A. Dunker

  • 28960 Citations
  • 82 h-Index
1969 …2019
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Publications 1969 2019

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Article
2019

Entropy, fluctuations, and disordered proteins

Faraggi, E., Dunker, A., Jernigan, R. L. & Kloczkowski, A., Jan 1 2019, In : Entropy. 21, 8, 764.

Research output: Contribution to journalArticle

Open Access
disorders
entropy
proteins
dihedral angle
mutations
1 Citation (Scopus)

Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships

Zhou, J., Oldfield, C. J., Yan, W., Shen, B. & Dunker, A., Jan 1 2019, In : Protein Science. 28, 9, p. 1652-1663 12 p.

Research output: Contribution to journalArticle

Conserved Sequence
Seed
Molecular recognition
Seeds
Bioinformatics
2018
1 Citation (Scopus)

Evolution of protein ductility in duplicated genes of plants

Yruela, I., Contreras-Moreira, B., Dunker, A. & Niklas, K. J., Aug 20 2018, In : Frontiers in Plant Science. 9, 1216.

Research output: Contribution to journalArticle

algae
genes
proteins
chromosomes
genetic recombination
13 Citations (Scopus)
Intrinsically Disordered Proteins
Alternative Splicing
Post Translational Protein Processing
Inosine Diphosphate
NFATC Transcription Factors
2017

Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder

Faraggi, E., Dunker, A., Sussman, J. L. & Kloczkowski, A., Aug 8 2017, (Accepted/In press) In : Journal of Biomolecular Structure and Dynamics. p. 1-11 11 p.

Research output: Contribution to journalArticle

X-Rays
Proteins
65 Citations (Scopus)

DisProt 7.0: A major update of the database of disordered proteins

Piovesan, D., Tabaro, F., Mičetić, I., Necci, M., Quaglia, F., Oldfield, C. J., Aspromonte, M. C., Davey, N. E., Davidović, R., Dosztányi, Z., Elofsson, A., Gasparini, A., Hatos, A., Kajava, A. V., Kalmar, L., Leonardi, E., Lazar, T., Macedo-Ribeiro, S., Macossay-Castillo, M., Meszaros, A. & 20 others, Minervini, G., Murvai, N., Pujols, J., Roche, D. B., Salladini, E., Schad, E., Schramm, A., Szabo, B., Tantos, A., Tonello, F., Tsirigos, K. D., Veljković, N., Ventura, S., Vranken, W., Warholm, P., Uversky, V. N., Dunker, A., Longhi, S., Tompa, P. & Tosatto, S. C. E., Jan 1 2017, In : Nucleic Acids Research. 45, D1, p. D219-D227

Research output: Contribution to journalArticle

Inosine Diphosphate
Protein Databases
Intrinsically Disordered Proteins
X Ray Crystallography
Proteins
7 Citations (Scopus)

Evidence for a strong correlation between transcription factor protein disorder and organismic complexity

Yruela, I., Oldfield, C. J., Niklas, K. J. & Dunker, A., 2017, In : Genome Biology and Evolution. 9, 5, p. 1248-1265 18 p.

Research output: Contribution to journalArticle

Transcription Factors
transcription factors
protein
Cell Count
algae
3 Citations (Scopus)

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions

Saravanan, K. M., Dunker, A. & Krishnaswamy, S., Dec 28 2017, (Accepted/In press) In : Journal of Biomolecular Structure and Dynamics. p. 1-14 14 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Dermatoglyphics
Amino Acids
Asparagine
Amino Acid Sequence
3 Citations (Scopus)

Time, space, and disorder in the expanding proteome universe

Minde, D. P., Dunker, A. & Lilley, K. S., Apr 1 2017, In : Proteomics. 17, 7, 1600399.

Research output: Contribution to journalArticle

Proteome
Proteins
Structural dynamics
Biomolecules
Conformations
2016
6 Citations (Scopus)

Correlating: Flavivirus virulence and levels of intrinsic disorder in shell proteins: Protective roles vs. immune evasion

Goh, G. K. M., Dunker, A. & Uversky, V. N., 2016, In : Molecular BioSystems. 12, 6, p. 1881-1891 11 p.

Research output: Contribution to journalArticle

Immune Evasion
Flavivirus
Virulence
Protein C
Tick-Borne Encephalitis Viruses
1 Citation (Scopus)

Lipopolysaccharide treatment induces genome-wide pre-mRNA splicing pattern changes in mouse bone marrow stromal stem cells

Zhou, A., Li, M., He, B., Feng, W., Huang, F., Xu, B., Dunker, A., Balch, C., Li, B., Liu, Y. & Wang, Y., Aug 22 2016, In : BMC Genomics. 17, 509.

Research output: Contribution to journalArticle

RNA Precursors
Mesenchymal Stromal Cells
Lipopolysaccharides
Stem Cells
Genome
35 Citations (Scopus)

Molecular recognition features (MoRFs) in three domains of life

Yan, J., Dunker, A., Uversky, V. N. & Kurgan, L., Mar 1 2016, In : Molecular BioSystems. 12, 3, p. 697-710 14 p.

Research output: Contribution to journalArticle

Eukaryota
Proteins
Archaea
Intrinsically Disordered Proteins
Bacteria
2015
3 Citations (Scopus)

Detection of links between Ebola nucleocapsid and virulence using disorder analysis

Goh, G. K. M., Dunker, A. & Uversky, V. N., May 22 2015, In : Molecular BioSystems. 11, 8, p. 2337-2344 8 p.

Research output: Contribution to journalArticle

Ebolavirus
Nucleocapsid
Virulence
Nucleocapsid Proteins
Viral RNA

Erratum to: A new hydropathy scale that improves disorder prediction, [BMC Bioinformatics, 15(Suppl 17) (2014), 54]

Huang, F., Oldfield, C. J., Xue, B., Hsu, W. L., Meng, J., Liu, X., Shen, L., Romero, P., Uversky, V. N. & Dunker, A., Jul 31 2015, In : BMC Bioinformatics. 16, 1, 241.

Research output: Contribution to journalArticle

Bioinformatics
54 Citations (Scopus)

Intrinsically disordered proteins and multicellular organisms

Dunker, A., Bondos, S. E., Huang, F. & Oldfield, C. J., Jan 1 2015, In : Seminars in Cell and Developmental Biology. 37, p. 44-55 12 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Post Translational Protein Processing
Alternative Splicing
Protein Splicing
RNA Precursors
24 Citations (Scopus)

Intrinsic disorder mediates hepatitis C virus core-host cell protein interactions

Dolan, P. T., Roth, A. P., Xue, B., Sun, R., Dunker, A., Uversky, V. N. & Lacount, D. J., Feb 1 2015, In : Protein Science. 24, 2, p. 221-235 15 p.

Research output: Contribution to journalArticle

Molecular recognition
Viruses
Cell Communication
Hepacivirus
Viral Proteins
3 Citations (Scopus)

Shell disorder, immune evasion and transmission behaviors among human and animal retroviruses

Goh, G. K. M., Dunker, A. & Uversky, V. N., May 22 2015, In : Molecular BioSystems. 11, 8, p. 2312-2323 12 p.

Research output: Contribution to journalArticle

Immune Evasion
Retroviridae
HIV-1
Nucleocapsid
Capsid
2014
51 Citations (Scopus)

A creature with a hundred waggly tails: Intrinsically disordered proteins in the ribosome

Peng, Z., Oldfield, C. J., Xue, B., Mizianty, M. J., Dunker, A., Kurgan, L. & Uversky, V. N., 2014, In : Cellular and Molecular Life Sciences. 71, 8, p. 1477-1504 28 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Ribosomes
Ribosomal Proteins
Proteins
RNA-Binding Proteins
6 Citations (Scopus)

Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms

Yang, J. Y., Dunker, A., Liu, J. S., Qin, X., Arabnia, H. R., Yang, W., Niemierko, A., Chen, Z., Luo, Z., Wang, L., Liu, Y., Xu, D., Deng, Y., Tong, W. & Yang, M. Q., Dec 16 2014, In : BMC Bioinformatics. 15, 17, I1.

Research output: Contribution to journalArticle

Bioinformatics
Computational Biology
Genes
Promoter
Protein
534 Citations (Scopus)

Classification of intrinsically disordered regions and proteins

Van Der Lee, R., Buljan, M., Lang, B., Weatheritt, R. J., Daughdrill, G. W., Dunker, A., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D. T., Kim, P. M., Kriwacki, R. W., Oldfield, C. J., Pappu, R. V., Tompa, P., Uversky, V. N., Wright, P. E. & Babu, M. M., Jul 9 2014, In : Chemical Reviews. 114, 13, p. 6589-6631 43 p.

Research output: Contribution to journalArticle

Proteins
Genes
30 Citations (Scopus)

Identification of genes and pathways involved in kidney renal clear cell carcinoma

Yang, W., Yoshigoe, K., Qin, X., Liu, J. S., Yang, J. Y., Niemierko, A., Deng, Y., Liu, Y., Dunker, A., Chen, Z., Wang, L., Xu, D., Arabnia, H. R., Tong, W. & Yang, M. Q., Dec 16 2014, In : BMC Bioinformatics. 15, 17, S2.

Research output: Contribution to journalArticle

Kidney
Renal Cell Carcinoma
Pathway
Genes
Cells
17 Citations (Scopus)

Improving protein order-disorder classification using charge-hydropathy plots

Huang, F., Oldfield, C. J., Xue, B., Hsu, W. L., Meng, J., Liu, X., Shen, L., Romero, P., Uversky, V. N. & Dunker, A., Dec 16 2014, In : BMC Bioinformatics. 15, 17, S4.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Order disorder transitions
Disorder
Charge
Proteins
276 Citations (Scopus)

Intrinsically disordered proteins and intrinsically disordered protein regions

Oldfield, C. J. & Dunker, A., 2014, In : Annual Review of Biochemistry. 83, p. 553-584 32 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Bioactivity
Proteins
Biochemistry
Textbooks

Pacific symposium on biocomputing 2014

Altman, R. B., Dunker, A., Hunter, L., Klein, T. E. & Ritchie, M. D., 2014, In : Unknown Journal. p. v-vi

Research output: Contribution to journalArticle

110 Citations (Scopus)

PE-DB: A database of structural ensembles of intrinsically disordered and of unfolded proteins

Varadi, M., Kosol, S., Lebrun, P., Valentini, E., Blackledge, M., Dunker, A., Felli, I. C., Forman-Kay, J. D., Kriwacki, R. W., Pierattelli, R., Sussman, J., Svergun, D. I., Uversky, V. N., Vendruscolo, M., Wishart, D., Wright, P. E. & Tompa, P., Jan 1 2014, In : Nucleic Acids Research. 42, D1

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Databases
Proteins
Magnetic Resonance Spectroscopy
X-Rays
3 Citations (Scopus)

The emerging genomics and systems biology research lead to systems genomics studies

Yang, M. Q. U., Yoshigoe, K., Yang, W., Tong, W., Qin, X., Dunker, A., Chen, Z., Arbania, H. R., Liu, J. S., Niemierko, A. & Yang, J. Y., 2014, In : BMC Genomics. 15, p. I1

Research output: Contribution to journalArticle

Systems Biology
Genomics
Computational Biology
Research
Protein Isoforms
8 Citations (Scopus)

The number of cell types, information content, and the evolution of complex multicellularity

Niklas, K. J., Cobb, E. D. & Dunker, A., 2014, In : Acta Societatis Botanicorum Poloniae. 83, 4, p. 337-347 11 p.

Research output: Contribution to journalArticle

proteome
cells
genome
organisms
Phaeophyceae
122 Citations (Scopus)

The structural and functional signatures of proteins that undergo multiple events of post-translational modification

Pejaver, V., Hsu, W. L., Xin, F., Dunker, A., Uversky, V. N. & Radivojac, P., 2014, In : Protein Science. 23, 8, p. 1077-1093 17 p.

Research output: Contribution to journalArticle

Post Translational Protein Processing
Proteins
Crosstalk
Molecular recognition
Modulation
2013
91 Citations (Scopus)

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

Buljan, M., Chalancon, G., Dunker, A., Bateman, A., Balaji, S., Fuxreiter, M. & Babu, M. M., Jun 2013, In : Current Opinion in Structural Biology. 23, 3, p. 443-450 8 p.

Research output: Contribution to journalArticle

Alternative Splicing
Proteins
Post Translational Protein Processing
Protein Isoforms
Messenger RNA
13 Citations (Scopus)

An assignment of intrinsically disordered regions of proteins based on NMR structures

Ota, M., Koike, R., Amemiya, T., Tenno, T., Romero, P. R., Hiroaki, H., Dunker, A. & Fukuchi, S., Jan 2013, In : Journal of Structural Biology. 181, 1, p. 29-36 8 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Magnetic Resonance Spectroscopy
Proteins
X-Rays
Biological Phenomena
2 Citations (Scopus)

Another disordered chameleon: The micro-exon gene 14 protein from schistosomiasis

Dunker, A., Jun 4 2013, In : Biophysical Journal. 104, 11, p. 2326-2328 3 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Lizards
Schistosomiasis
Protein Folding
Exons
204 Citations (Scopus)

D2P2: Database of disordered protein predictions

Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., Dosztányi, Z., Uversky, V. N., Obradovic, Z., Kurgan, L., Dunker, A. & Gough, J., Jan 1 2013, In : Nucleic Acids Research. 41, D1

Research output: Contribution to journalArticle

Protein Databases
Genome
Proteome
Proteins
History
92 Citations (Scopus)

Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding

Hsu, W. L., Oldfield, C. J., Xue, B., Meng, J., Huang, F., Romero, P., Uversky, V. N. & Dunker, A., Mar 2013, In : Protein Science. 22, 3, p. 258-273 16 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Molecular recognition
Alternative Splicing
Post Translational Protein Processing
Proteins
10 Citations (Scopus)

Interplay between estrogen receptor and AKT in Estradiol-induced alternative splicing

Bhat-Nakshatri, P., Song, E. K., Collins, N. R., Uversky, V. N., Dunker, A., O'Malley, B. W., Geistlinger, T. R., Carroll, J. S., Brown, M. & Nakshatri, H., 2013, In : BMC Medical Genomics. 6, 1, 21.

Research output: Contribution to journalArticle

Estrogen Receptor alpha
Alternative Splicing
Estrogen Receptors
Estradiol
Recombinant DNA
37 Citations (Scopus)

Intrinsically disordered regions of p53 family are highly diversified in evolution

Xue, B., Brown, C. J., Dunker, A. & Uversky, V. N., Apr 2013, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1834, 4, p. 725-738 14 p.

Research output: Contribution to journalArticle

Substitution reactions
DNA
Proteins
Missense Mutation
Invertebrates

Pacific symposium on biocomputing 2013

Altman, R. B., Dunker, A., Hunter, L. & Klein, T. E., 2013, In : Unknown Journal. p. 1-4 4 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Prediction of intrinsic disorder in MERS-CoV/HCoV-EMC supports a high oral-fecal transmission

Goh, G. K. M., Dunker, A. & Uversky, V., 2013, In : PLoS Currents. 5, Outbreaks

Research output: Contribution to journalArticle

Coronavirus
Middle East
Hardness
Saliva
Urine
3 Citations (Scopus)

Sequences and topology: Disorder, modularity, and post/pre translation modification

Gough, J. & Dunker, A., Jun 2013, In : Current Opinion in Structural Biology. 23, 3, p. 417-419 3 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Post Translational Protein Processing
Tertiary Protein Structure
Amino Acid Sequence
24 Citations (Scopus)

Stochastic machines as a colocalization mechanism for scaffold protein function

Xue, B., Romero, P. R., Noutsou, M., Maurice, M. M., Rüdiger, S. G. D., William, A. M., Mizianty, M. J., Kurgan, L., Uversky, V. N. & Dunker, A., Jun 5 2013, In : FEBS Letters. 587, 11, p. 1587-1591 5 p.

Research output: Contribution to journalArticle

Catenins
Scaffolds
Casein Kinase I
Glycogen Synthase
Phosphorylation
52 Citations (Scopus)
Intrinsically Disordered Proteins
Molecular recognition
Catalysis
Static Electricity
Electrostatics
29 Citations (Scopus)

Utilization of protein intrinsic disorder knowledge in structural proteomics

Oldfield, C. J., Xue, B., Van, Y. Y., Ulrich, E. L., Markley, J. L., Dunker, A. & Uversky, V. N., Feb 2013, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1834, 2, p. 487-498 12 p.

Research output: Contribution to journalArticle

Proteomics
Proteins
Intrinsically Disordered Proteins
Pipelines
Crystal structure
2012
2 Citations (Scopus)

Erratum: A protein domain-based interactome network for C. elegans early embryogenesis (Cell (2008) 134 (534-545))

Boxem, M., Maliga, Z., Klitgord, N., Li, N., Lemmens, I., Mana, M., De Lichtervelde, L., Mul, J. D., Van De Peut, D., Devos, M., Simonis, N., Yildirim, M. A., Cokol, M., Kao, H. L., De Smet, A. S., Wang, H., Schlaitz, A. L., Hao, T., Milstein, S., Fan, C. & 17 others, Tipsword, M., Drew, K., Galli, M., Rhrissorrakrai, K., Drechsel, D., Koller, D., Roth, F. P., Iakoucheva, L. M., Dunker, A., Bonneau, R., Gunsalus, K. C., Hill, D. E., Piano, F., Tavernier, J., Van Den Heuvel, S., Hyman, A. A. & Vidal, M., Dec 21 2012, In : Cell. 151, 7, p. 1633 1 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative

Johnson, D. E., Xue, B., Sickmeier, M. D., Meng, J., Cortese, M. S., Oldfield, C. J., Le Gall, T., Dunker, A. & Uversky, V. N., Oct 2012, In : Journal of Structural Biology. 180, 1, p. 201-215 15 p.

Research output: Contribution to journalArticle

Proteins
Circular Dichroism
Digestion
Intrinsically Disordered Proteins
Myoglobin
2 Citations (Scopus)

Intrinsically disordered proteins: Analysis, prediction, simulation, and biology

Chen, J., Cheng, J. & Dunker, A., 2012, In : Unknown Journal. p. 67-69 3 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Proteins
45 Citations (Scopus)

Intrinsic protein disorder and protein-protein interactions.

Hsu, W. L., Oldfield, C., Meng, J., Huang, F., Xue, B., Uversky, V. N., Romero, P. & Dunker, A., 2012, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 116-127 12 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Artifacts
Proteins
Amino Acids
Weights and Measures
5 Citations (Scopus)

Molecular profiling - An essential technology enabling personalized medicine in breast cancer

Liu, J., Li, S., Dunker, A. & Uversky, V. N., Apr 2012, In : Current Drug Targets. 13, 4, p. 541-554 14 p.

Research output: Contribution to journalArticle

Precision Medicine
Medicine
Tumors
Breast Neoplasms
Technology
174 Citations (Scopus)

MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins

Disfani, F. M., Hsu, W. L., Mizianty, M. J., Oldfield, C. J., Xue, B., Dunker, A., Uversky, V. N. & Kurgan, L., Jun 2012, In : Bioinformatics. 28, 12, bts209.

Research output: Contribution to journalArticle

Feature Recognition
Molecular recognition
Disorder
Proteins
Protein
48 Citations (Scopus)

Multiparametric analysis of intrinsically disordered proteins: Looking at intrinsic disorder through compound eyes

Uversky, V. N. & Dunker, A., Mar 6 2012, In : Analytical Chemistry. 84, 5, p. 2096-2104 9 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Proteome
Proteins
219 Citations (Scopus)
Proteome
Viruses
Eukaryota
Intrinsically Disordered Proteins
Proteins

Pacific symposium on biocomputing 2012

Altman, R. B., Dunker, A., Hunter, L. & Klein, T. E., 2012, In : Unknown Journal. p. v-vi

Research output: Contribution to journalArticle