Projects: (1) Rad51-Rad54 interaction during homologous recombination (2) Structure and function of Rad51 and Rad54
Interests: Protein structure, function and protein-protein interaction.
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
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
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
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
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.
(1) Heyer lab hikes: 2012 (2) Heyer lab hikes: 2011
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 ...
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
