Bin XUE

Department of Molecular Medicine, Morsani College of Medicine

University of South Florida 813-***-****

***** ***** * ***** ****. MDC 7 abpolp@r.postjobfree.com

Tampa, FL, USA 33612

WORKING HISTORY

Res. Asst. Prof. Dept. of Molecular Medicine, Morsani College of Medicine

2010 Present Uni. of South Florida

Visiting Res. Asst. Prof. Institute of Intrinsically Disordered Proteins

2009 2010 Center for Computational Biology and Bioinformatics

Indiana Uni. & Purdue Uni. at Indianapolis

Postdoc Institute of Intrinsically Disordered Proteins

2008 2009 Center for Computational Biology and Bioinformatics

Indiana Uni. & Purdue Uni. at Indianapolis

Postdoc School of Informatics

2006 - 2008 Indiana Uni. & Purdue Uni. at Indianapolis

Postdoc Dept of Physiology and Biophysics

2005 2006 State University of New York, at Buffalo

EDUCATION: Ph.D. Condensed Matter Physic - Protein Computational Simulation, Nanjing Univ. 2005

PROFESSIONAL EXPERIENCE

- Bioinformatics data mining

- Machine learning and prediction

- Software and databases

- Computational Modeling and Simulation

- Protein-partner interaction

- Protein Interaction Networks and Pathways

- Gene Expression Analysis

- Protein Evolution and Phylogenetic Analysis

OTEHR ACADEMIC EXPERIENCE

- Associate faculty member of Faculty 1000 Biology

- Associate Editor of International Journal of Bioinformatics Research

- Academic Editor of PLoS ONE

- Member of Editorial Board of Protein and Peptide Letters

- Member of Editorial Board of IIOAB Journal (Institute of Integrative Omics and Applied Biotechnology Journal)

- Reviewer of Protein and Peptide Letters; PLoS ONE; Journal of Computational Chemistry; Proteins: structure function and

bioinformatics; BMC bioinformatics; Protein Engineering; Neurocomputing; Biomolecules; etc.

- Member of Biophysics Society

TEACHING

- Structural Biology, Spring

- Bioinformatics, Fall

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PEER-REVIEWED PUBLICATIONS

1.) Review

- Uversky V.N., Oldfield C.J, Midic U., Xie H., Vucetic S., Xue B., Iakoucheva L.M., Obradovic Z., Dunker A.K.

Unfoldomics of human diseases: Linking protein intrinsic disorder with diseases. BMC Genomics, 10 Suppl 1:S7 (2009)

- Bo He, Kejun Wang, Yunlong Liu, Bin Xue, Vladimir N. Uversky, A. Keith Dunker. Predicting intrinsic disorder in

proteins: an overview. Cell Research, 19:929-49 (2009)

- Bin Xue, RW Williams, CJ Oldfield, A GK Goh, AK Dunker, and Vladimir Uversky. Viral disorder or disordered viruses:

Do viral proteins possess unique features? Protein & peptide Lett. 17(8):932-951(2010)

- Sandy Westerheide, Rachel Raynes, Chase Powell, Bin Xue, and Vladimir Uversky. HSF transcription factor family, heat

shock response, and protein intrinsic disorder. Curr. Protein Pept. Sci. (2011 accepted)

2.) Functional Analysis of Intrinsically Disordered Proteins

- Bin Xue, A. Keith Dunker, and Vladimir N. Uversky. The roles of intrinsic disorder in orchestrating the Wnt-pathway. J.

Biomol. Struct. Dyn. 29:843-61(2012)

- Wei-Lun Hsu, Christopher J. Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A

Keith Dunker. Intrinsic Protein Disorder and Protein-Protein Interactions . Pac. Symp. Biocomput. 128-39(2012)

- Fei Huang, Christopher J. Oldfield, Jingwei Meng, Wei-Lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A

Keith Dunker. Subclassifying Disordered Proteins by the CH-CDF Plot Method . Pac. Symp. Biocomput. 116-27(2012)

- Bin Xue, Christopher J. Oldfield, Ya-Yue Van, A. Keith Dunker, and Vladimir N. Uversky. Protein intrinsic disorder and

induced pluripotent stem cells. Mol. Biosyst. 8:134-50(2012)

- Bin Xue, Marcin J. Mizianty, Lukasz Kurgan, and Vladimir Uversky. Protein intrinsic disorder as a flexible armor and a

weapon of HIV-1. Cell Mol. Life Sci. (2011 accepted)

- Franck Peysselon, Bin Xue, Vladimir Uversky, and Sylvie Richard-Blum. Intrinsic disorder of the extracellular matrix. Mol.

Biosyst. 7:3353-65(2011)

- Xiaolin Sun, Bin Xue, William T. Jones, Erik Rikkerink, A. Keith Dunker, Vladimir N. Uversky. A functionally required

unfoldome from the plant kingdom: Intrinsically disordered N-terminal domains of GRAS proteins are involved in

molecular recognition during plant development. Plant Molecular Biology. 77:205-23(2011)

- Bin Xue, Daniel Soeria-Atmadja, Mats G. Gustafsson, Ulf Hammerling, A. Keith Dunker, and Vladimir N. Uversky.

Abundance and functional roles of intrinsic disorder in allergenic proteins and allergen representative peptides. Proteins.

79:2595-606(2011)

- Sergei E. Permyakov, Ramis G. Ismailov, Bin Xue, Alexander I. Denesyuk, Vladimir N. Uversky, and Eugene A.

Permyakov. Intrinsic disorder in S100 proteins. Mol. Biosyst. 7:2164-80(2011)

- Bin Xue, AK Dunker, and Vladimir Uversky. Retro-MoRFs: Identifying protein binding sites by normal and reverse

alignment and intrinsic disorder prediction. Int. J. Mol. Sci. 11(10):3725-3747(2010)

- Julian Jorda, Bin Xue, Vladimir Uversky, and Andrey Kajava. Protein tandem repeats: the more perfect the less structured.

FEBS Journal, 277(12):2673-82(2010)

- Bin Xue, Liwei Li, Samy Meroueh, A. Keith Dunker, Vladimir N. Uversky. Analysis of structured and intrinsically

disordered regions of trans-membrane proteins. Molecular BioSystems, 5:1688-1702 (2009)

- Xiaolin Sun, William T. Jones, Dawn Harvey, Pat Edwards, Steve Pascal, Christopher Kirk, Th r se Considine, Jasna

Rakonjac, Bin Xue, A. Keith Dunker, and Vladimir N. Uversky. N-terminal domains of della proteins are intrinsically

unstructured proteins in the absence of interaction with gid1ga receptors. Journal of Biological Chemistry, 285:11557-71

(2010)

3.) Methionine Oxidation

- Kuiran Xu, Vladimir Uversky, Bin Xue. Local flexibility facilitates oxidation of buried methionine residues. Protein &

peptide Lett. (2011 accepted)

- Hu Dongmei, Qin Zhijie, Xue Bin, Fink Anthony L. and Uvrsky Vladimir N. Effect of methionine oxidation on the

structural properties, conformational stability, and aggregation of immunoglobulin light chain LEN. Biochemistry, 47, 8665-

8677 (2008)

4.) Intrinsic Disorder and Evolution

-Bin Xue, Robert W. Williams, Christopher J. Oldfield, A. Keith Dunker, Vladimir N. Uversky. Archaic chaos: Intrinsically

disordered proteins in archaea. BMC-Systems Biology, 4:S1:S1 (2010)

5.) Predictors for Intrinsical Disorder

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- Tuo Zhang, Eshel Faraggi, Bin Xue, Vladimir Uversky, A Keith Dunker, and Yaoqi Zhou, SPINE-D: Accurate prediction

of short and long disordered regions by a single neural-network based method. J. Biomolecular Structure and Dynamics,

29:799-813(2012)

- Marcin J. Mizianty, Tuo Zhang, Bin Xue, Yaoqi Zhou, A. Keith Dunker, Vladimir N. Uversky, and Lukasz Kurgan. In-

silico prediction of disorder content using hybrid sequence representation. BMC Bioinformatics, 12:245 (2011)

- Bin Xue, Christopher J. Oldfield, Weilun Hsu, Vladimir N. Uversky, and A. Keith Dunker. Development of new predictors

on intrinsically disordered proteins and residues. Biophys. J. 98:256-256(2010)

- Bin Xue, Weilun Hsu, Hua Lu, A. Keith Dunker, Vladimir N. Uversky. SPA: Short peptide analyzer for disordered status.

Genes to Cells, 15(6):635-46(2010)

- Bin Xue, Roland L. Dunbrack, Robert W. Williams, A. Keith Dunker, Vladimir N. Uversky. PONDR-FIT: A meta-

predictor of intrinsically disordered amino acid. Biochimica et Biophysica Acta Proteins and Proteomics, 1804:996-

1010(2010)

- Bin Xue, Christopher J. Oldfield, A. Keith Dunker, Vladimir N. Uversky. CDF It All: Consensus prediction of intrinsically

disordered proteins based on various cumulative distribution functions. FEBS Lett. 583, 1469-74(2009)

6.) Translational Bioinformatics

-Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters B, Sathyesh R, Li B, Sun Y, Xue B, Shah N,

Kann M, Cooper DN, Radivojac P, Mooney SD. In Silico functional profiling of human disease-associated and polymorphic

amino acid substitutions. Human Mutation, 31:335-346 (2010)

7.) Algorithms of Artificial Neural Networks

- Bin Xue, Ofer Dor, Eshel Faragi, and Yaoqi Zhou. Real value prediction of backbone torsion angle. Proteins, 72, 427-

33(2008)

8.) Prediction on Protein Structural Properties

- Bin Xue, Eshel Faragi, and Yaoqi Zhou. Predicting residue-residue contact map by a two-layer, integrated neural-network

method. Proteins, 76, 176-83(2009)

- Eshel Faragi, Bin Xue, and Yaoqi Zhou. Improving the prediction accuracy of residue solvent accessibility and real-value

backbone torsion angles of proteins by fast guided-learning through a two-layer neural network. Proteins, 74, 847-56(2009)

- Hongyi Zhou, Bin Xue, and Yaoqi Zhou. DDomain: Dividing structures into domains using a normalized domain-domain

interaction profile. Protein Sci. 16: 947(2007)

9.) Inter-residue Interaction Potential

- Yin Chen, Jun Wang, Bin Xue and Wei Wang. The orientational preferences of backbones of Proteins. Chinese Science

Bulletin, 51,2559( 2006)

10.) Protein Dynamics and Function

- Zuo Guanghong, Wang Jun, Qin Meng, Xue Bin and Wang Wei. Effect of salvation-related interaction on the low-

temperature dynamics of proteins. Phys. Rev. E 81:031917(2010)

- Bin Xue and Wei Wang. Influence of external vibration on tether chain in ligand-receptor binding. J. Chem. Phys. 122,

194912(2005)

- Bin Xue, Yu Su, and Wei Wang. Permeation of particle through a four-helix-bundle model channel. J. Chem. Phys. 122,

104703(2005)

11.) Protein Folding Mechanisms, Monte Carlo and Molecular Dynamics

- Zheng Hua, Wang Jun, Xue Bin, Jiang Changzhong. Investigation on mechanisms of two-state and three-state protein

folding with discrete molecular dynamics simulations. Journal of Wuhan University, 51,579(2005)

- Ji Gaofeng, Xue Bin, and Wang Wei. Folding of lattice protein model chains with fixed ends. Chin. Phys. 13, 1574 -

1581(2004)

- Bin Xue, Jun Wang, and Wei Wang. The folding behaviors of homopolymers with one end fixed. Int. J. Mod. Phys. B 18,

2123-2139(2004)

- Bin Xue, Jun Wang, and Wei Wang. Collapse of homopolymer chains with two fixed terminals. J. Chem. Phys. 119, 7534-

7542(2003)

POSTERS AND ABSTRACTS

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- Bin Xue, Eshel Faragi, and Yaoqi Zhou. Improving dihedral angle prediction using neural networks, Biochemistry

Research Day 2007, School of Medicine, IUPUI, Indianapolis, Indiana, USA

- Matthew Mort, Uday Uvani, Peter H. Baenziger, Brandon Peters, Rakesh Sayeth, Yanan Sun, Bin Xue, Yaoqi Zhou, David

N. Cooper, Eunseog Youn, Matthew Hahn, Maricel Kann, Predrag Radivojac, Sean D. Mooney. Predicting molecular

functions disrupted by mutations using in silico functional profiling, Automated Function Prediction (AFP) SIG at ISMB

2008, Toronto, Canada.

- Bin Xue, Christopher J. Oldfield, Weilun Hsu, Vladimir N. Uversky, and A. Keith Dunker. Development of new

predictors on intrinsically disordered proteins and residues, 54th Annual Meeting of Biophysical Society (2010), San

Francisco, California, USA

- A. Keith Dunker, Bin Xue, Albert William, and Vladimir N. Uversky Intrinsic disorder, scaffolds, and stochastic

machines, 54th Annual Meeting of Biophysical Society (2010), San Francisco, California, USA

- Wei-Lun Hsu, Christopher J. Oldfield, Bin Xue, Jingwei Meng, Vladimir N. Uversky, and A. Keith Dunker, Exploring the

binding diversity of intrinsically disordered proteins, 54th Annual Meeting of Biophysical Society (2010), San Francisco,

California, USA

- A. Keith Dunker, Bin Xue, Albert William, and Vladimir N. Uversky Intrinsic disorder, scaffolds, and stochastic

machines, 2010 IUPUI Research Day (2010), Indianapolis, IN, USA

- A. Keith Dunker, Bin Xue, Christopher J. Oldfield, Vladimir N. Uversky, Wei-Lun Hsu, and Richard Kriwacki,

Signalling-associated molecular recognition with intrinsically disordered protein regions, 1th Aegean International

Conference on Molecular Recognition (2010), Crete, Greece

- A. Keith Dunker, Vladimir N. Uversky, Bin Xue, Intrinsically disordered proteins and cancer pathology, 2010 IUPUI

Cancer Research Day (2010), Indianapolis, IN, USA

- Bin Xue, Robert W. Williams, Christopher J. Oldfield, A. Keith Dunker, and Vladimir N. Uversky, Where are the

intrinsically Disordered Proteins? 2010 Gordon Conference on Intrinsically Disordered Proteins, Davidson, NC, USA

- Vladimir N. Uversky and Bin Xue, Intrinsically disordered proteins: Past, present, and future. 2010 University of South

Florida ResearchOne, Tampa, FL, USA

- Bin Xue, A Keith Dunker, and Vladimir N. Uversky. Prediction of Protein Intrinsic disorder: from General to Specific.

2011 Pacific Symposium of Bio-computing, Big Island, HA, USA

- Wei-Lun Hsu, Christopher J. Oldfield, Bin Xue, Jingwei Meng, Vladimir N. Uversky, and A Keith Dunker. Exploring the

Binding Diversity of Intrinsically Disordered Proteins. 2011 Pacific Symposium of Bio-computing, Big Island, HA, USA

- Fei Huang, Christopher J. Oldfield, Bin Xue, Jingwei Meng, Wei-Lun Hsu, Vladimir N. Uversky, and A Keith Dunker.

Investigating differences in disorder prediction by VSL2 and charge-hydropathy plot. 2011 Pacific Symposium of Bio-

computing, Big Island, HA, USA

- Robert W. Williams, Bin Xue, Vladimir N. Uversky, and A Keith Dunker. Natural Selection of 100% intrinsically

Disordered Biologically Functional Disease Related PFAM Protein Domains. 2011, 55th Biophysical Society Annual

Meeting, Baltimore, MA, USA

- Wei-Lun Hsu, Christopher J. Oldfield, Bin Xue, Vladimir N. Uversky, and A Keith Dunker. Molecular Recognition

Features Facilitate the Binding Diversity of Hub Proteins . 2011, 55th Biophysical Society Annual Meeting, Baltimore, MA,

USA

- Fei Huang, Christopher J. Oldfield, Bin Xue, Jingwei Meng, Wei-Lun Hsu, Vladimir N. Uversky, and A Keith Dunker.

Understanding Disordered Protein Sub-groups by Four-quadrant-plot Derived from VSL2 and Charge-hydropathy Plot

Disorder Prediction. 2011, 55th Biophysical Society Annual Meeting, Baltimore, MA, USA

- Wei-Lun Hsu, Christopher J. Oldfield, Jingwei Meng, Fei Huang, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A

Keith Dunker. Intrinsic Protein Disorder and Protein-Protein Interactions . 2012 Pacific Symposium of Bio-computing,

Big Island, HA, USA

- Fei Huang, Christopher J. Oldfield, Jingwei Meng, Wei-Lun Hsu, Bin Xue, Vladimir N. Uversky, Pedro Romero, and A

Keith Dunker. Subclassifying Disordered Proteins by the CH-CDF Plot Method . 2012 Pacific Symposium of Bio-

computing, Big Island, HA, USA

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