptor and Ion-Channel Trafficking: Cell Biology of Ligand-Gated and Voltage-Sensitive Ion Channels. Oxford University Press

Research output: Chapter in Book/Report/Conference proceedingChapter

GABA-A Receptors
gamma-Aminobutyric Acid
Cluster Analysis
Neural Inhibition
Aminobutyrates

Gene Function Prediction and Functional Network: The Role of Gene Ontology

Zeng, E., Ding, C., Mathee, K., Schneper, L. & Narasimhan, G., Dec 1 2012, Data Mining: Foundations and Intelligent Paradigms: Volume 3:Medical,Health, Social, Biological and other Applications. Holmes, D. & Jain, L. (eds.). p. 123-162 40 p. (Intelligent Systems Reference Library; vol. 25).

Research output: Chapter in Book/Report/Conference proceedingChapter

ontology
Ontology
Genes
semantics
Semantics

Role of Ca2+-Mediated signaling in als pathology

Kotelnikova, E. A., Pyatnitskiy, M. A., Redler Rachel L., R. L. & Dokholyan, N., Dec 1 2012, From Knowledge Networks to Biological Models. Bentham Science Publishers Ltd., p. 24-72 49 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Pathology
Calcium
Transcription factors
Neurons
Transcription Factors
90 Citations (Scopus)

The complex molecular biology of Amyotrophic Lateral Sclerosis (ALS)

Redler, R. L. & Dokholyan, N., Jan 1 2012, Progress in Molecular Biology and Translational Science. Elsevier B.V., p. 215-262 48 p. (Progress in Molecular Biology and Translational Science; vol. 107).

Research output: Chapter in Book/Report/Conference proceedingChapter

Amyotrophic Lateral Sclerosis
Molecular Biology
Axonal Transport
Poisons
Nerve Growth Factors
2011

Isolation and characterization of the nuclear serpin MENT

Grigoryev, S. & McGowan, S., Jan 1 2011, Methods in Enzymology. Academic Press Inc., p. 29-47 19 p. (Methods in Enzymology; vol. 501).

Research output: Chapter in Book/Report/Conference proceedingChapter

Serpins
Peptide Hydrolases
Chromatin
DNA
Proteins
6 Citations (Scopus)

Methyl-coenzyme M reductase from Methanothermobacter marburgensis

Duin, E. C., Prakash, D. & Brungess, C., Jan 1 2011, Methods in Enzymology. Academic Press Inc., p. 159-187 29 p. (Methods in Enzymology; vol. 494).

Research output: Chapter in Book/Report/Conference proceedingChapter

Methanobacteriaceae
Purification
Methanobacterium
Archaea
Methane
2010
7 Citations (Scopus)

Computational evaluation of protein stability change upon mutations

Yin, S., Ding, F. & Dokholyan, N., Dec 1 2010, In Vitro Mutagenesis Protocols: Third Edition. Jeff, B. (ed.). p. 189-201 13 p. (Methods in Molecular Biology; vol. 634).

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein Stability
Mutation
Mutant Proteins
Tertiary Protein Structure
Mutagenesis
1 Citation (Scopus)

Making Mutations is an Active Process: Methods to Examine DNA Polymerase Errors

Eckert, K. & Gestl, E. E., Mar 30 2010, The Handbook of Plant Mutation Screening: Mining of Natural and Induced Alleles. Wiley-VCH, p. 55-82 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA-Directed DNA Polymerase
Mutation
Genetic Templates
DNA
Molecular Biology
2 Citations (Scopus)

Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics

Yin, S., Ding, F. & Dokholyan, N., Sep 7 2010, Introduction to Protein Structure Prediction: Methods and Algorithms. John Wiley and Sons, p. 453-476 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Mutation
Molecules
Proteins
2009
12 Citations (Scopus)

Chapter 20 Expression of CXCR4, a G-Protein-Coupled Receptor for CXCL12 in Yeast. Identification of New-Generation Inverse Agonists

Evans, B. J., Wang, Z., Broach, J., Oishi, S., Fujii, N. & Peiper, S. C., May 14 2009, Chemokines, Part A. Abelson, J. & Simon, M. (eds.). A ed. p. 399-412 14 p. (Methods in Enzymology; vol. 460, no. A).

Research output: Chapter in Book/Report/Conference proceedingChapter

G-Protein-Coupled Receptors
Yeast
Yeasts
Pheromones
Reporter Genes
2008
2 Citations (Scopus)

Demystifying skin color and race

Cheng, K., Dec 1 2008, Racism in the 21st Century: An Empirical Analysis of Skin Color. Springer New York, p. 3-23 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

racism
tribalism
science
kinship
education
2007

A novel clustering approach: Global optimum search with enhanced positioning

P. Tan, M., Broach, J. & A. Floudas, C., Dec 1 2007, 17th European Symposium on Computer Aided Process Engineering. Plesu, V. & Agachi, P. S. (eds.). p. 983-988 6 p. (Computer Aided Chemical Engineering; vol. 24).

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA
Cluster analysis
Microarrays
Clustering algorithms
Genes

MENT, a chromatin-associated serpin from avian blood cells: Structure and function

Grigoryev, S. A., Bulynko, Y. A., Pike, R. N. & Whisstock, J. C., Jan 1 2007, Molecular and Cellular Aspects of the Serpinopathies and Disorders in Serpin Activity. World Scientific Publishing Co., p. 243-259 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Serpins
Chromatin
Blood Cells
2006
8 Citations (Scopus)

Role of Chondroitin-4-Sulfate in Pregnancy-Associated Malaria

Gowda, C., Dec 1 2006, Chondroitin Sulfate: Structure, Role and Pharmacological Activity. Volpi, N. (ed.). p. 375-400 26 p. (Advances in Pharmacology; vol. 53).

Research output: Chapter in Book/Report/Conference proceedingChapter

Parasitic Pregnancy Complications
Chondroitin Sulfates
Plasmodium falciparum
Cell Adhesion
Placenta
2003
23 Citations (Scopus)

Expression of meprins in health and disease

Norman, L. P., Matters, G., Crisman, J. M. & Bond, J. S., Dec 1 2003, Current Topics in Developmental Biology. p. 145-166 22 p. (Current Topics in Developmental Biology; vol. 54).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cell Surface Extensions
Metalloendopeptidases
Neoplastic Cell Transformation
Tiopronin
Tertiary Protein Structure
1994
18 Citations (Scopus)

Application of Equilibrium and Stopped-Flow 19F NMR Spectroscopy to Protein Folding: Studies of E. coli Dihydrofolate Reductase

Hoeltzli, S. D., Ropson, I. & Frieden, C., Jan 1 1994, Techniques in Protein Chemistry. C ed. p. 455-465 11 p. (Techniques in Protein Chemistry; vol. 5, no. C).

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein folding
Tetrahydrofolate Dehydrogenase
Protein Folding
Escherichia coli
Nuclear magnetic resonance spectroscopy