Alejandro A. Schäffer

Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer: Database indexing for production MegaBLAST searches. Bioinformatics 24(16): 1757-1764 (2008)

Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer: Database indexing for production MegaBLAST searches. Bioinformatics 24(24): 2942 (2008)

Alejandro A. Schäffer, Edward Stallknecht Rice, William Cook, Richa Agarwala: rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. Bioinformatics 23(9): 1156-1158 (2007)

Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, Richa Agarwala: Improved BLAST searches using longer words for protein seeding. Bioinformatics 23(21): 2949-2951 (2007)

Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala: WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22(2): 134-141 (2006)

Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala: A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. Journal of Computational Biology 13(5): 1028-1040 (2006)

Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, Stephen H. Bryant: A structure-based method for protein sequence alignment. Bioinformatics 21(8): 1451-1456 (2005)

Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schäffer: Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations. Discrete Applied Mathematics 104(1-3): 3-44 (2000)

Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer: Distance-Based Reconstruction of Tree Models for Oncogenesis. Journal of Computational Biology 7(6): 789-803 (2000)

Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul: IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 15(12): 1000-1011 (1999)

Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer: Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data. Journal of Computational Biology 6(1): 37-51 (1999)

Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schäffer: Inverse Inbreeding Coefficient Problems with an Application to Linkage Analysis of Recessive Diseases in Inbred Populations. SODA 1999: 840-841

S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker: Approximation Algorithms for a Genetic Diagnostics Problem. Journal of Computational Biology 5(1): 9-26 (1998)

S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker: Approximation Algorithms for a Genetic Diagnostics Problem. WADS 1997: 69-92

Ramana M. Idury, Alejandro A. Schäffer: Multiple Matching of Parametrized Patterns. Theor. Comput. Sci. 154(2): 203-224 (1996)

Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer: Optimal Edge Ranking of Trees in Polynomial Time. Algorithmica 13(6): 592-618 (1995)

Ramana M. Idury, Alejandro A. Schäffer: Multiple Matching of Rectangular Patterns. Inf. Comput. 117(1): 78-90 (1995)

Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer: Improved Dynamic Dictionary Matching. Inf. Comput. 119(2): 258-282 (1995)

Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer: Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment. Journal of Computational Biology 2(3): 459-472 (1995)

Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer: Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract). CPM 1995: 128-143

Franz Aurenhammer, Michael Formann, Ramana M. Idury, Alejandro A. Schäffer, Frank Wagner: Faster Isometric Embedding in Products of Complete Graphs. Discrete Applied Mathematics 52(1): 17-28 (1994)

Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman: Markov Analysis of Multiple-Disk Prefetching Strategies for External Merging. Theor. Comput. Sci. 128(1&2): 211-239 (1994)

Ramana M. Idury, Alejandro A. Schäffer: Dynamic Dictionary Matching with Failure Functions. Theor. Comput. Sci. 131(2): 295-310 (1994)

Ramana M. Idury, Alejandro A. Schäffer: Multiple Matching of Parameterized Patterns. CPM 1994: 226-239

Alejandro A. Schäffer: A Faster Algorithm to Recognize Undirected Path Graphs. Discrete Applied Mathematics 43(2): 261-295 (1993)

Ramana M. Idury, Alejandro A. Schäffer: Triangulating Three-Colored Graphs in Linear Time and Linear Space. SIAM J. Discrete Math. 6(2): 289-293 (1993)

Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer: Optimal Edge Ranking of Trees in Polynomial Time. SODA 1993: 138-144

Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer: Improved Dynamic Dictionary Matching. SODA 1993: 392-401

Ramana M. Idury, Alejandro A. Schäffer: Multiple matching of rectangular patterns. STOC 1993: 81-90

Joan Feigenbaum, Alejandro A. Schäffer: Finding the prime factors of strong direct product graphs in polynomial time. Discrete Mathematics 109(1-3): 77-102 (1992)

Ramana M. Idury, Alejandro A. Schäffer: Dynamic Dictionary Matching with Failure Functions (Extended Abstract). CPM 1992: 276-287

Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman: Markov Analysis of Multiple-Disk Prefetching for External Mergesort. ICPP (3) 1992: 272-279

Alejandro A. Schäffer: Recognizing brittle graphs: remarks on a paper of Hoàng and Khouzam. Discrete Applied Mathematics 31(1): 29-35 (1991)

Amos Fiat, J. Ian Munro, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel: An Implicit Data Structure for Searching a Multikey Table in Logarithmic Time. J. Comput. Syst. Sci. 43(3): 406-424 (1991)

Alejandro A. Schäffer, Mihalis Yannakakis: Simple Local Search Problems That are Hard to Solve. SIAM J. Comput. 20(1): 56-87 (1991)

Christos H. Papadimitriou, Alejandro A. Schäffer, Mihalis Yannakakis: On the Complexity of Local Search (Extended Abstract). STOC 1990: 438-445

Alejandro A. Schäffer: Optimal Node Ranking of Trees in Linear Time. Inf. Process. Lett. 33(2): 91-96 (1989)

David Peleg, Alejandro A. Schäffer: Graph spanners. Journal of Graph Theory 13(1): 99-116 (1989)

David Peleg, Alejandro A. Schäffer: Time bounds on fault-tolerant broadcasting. Networks 19(7): 803-822 (1989)

Joseph Naor, Moni Naor, Alejandro A. Schäffer: Fast Parallel Algorithms for Chordal Graphs. SIAM J. Comput. 18(2): 327-349 (1989)

Alejandro A. Schäffer: A Tighter Upper Bound on the Worst Case Behavior of Conway's Parallel Sorting Algorithm. J. Algorithms 9(3): 321-342 (1988)

Ramsey W. Haddad, Alejandro A. Schäffer: Recognizing Bellman-Ford-Orderable Graphs. SIAM J. Discrete Math. 1(4): 447-471 (1988)

Amos Fiat, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel: Storing and Searching a Multikey Table (Extended Abstract). STOC 1988: 344-353

Alejandro A. Schäffer: Shortest prefix strings containing all subset permutations. Discrete Mathematics 64(2-3): 239-252 (1987)

Alejandro A. Schäffer, Christopher J. Van Wyk: Convex Hulls of Piecewise-Smooth Jordan Curves. J. Algorithms 8(1): 66-94 (1987)

Joseph Naor, Moni Naor, Alejandro A. Schäffer: Fast Parallel Algorithms for Chordal Graphs (Extended Abstract). STOC 1987: 355-364

Joan Feigenbaum, Alejandro A. Schäffer: Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism. SIAM J. Comput. 15(2): 619-627 (1986)