The following is a list of my publications organized by subject areas. Within each topic, the most relevant ones appear first. Some publications are included in more than one subject area. The numbers correspond to the chronological order of publication (higher is more recent).

See also PubMed entries.

The subject areas used are:

• 10 Most Cited Papers
• Meta 3D protein structure prediction
• Genomic ORFans and Evolution
• Protein Structure Prediction Methods
• Bioinformatics and Structure Determination
• Genome-wide Structural Assignments, Structural Genomics
• Assessment of Structure Prediction Methods: Benchmarks, Assesment Methods
• CASP "winner" papers
• Miscelaneous Topics
• Structure Comparison
• Docking
• Reviews

• 10 Most Cited Papers (as of Jan. 2004 in ISI). Notice that higher-impact, recently published papers may not have had time to accumulate enough citations. The 10 most cited papers together have accumulated over 700 citations, or 70 citations per paper on average. The papers with most citations are listed first.
  
  
  
  • Over 200 citations:
    
    
    • 14. Fischer, D. and Eisenberg, D. Fold Recognition Using Sequence-Derived Properties. Protein Science, 5, 947-955, 1996.
      
      
  • Over 40 citations:
    
    
    • 17. Fischer, D. and Eisenberg, D. Assigning Folds to the Proteins Encoded by the Genome of Mycoplasma genitalium. Proc. Nat. Academy of Sciences, 94, 11929-11934, 1997 pdf.
      
      
    • 8. Fischer, D., Lin, S.L., Wolfson, H. and Nussinov, R. A Geometry-Based Suite of Molecular Docking Processes. J. Mol. Biol., 248, 459-477, 1995.
      
      
    • 33. Bujnicki JM, Elofsson A, Fischer D and Rychlewski L. Structure prediction meta server. Bioinformatics 17, 750-751, 2001.
      
      
    • 6. Lin, L. S., Nussinov, R., Fischer, D. and Wolfson, H. Molecular Surface Representation by Sparse Critical Points. Proteins: Structure, Function and Genetics, 18, 94-101, 1994.
      
      
    • 13. Fischer, D., Rice, D.W., Bowie, J.U. and Eisenberg, D. Assigning Amino Acid Sequences to 3D Protein Folds. FASEB J., 10, 126-136, 1996.
      
      
    • 4. Bachar, O., Fischer, D., Nussinov, R. & Wolfson, H. A Computer Vision Based Technique for Sequence Independent Structural Comparison of Proteins. Protein Engineering, 6, 279-288, 1993.
      
      
    • 5. Fischer, D., Wolfson, H., Lin, S. L. and Nussinov, R. Three-Dimensional, Sequence Order-Independent Structural Comparison of a Serine Protease Against the Crystallographic Database Reveals Active Site Similarities: Potential Implications to Evolution and to Protein Folding. Protein Science, 3, 769-768, 1994.
      
      
    • 29. Buhnicki, J. M., Elofsson, A., Fischer, D. and Rychlewski, L. LiveBench1: Continuous Benchmarking of Protein Structure Prediction Servers. Prot. Sci. , 10: 352-361, 2001. pdf .
      
      
    • 1. Fischer, D., Bachar. O., Nussinov, R. & Wolfson, H. An Efficient Automated Computer Vision Based Technique for Detection of Three-Dimensional Structural Motifs in Proteins. J. Biom. Struct. & Dynamics, 9, 769-789, 1992.
      
      
    • 9. Fischer, D., Tsai, C.J., Nussinov, R. and Wolfson, H. A 3-D Sequence-Independent Representation of the Protein Data Bank. Protein Engineering, 8, 981-997, 1995.
  
  
  
  
• Meta 3D protein structure prediction
  
  
  
  • 38. Fischer, D. 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor. Proteins, 51:434-441, 2003. ps.
    
    
  • 47. Fischer, D. The 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3. Proteins, 53: 517-523, 2003. pdf .
    
    
  • 51. Bujnicki, J. and Fischer, D. Meta Approaches to Protein Structure Prediction. Chapter in Nucleic Acids and Molecular Biology, Vol. 15. pp 23-34. Janusz M. Bujnicki (Ed.). Practical Bioinformatics. Springer-Verlag Berlin Heidelberg, 2004. pdf .
    
    
  • 42. Ginalski, K., Elofsson, A., Fischer, D. and Rychlewski, L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19: 1015-1018, 2003.
    
    
  • 33. Bujnicki JM, Elofsson A, Fischer D and Rychlewski L. Structure prediction meta server. Bioinformatics 17, 750-751, 2001.
  
  
  
• Genomic ORFans and Evolution
  
  
  • 39. Siew, N and Fischer, D. 20,000 ORFan microbial protein families for the biologist? Structure , 11: 7-9, 2003. pdf .
    
    
  • 41. Siew, N and Fischer, D. Analysis of Singleton ORFans in Fully Sequenced Microbial Genomes. Proteins, 53: 241-251, 2003. pdf .
    
    
  • 53. Siew, N. and Fischer, D. Structural Biology Sheds Light on the ORFan Puzzle. J. Mol. Biol., 342:369-373, 2004. pdf .
    
    
  • 20. Fischer, D. and Eisenberg, D. Finding families for genomic ORFans: the role of bioinformatics and structural biology. Bioinformatics, 15: 759-762, 1999.
    
    
  • 45. Siew, N. and Fischer, D. Unravelling the ORFan puzzle. Comparative and Functional Genomics, 4: 432-441, 2003. pdf .
    
    
  • 24. Fischer, D. Structural genomics: affirmative action for ORFans and the growth in our structural knowledge. Prot. Eng., 12:1029-1030, 1999.
    
    
  • 50. Shmuely, H., Dinitz, E., Dahan, I., Eichler, J., Fischer, D. and Shaanan, B. Poorly-conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins. Bioinformatics, 20: 1248-1253, 2004. pdf .
    
    
  • 49. Siew, N., Azaria, Y. and Fischer, D. The ORFanage: An ORFan Database. Nucl. Acid. Research, 32,D281-D283, 2004. NAR .
    
  
  
  
• Protein Structure Prediction Methods
  
  
  
  • 38. Fischer, D. 3D-SHOTGUN: A Novel, Cooperative, Fold-Recognition Meta-Predictor. Proteins, 51:434-441, 2003. ps.
    
    
  • 17. Fischer, D. and Eisenberg, D. Assigning Folds to the Proteins Encoded by the Genome of Mycoplasma genitalium. Proc. Nat. Academy of Sciences, 94, 11929-11934, 1997 pdf.
    
    
  • 25. Fischer, D. Hybrid Fold Recognition: Combining Sequence Derived Properties with Evolutionary Information. Pacific Symp. Biocomputing, Hawaii, 119-130, January 2000. Editors: Altman, R.B., Dunker, A.K., Hunter, Lauderdale, K. and Klein, T.E. Publishers: World Scientific. scanned pdf.
    
    
  • 14. Fischer, D. and Eisenberg, D. Fold Recognition Using Sequence-Derived Properties. Protein Science, 5, 947-955, 1996.
    
    
  • 35. Naomi Siew and Daniel Fischer. A user's guide to fold recognition. In Protein Structure Prediction , IUL Biotechnology Series, Editor Igor F. Tsigelny, International University Line, La Jolla, California. Pages 355-376, 2002.
    
    
  • 13. Fischer, D., Rice, D.W., Bowie, J.U. and Eisenberg, D. Assigning Amino Acid Sequences to 3D Protein Folds. FASEB J., 10, 126-136, 1996.
    
    
  • 15. Elofsson, A., Fischer, D., Rice, D.W., LeGrand, S. and Eisenberg, D. A Study of Combined Structure-sequence Profiles. Folding and Design, 1, 451-461, 1996.
    
    
  
  
  
• Bioinformatics and Structure Determination
  
  
  • 37. Janusz Bujnicki, Marcin Feder, Leszek Rychlewski and Daniel Fischer. Errors in the D.radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools. FEBS letters 525, 174-175, 2002.
    
    
  • 36. Janusz Bujnicki, Leszek Rychlewski and Daniel Fischer. Fold-Recognition Detects an Error in the Protein Data Bank. Bioinformatics , 18: 1391-1395, 2002.
    
    
  • 28. Fischer, D., Baker, D. and Moult, J. We need both computer models and experiments (correspondence). Nature, 409: 558, 2001. ps .
    
    
  • 52. Fischer, D., Pas, J. and Rychlewski, L. The PDB-preview database: a repository of in-silico models of "on-hold" PDB entries. Bioinformatics, 20: 2482-2484, 2004.
    
    
  • 44. Rychlewski, L, Bujnicki, J and Fischer, D. Protein Fold-Recognition and Experimental Structure Determination. Chapter in, Book in press, 2003.
    
    
  
  
  
• Genome-wide Structural Assignments, Structural Genomics
  
  
  • 53. Siew, N. and Fischer, D. Structural Biology Sheds Light on the ORFan Puzzle. J. Mol. Biol., 342:369-373, 2004. pdf .
    
    
  • 17. Fischer, D. and Eisenberg, D. Assigning Folds to the Proteins Encoded by the Genome of Mycoplasma genitalium. Proc. Nat. Academy of Sciences, 94, 11929-11934, 1997 pdf.
    
    
  • 23. Fischer, D. and Eisenberg, D. Predicting structures for genome proteins. Curr. Opin. Structural Biology, 9:208-211, 1999.
    
    
  • 28. Fischer, D., Baker, D. and Moult, J. We need both computer models and experiments (correspondence). Nature, 409: 558, 2001. ps .
    
    
  • 24. Fischer, D. Structural genomics: affirmative action for ORFans and the growth in our structural knowledge. Prot. Eng., 12:1029-1030, 1999.
    
    
  • 52. Fischer, D., Pas, J. and Rychlewski, L. The PDB-preview database: a repository of in-silico models of "on-hold" PDB entries. Bioinformatics, 20: 2482-2484, 2004.
    
    
  • 20. Fischer, D. and Eisenberg, D. Finding families for genomic ORFans: the role of bioinformatics and structural biology. Bioinformatics, 15: 759-762, 1999.
    
  
  
  
• Assessment of Structure Prediction Methods: Benchmarks, Assesment Methods
  
  
  • CAFASP / LiveBench series
    
    
    
    • 54. Rychlewski, L and Fischer, D. LiveBench-8: The large-scale, continuous assessment of Automated Protein Structure Prediction. Protein Science , in press, 2004.
      
      
    • 48. Fischer, D., Rychlewski, L., Dunbrack, R. L., Ortiz, A. R. and Elofsson, A. CAFASP3: The Third Critical Assessment of Fully Automated Structure Prediction Methods. Proteins, 53: 503-516, 2003. pdf .
      
      
    • 46. Rychlewski, L. Fischer, D. and Elofsson, A. LiveBench-6: Large-Scale Evaluation of Protein Structure Prediction Servers. Proteins, 53: 542-547, 2003. pdf .
      
      
    • 40. Fischer,D and Rychlewski, L. The 2002 Olympic Games of Protein Structure Prediction Prot. Eng., 16: 157-160, 2003. pdf .
      
      
    • 32. Fischer, D., et al. CAFASP-2: The Second Critical Assessment of Fully Automated Structure Prediction Methods. Proteins, Suppl. 5, 171-183, 2001. pdf .
      
      
    • 31. Buhnicki, J. M. and Elofsson, A., Fischer, D. and Rychlewski, L. LiveBench-2: The Second Large-Scale Evaluation of Protein Structure Prediction Servers. Proteins, Suppl. 5, 184-191, 2001. pdf .
      
      
    • 30. Siew, N. and Fischer, D. Convergent Evolution of CAFASP and Computer Chess Tournaments: CASP, Kasparov and CAFASP. IBM Systems Journal , 40, No.2, 410-425, 2001. pdf .
      
      
    • 29. Buhnicki, J. M., Elofsson, A., Fischer, D. and Rychlewski, L. LiveBench1: Continuous Benchmarking of Protein Structure Prediction Servers. Prot. Sci. , 10: 352-361, 2001. pdf .
      
      
    • 28. Fischer, D., Baker, D. and Moult, J. We need both computer models and experiments (correspondence). Nature, 409: 558, 2001. ps .
      
      
    • 27. Fischer, D., Elofsson, A. and Rychlewski, L. The 2000 Olympic Games of Protein Structure Prediction. Prot. Eng. , 13(10):667-670, 2000.
      
      
    • 21. Fischer, D et al. Critical Assessment of Fully Automated Structure Prediction Methods - CAFASP1, Proteins, Dedicated CASP3 issue, 1999.
      
      
  • Assessment Methods
    
    
    • 26. Siew, N., Elofsson, A., Rychlewski, L. and Fischer, D. MaxSub: A Measure for Quality Assessment of Protein Structure Predictions. Bioinformatics 16(9):776-785, 2000. pdf .
      
      
    • 12. Fischer, D., Elofsson, A., Rice, D.W., LeGrand, S. and Eisenberg, D. Assessing the Performance of Fold Recognition Methods By Means of a Comprehensive Benchmark. in Proc. Pacific Symp. Biocomputing, Hawaii, 300-318 January 1996 scanned pdf.
      
      
    • 34. Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. A study of quality measures for protein threading models. BMC Bioinformatics 2:5, 2001.
      
      
  
  
  
• CASP "winner" papers
  
  
  • 47. Fischer, D. The 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3. Proteins, 53: 517-523, 2003. pdf .
    
    
  • 43. Sasson, I and Fischer, D. Modeling Three-Dimensional Protein Structures for CASP5 Using the 3D-SHOTGUN meta-predictors. Proteins, 53: 389-394, 2003. pdf .
    
    
  • 32. Fischer, D., et al. CAFASP-2: The Second Critical Assessment of Fully Automated Structure Prediction Methods. Proteins, Suppl. 5, 171-183, 2001. pdf .
    
    
  • 22. Fischer, D. Modeling 3D Protein Structures for the CASP3 experiment. Proteins, Dedicated CASP3 issue, 1999.
    
    
  • 16. Rice, D.W., Fischer, D., Weiss, R. & Eisenberg, D.. Fold Assignments for Amino Acid Sequences of the CASP2 Experiment. Proteins, Suppl. 1, 113-122, 1997.
  
  
  
• Miscelaneous Topics
  
  
  • 19. Landgraf, R., Pegram, M., Fischer, D., Slamon, D.J. and Eisenberg, D. Analysis of heregulin symmetry by evolutionary tracing. Prot. Eng, , 12: 943-951, 1999.
    
    
  • 18. Beamer, L, Fischer, D. and Eisenberg, D. Detecting distant relatives of mammalian LPS-binding and lipid transport proteins. Protein Science , 7,1643-1646, 1998.
    
    
  • 10. Naor, D., Fischer, D., Jernigan, R. L., Wolfson, H. J. and Nussinov, R. Amino Acid Pair Interchanges at Spatially Conserved Locations. J. Mol. Biol., 256, 924,938,1996.
  
  
  
• Structure Comparison
  
  
  • 26. Siew, N., Elofsson, A., Rychlewski, L. and Fischer, D. MaxSub: A Measure for Quality Assessment of Protein Structure Predictions. Bioinformatics 16(9):776-785, 2000. pdf .
    
    
  • 11. Alexandrov, N.N. and Fischer, D. Ensembles of the Similarly Arranged Secondary Structure Elements in Proteins. Proteins: Structure, Function and Genetics, 25, 354-365, 1996.
    
    
  • 34. Cristobal S, Zemla A, Fischer D, Rychlewski L, Elofsson A. A study of quality measures for protein threading models. BMC Bioinformatics 2:5, 2001.
    
    
  • 5. Fischer, D., Wolfson, H., Lin, S. L. and Nussinov, R. Three-Dimensional, Sequence Order-Independent Structural Comparison of a Serine Protease Against the Crystallographic Database Reveals Active Site Similarities: Potential Implications to Evolution and to Protein Folding. Protein Science, 3, 769-768, 1994.
    
    
  • 4. Bachar, O., Fischer, D., Nussinov, R. & Wolfson, H. A Computer Vision Based Technique for Sequence Independent Structural Comparison of Proteins. Protein Engineering, 6, 279-288, 1993.
    
    
  • 9. Fischer, D., Tsai, C.J., Nussinov, R. and Wolfson, H. A 3-D Sequence-Independent Representation of the Protein Data Bank. Protein Engineering, 8, 981-997, 1995.
    
    
  • 2. Fischer, D., Nussinov, R. & Wolfson, H. Spatial, Sequence-Order Independent Structural Comparison of alpha/beta Proteins: Evolutionary Implications. J. Biom. Struct. & Dynamics, 11, 367-380, 1993.
    
    
  • 1. Fischer, D., Bachar. O., Nussinov, R. & Wolfson, H. An Efficient Automated Computer Vision Based Technique for Detection of Three-Dimensional Structural Motifs in Proteins. J. Biom. Struct. & Dynamics, 9, 769-789, 1992.
  
  
  
• Docking
  
  
  • 8. Fischer, D., Lin, S.L., Wolfson, H. and Nussinov, R. A Geometry-Based Suite of Molecular Docking Processes. J. Mol. Biol., 248, 459-477, 1995.
    
    
  • 7. Norel, R., Fischer, D., Wolfson, H & Nussinov, R. Molecular Surface Recognition by a Computer Vision Based Technique. Protein Engineering, 7, 39-46, 1994.
    
    
  • 6. Lin, L. S., Nussinov, R., Fischer, D. and Wolfson, H. Molecular Surface Representation by Sparse Critical Points. Proteins: Structure, Function and Genetics, 18, 94-101, 1994.
    
    
  • 3. Fischer, D., Norel, R., Wolfson, H & Nussinov, R. Surface Motifs by a Computer Vision Technique: Searches, Detection and Implications for Protein-Ligand Recognition. Proteins: Structure, Function and Genetics, 16, 278-292, 1993.
  
  
  
• Reviews
  
  
  • 51. Bujnicki, J. and Fischer, D. Meta Approaches to Protein Structure Prediction. Chapter in Nucleic Acids and Molecular Biology, Vol. 15. pp 23-34. Janusz M. Bujnicki (Ed.). Practical Bioinformatics. Springer-Verlag Berlin Heidelberg. In press, 2004. pdf .
    
    
  • 45. Siew, N. and Fischer, D. Unravelling the ORFan puzzle. Comparative and Functional Genomics, 4: 432-441, 2003. pdf .
    
    
  • 44. Rychlewski, L, Bujnicki, J and Fischer, D. Protein Fold-Recognition and Experimental Structure Determination. Chapter in, Book in press, 2003.
    
    
  • 35. Naomi Siew and Daniel Fischer. A user's guide to fold recognition. In Protein Structure Prediction , IUL Biotechnology Series, Editor Igor F. Tsigelny, International University Line, La Jolla, California. Pages 355-376, 2002.
    
    
  • 30. Siew, N. and Fischer, D. Convergent Evolution of CAFASP and Computer Chess Tournaments: CASP, Kasparov and CAFASP. IBM Systems Journal , 40, No.2, 410-425, 2001. pdf .
    
    
  • 23. Fischer, D. and Eisenberg, D. Predicting structures for genome proteins. Curr. Opin. Structural Biology, 9:208-211, 1999.
    
    
  • 13. Fischer, D., Rice, D.W., Bowie, J.U. and Eisenberg, D. Assigning Amino Acid Sequences to 3D Protein Folds. FASEB J., 10, 126-136, 1996.