Projects & Interests

Projects:
(1) Rad51-Rad54 interaction during homologous recombination
(2) Structure and function of Rad51 and Rad54

Interests:
Protein structure, function and protein-protein interaction.

Education

2001 - PhD, Biochemistry, Stockholm University, Sweden
1989 - MSc, Plant Physiology, Lanzhou University, Lanzhou, P. R. China
1983 - BSc, Botany, Lanzhou University, Lanzhou, P. R. China

Work experience

2007 -             Project scientist
2002 - 2007 - Post Doctoral Fellow, Section of Microbiology, UC Davis, USA
2002 - Post Doctoral Fellow, Drexel University College of Medicine, Drexel Univ., USA
1996 - 2001 - PhD student, Dept. of Biochem. & Biophys, Stockholm University, Sweden
1993 -1995 - Visiting Scholar, Hong Kong Baptist University, HK
1983 -1993 - Teacher and Researcher, Dept. of Biology, Lanzhou University, P. R. China

Honors and awards

2004 - 2007 Post-doctoral Fellowship, Susan G. Komen Breast Cancer Foundation
1999 - The Best Poster Prize from Bioinformatics '99, the international bioinformatics meeting in Scandinavia, April 15-18, Lund, Sweden

Publications

Zhang, X.-P., Galkin, V., Yu, X., Egelman, E. and Heyer, W.-D. (2009) Loop 2 in S. Cerevisiae Rad51 protein regulates filament formation and ATPase activity. Nucleic Acid Res. 37:158-171 [PDF]

Li, X., Zhang, X.-P., Solinger, J., Kiianitsa, K., Yu, X., Egelman, E. and Heyer, W.-D. (2007) Rad51 and Rad54 ATPase activites are both required to modulate Rad51-dsDNA filament dynamics. Nucleic Acid Res. 35(12): 4124-4140. [PubMed] [PDF].

Heyer, W.-D., Li, X., Rolfsmeier, M. and Zhang, X.-P. (2006) Rad54, the Swiss Army knife of homologous recombination? Nucleic Acid Res, 34(15): 4115-4125 .[PubMed] [PDF]

Galkin, V.E., Wu, Y., Zhang, X.-P., Qian, X., He, Y., Yu, X., Heyer, E.-D., Luo, Y. and Egelman, E.H. (2006) The Rad51/RadA N-terminal domain activates Nucleoprotein Filaments. STRUCTURE, 14, 983-992. [PubMed] [PDF] [Cover Illustration] [Preview by Wyman, C. (2006) Monomer Networking Activates Recombinases. Structure 14(6): 949-950 [PDF]]

Zhang, X.-P., Lee, K.-I., Solinger, J.A., Kiianitsa, K., and Heyer, W.-D. (2005) Gly103 in the N-terminal domain of S. cerevisiae Rad51 protein is critical for DNA binding. J. Biol. Chem. 280, 26303-26311.[Pubmed][Pdf file]

Zhang, X.-P., and Glaser, E. (2002) Interaction of chloroplast and mitochondrial signal sequences with organellar hsp70. Trends in Plant Science, 7(1): 14-21 [PubMed] [Pdf file]

Zhang, X.-P., Sjöling, S., Tanudji, M., Somogyi, L., Andreu, D., Eriksson, L. E. G., Gräslund, A., Whelan, J. and Glaser, E. (2001) Mutagenesis and computer modelling approach to study determinants for recognition of signal peptides by the mitochondrial processing peptidase. Plant J., 27 (5):427-438[PubMed] [Pdf file]

Zhang, X.-P., Elofsson, A., Andreu, D. and Glaser, E. (1999) Interaction of mitochondrial presequence with DnaK and mitochondrial hsp70. J. Mol. Biol. 288(1):177-190 [PubMed] [Pdf file]

Pavlov, P. F., Moberg, P., Zhang, X.-P. and Glaser, E. (1999) CNBr chemical cleavage of the overexpressed mitochondrial precursors: a new strategy of construct import competent preproteins. Biochem. J., 341:95-103 [PubMed] [Pdf file]

Full publication list

Other Interests

Bioinformatitics

Linux/MS Windows Server Administration

Database development and administration

Photography (see my photos) and website design (see my first design )

Computer hardware:

Intel processors, AMD processors, Graphic Cards, visit the CPU Benchmarks before you decide to buy a computer.

Photo Album

(1) Heyer lab hikes: 2012
(2) Heyer lab hikes: 2011

Favorite Tools/Sites

LINKS FOR BIOINFORMATIC PROGRAMS / WEBSERVERS

Homology Searching - BLAST
Molecular Modeling - ICM, Modeller, Whatif, ECEPPAK
Model Verification - Procheck, Whatif, ProsaII, Verify3D, ProQ, ModFOLD, MetaMQAPII, QMEANclust
Molecular Docking - Autodock, Vina,
Molecular Docking servers: GRAMM-X,
Molecular Graphics - PyMol, Molscript, Raster3D, Grasp, Swiss PdbViewer
Residue Conservation - Sequence logo
Sequence Alignment - Jalview, ClustalΩ, ClustalX, CLustalW, MUSCLE, T-Coffee, MUFFT, Vector NTI, Bioedit, EMBOSS, eBioX (Mac) and eBioTools (Mac)
Alignment Editing/Publishing - Jalview, CINEMA, Bioedit, Gendoc, BOXSHADE
DNA modeling - W3DNA or use 3DNA locally; or 3D-DART Web server

NEXT GENERATION SEQUENCING (NGS)
Systems
Roche 454, Illumina/Solexa, ABI SOLid, Life/APG, Helicos BioSciences, Pacific Biosystems
Software
Evaluation of next-generation sequencing software in mapping and assembly
Assembly algorithms for next-generation sequencing data
A software list from SEQanswers
Liturature
Sequencing technologies-the next generation
Next-Generation DNA Sequencing Methods
Next Generation Sequencing from Bioinformatics
......

MOLECULAR BIOLOGY

DNA double digest table
Restriction Enzyme Database
NEBcutter
Protein interaction
Protease inhibitors
Tools from Gene infinity
Sequence Manupulation Suite" (Mirror) by Paul Stothard

QUESTIONS AND ANSWERS

1. How to visualize sequencing chromatogram (ABI) files on PC, Mac and Linux:
PC users: Chromas Lite(Pro), SequenceScanner, Bioedit, Staden, EMBOSS, VectorNTI.
Mac users: 4peaks, Staden, EMBOSS, "Edit View ???
Linux users: EMBOSS, Staden, or the PC/Windows programs through Wine, or VMware.

2. How to run Windows and Linux (Unix) applications on the same computer?
(1)Dual/multi-operating systems may be the best way if you don't need to talk between Windows application and Linux application.
(2)If you do and mainly depend on Windows, Cygwin may help.
(3) Wine and VMware Player may be the good solution for Linux (Unix) users. Based on my experience, VMware is extremely slow on old computers. A PC with multi-core processor, physical memmory more tha 4 GB, runs VMware player beatifully.

3. How to ...



OTHER USEFUL LINLKS

Links for Linux fans
Phoronix

Databases
- NCBI, Swiss-Prot, PDB, Yeast Genome Database, Human Pathway Interactions, MIPS, Protein interaction (based on structure), Protein interaction (Genetic and Physical interaction), Finley Lab Interactions Databases, BioGRID,DIP
Protein lounge (Commercial databases)

Protein secondary structure prediction
- APSSP2 at the Institute of Microbial Technology Chandigarh, India
- Jpred 3 by Dr. Geoffrey J. Barton
- JSSPrediction at University of Calabria, Italy
- Jufo by Meiler Lab
- PHD by Rost Lab
- Porter at the University College Dublin
- PROF by Dr. Ross D. King
- Psipred by Dr. David Jones
- SAM-T06 by Dr. Kevin Karplus
- SAM-T08 by Dr. Kevin Karplus
- SSPro at UC Irvine
- YASPIN at the UV University Amsterdam
- Protein secondary structure prediction at Baylor College of Medicine
- SYMPRED consensus secondary structure prediction at the UV University Amsterdam
- NPSA at the Institute of Biology and Chemistry of Proteins in France

Protein motif search servers
- Motif Search from Japan, search a motif against well known databases
- InterProScan from EBI
- Motif Search from Canada, search all known motifs from your sequence.

Full length protein 3D structural prediction servers
- I-TASSER from Zhang lab at the University of Michigan
- Robetta Server at the University of Washington

Concensus fold recognition servers
- Meta server (currently unavailable) from bioinfo Bank, Poland
- Pcons
- MetaTASSER at the Georgia Institute of Technology (includes SPARKS, SP3 and PROSPECTOR_3)
- LOMETS at the University of Michigan (includes FFAS, HHsearch, MUSTER, PPA, PROSPECT2, SAM-T02, SPARKS, PRC and SP3)
- @TOME includes HHsearch, Fugue, PS3 and Psiblast

Other homology template searching servers
- HHpred from Germany
- RAPTOR Server at the University of Chicago
- SP3 fold recognition, improved versions SPARKSX
- PSIPRED Protein Structure Prediction Server (GenTHREADER, pGenTHREADER and pDomTHREADER)
- FUGUE at the National Institute of Biomedical Innovation in Japan
- FFAS at Sanford Burnham Medical Research Institute
- 3D-PSSM at the Imperil College, London, improved versions:Phyre2
- SAMT08 at UCSC

On-line molecular docking server
- ClusPro
- FiberDOCK
- FireDOCK
- GRAMM-X
- HADDOCK
- Hex Server
- PatchDock
- PSiFR (structure and function prediction suite)
- RosettaDock
- SKE-DOCK(e-mail server)
- ZDOCK

Critical Assessment of protein Structure Prediction (CASP)

Critical Assessment of PRediction of Interactions (CAPRI)

Signal peptide prediction and protein localization
- MitoProt, SignalP (V4.0), SignalP (V2.0b2), TargetP, ChloroP, Predotar, ProtComP, NNPSL, PSORT, Yeast protein localization, PredictNLS

Bacterial signal peptide
- Bacterial signal peptide database

Prediction of Bacterial Signal peptide
- PrediSi
- SignalP
- SIG-Pred
- Signal BLAST

win arginine signal prediction
- TatP 1.0

Phosphorylation site prediction
- NetPhos, PhosphoBase

Links for DNA repair
DNA Repair Wiki
DNA Repair Interest Group at NIH
DNA Damage Response and Repair Mechanisms
DNA Repair at ELSEVIER
DNA Repair by John W. Kimball
Mutation, Mutagens, and DNA Repair by Beth A. Montelone
Human DNA Repair Genes by Cancer Research UK
The book of "DNA Repair and Mutagenesis" DNA Repair from WormBook
DNA Repair from Reactome

Other info:

Updated on Jan. 09, 2009