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ORCIDAlejandro A. Schäffer
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2020 – today
- 2022
[c15]Abdurrahman Elbasir, Ying Ye, Daniel E. Schäffer, Jayamanna Wickramasinghe, Xue Hao, Paul M. Lieberman, Quaid Morris, Rugang Zhang, Alejandro A. Schäffer, Noam Auslander:
Characterizing The Landscape Of Viral Expression In Cancer By Deep Learning. BIBM 2022: 3801-3803- 2021
- [j49]Haoyun Lei, E. Michael Gertz, Alejandro A. Schäffer, Xuecong Fu, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Guibo Li
, Liqin Xu, Yong Hou, Kui Wu, Xulian Shi, Michael Dean, Thomas Ried, Russell Schwartz:
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinform. 37(24): 4704-4711 (2021) - [j48]Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki:
Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation. BMC Bioinform. 22(1): 400 (2021) - [j47]Kelly Finke, Michael Kourakos, Gabriela Brown, Huyen Trang Dang, Shi Jie Samuel Tan, Yuval B. Simons, Shweta Ramdas, Alejandro A. Schäffer, Rachel L. Kember, Maja Bucan, Sara Mathieson:
Ancestral haplotype reconstruction in endogamous populations using identity-by-descent. PLoS Comput. Biol. 17(2) (2021) - 2020
- [j46]Erfan Sadeqi Azer, Farid Rashidi Mehrabadi, Salem Malikic, Xuan Cindy Li, Osnat Bartok, Kevin Litchfield, Ronen Levy, Yardena Samuels, Alejandro A. Schäffer, E. Michael Gertz, Chi-Ping Day, Eva Pérez-Guijarro, Kerrie Marie, Maxwell P. Lee, Glenn Merlino, Funda Ergün, Süleyman Cenk Sahinalp:
PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. Bioinform. 36(Supplement-1): i169-i176 (2020) - [j45]Alejandro A. Schäffer, Eneida Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi, Eric P. Nawrocki:
VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinform. 21(1): 211 (2020) - [j44]Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz:
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. J. Comput. Biol. 27(4): 565-598 (2020)
2010 – 2019
- 2019
- [c14]Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz:
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. RECOMB 2019: 174-189 - 2018
- [j43]Alejandro A. Schäffer, Eric P. Nawrocki, Yoon Choi, Paul A. Kitts, Ilene Karsch-Mizrachi, Richard McVeigh:
VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening. Bioinform. 34(5): 755-759 (2018) - [c13]Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Russell Schwartz:
Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data. ICCABS 2018: 1 - 2017
- [j42]Eneida Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister:
Virus Variation Resource - improved response to emergent viral outbreaks. Nucleic Acids Res. 45(Database-Issue): D482-D490 (2017) - 2016
- [j41]Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schäffer, Russell Schwartz:
Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study. IEEE ACM Trans. Comput. Biol. Bioinform. 13(4): 643-655 (2016) - 2015
- [j40]Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
Inferring models of multiscale copy number evolution for single-tumor phylogenetics. Bioinform. 31(12): 258-267 (2015) - 2014
- [j39]Edward Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D. Terwilliger, Alejandro A. Schäffer:
PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD. BMC Bioinform. 15: 47 (2014) - [j38]Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics. PLoS Comput. Biol. 10(7) (2014) - 2013
- [j37]Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. Bioinform. 29(13): 189-198 (2013)
2000 – 2009
- 2008
- [j36]Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer:
Database indexing for production MegaBLAST searches. Bioinform. 24(16): 1757-1764 (2008) - [j35]Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer:
Database indexing for production MegaBLAST searches. Bioinform. 24(24): 2942 (2008) - 2007
- [j34]Alejandro A. Schäffer, Edward Stallknecht Rice, William J. Cook, Richa Agarwala:
rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. Bioinform. 23(9): 1156-1158 (2007) - [j33]Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, Richa Agarwala:
Improved BLAST searches using longer words for protein seeding. Bioinform. 23(21): 2949-2951 (2007) - 2006
- [j32]Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala:
WindowMasker: window-based masker for sequenced genomes. Bioinform. 22(2): 134-141 (2006) - [j31]Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala:
A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. J. Comput. Biol. 13(5): 1028-1040 (2006) - 2005
- [j30]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. Bioinform. 21(8): 1451-1456 (2005) - 2000
- [j29]Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schäffer:
Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations. Discret. Appl. Math. 104(1-3): 3-44 (2000) - [j28]Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer:
Distance-Based Reconstruction of Tree Models for Oncogenesis. J. Comput. Biol. 7(6): 789-803 (2000)
1990 – 1999
- 1999
- [j27]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. Bioinform. 15(12): 1000-1011 (1999) - [j26]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. J. Comput. Biol. 6(1): 37-51 (1999) - [c12]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 - 1998
- [j25]S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker:
Approximation Algorithms for a Genetic Diagnostics Problem. J. Comput. Biol. 5(1): 9-26 (1998) - 1997
- [c11]S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker:
Approximation Algorithms for a Genetic Diagnostics Problem. WADS 1997: 69-92 - 1996
- [j24]Ramana M. Idury, Alejandro A. Schäffer:
Multiple Matching of Parametrized Patterns. Theor. Comput. Sci. 154(2): 203-224 (1996) - 1995
- [j23]Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer:
Optimal Edge Ranking of Trees in Polynomial Time. Algorithmica 13(6): 592-618 (1995) - [j22]Ramana M. Idury, Alejandro A. Schäffer:
Multiple Matching of Rectangular Patterns. Inf. Comput. 117(1): 78-90 (1995) - [j21]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) - [j20]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. J. Comput. Biol. 2(3): 459-472 (1995) - [c10]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 - 1994
- [j19]Franz Aurenhammer, Michael Formann, Ramana M. Idury, Alejandro A. Schäffer, Frank Wagner:
Faster Isometric Embedding in Products of Complete Graphs. Discret. Appl. Math. 52(1): 17-28 (1994) - [j18]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) - [j17]Ramana M. Idury, Alejandro A. Schäffer:
Dynamic Dictionary Matching with Failure Functions. Theor. Comput. Sci. 131(2): 295-310 (1994) - [c9]Ramana M. Idury, Alejandro A. Schäffer:
Multiple Matching of Parameterized Patterns. CPM 1994: 226-239 - 1993
- [j16]Alejandro A. Schäffer:
A Faster Algorithm to Recognize Undirected Path Graphs. Discret. Appl. Math. 43(2): 261-295 (1993) - [j15]Ramana M. Idury, Alejandro A. Schäffer:
Triangulating Three-Colored Graphs in Linear Time and Linear Space. SIAM J. Discret. Math. 6(2): 289-293 (1993) - [c8]Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer:
Optimal Edge Ranking of Trees in Polynomial Time. SODA 1993: 138-144 - [c7]Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer:
Improved Dynamic Dictionary Matching. SODA 1993: 392-401 - [c6]Ramana M. Idury, Alejandro A. Schäffer:
Multiple matching of rectangular patterns. STOC 1993: 81-90 - 1992
- [j14]Joan Feigenbaum, Alejandro A. Schäffer:
Finding the prime factors of strong direct product graphs in polynomial time. Discret. Math. 109(1-3): 77-102 (1992) - [c5]Ramana M. Idury, Alejandro A. Schäffer:
Dynamic Dictionary Matching with Failure Functions (Extended Abstract). CPM 1992: 276-287 - [c4]Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman:
Markov Analysis of Multiple-Disk Prefetching for External Mergesort. ICPP (3) 1992: 272-279 - 1991
- [j13]Alejandro A. Schäffer:
Recognizing brittle graphs: remarks on a paper of Hoàng and Khouzam. Discret. Appl. Math. 31(1): 29-35 (1991) - [j12]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) - [j11]Alejandro A. Schäffer, Mihalis Yannakakis:
Simple Local Search Problems That are Hard to Solve. SIAM J. Comput. 20(1): 56-87 (1991) - 1990
- [c3]Christos H. Papadimitriou, Alejandro A. Schäffer, Mihalis Yannakakis:
On the Complexity of Local Search (Extended Abstract). STOC 1990: 438-445
1980 – 1989
- 1989
- [j10]Alejandro A. Schäffer:
Optimal Node Ranking of Trees in Linear Time. Inf. Process. Lett. 33(2): 91-96 (1989) - [j9]David Peleg, Alejandro A. Schäffer:
Graph spanners. J. Graph Theory 13(1): 99-116 (1989) - [j8]David Peleg, Alejandro A. Schäffer:
Time bounds on fault-tolerant broadcasting. Networks 19(7): 803-822 (1989) - [j7]Joseph Naor, Moni Naor, Alejandro A. Schäffer:
Fast Parallel Algorithms for Chordal Graphs. SIAM J. Comput. 18(2): 327-349 (1989) - 1988
- [b1]Alejandro A. Schäffer:
Algorithmic problems on intersection graphs. Stanford University, USA, 1988 - [j6]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) - [j5]Ramsey W. Haddad, Alejandro A. Schäffer:
Recognizing Bellman-Ford-Orderable Graphs. SIAM J. Discret. Math. 1(4): 447-471 (1988) - [c2]Amos Fiat, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel:
Storing and Searching a Multikey Table (Extended Abstract). STOC 1988: 344-353 - 1987
- [j4]Alejandro A. Schäffer:
Shortest prefix strings containing all subset permutations. Discret. Math. 64(2-3): 239-252 (1987) - [j3]Alejandro A. Schäffer, Christopher J. Van Wyk:
Convex Hulls of Piecewise-Smooth Jordan Curves. J. Algorithms 8(1): 66-94 (1987) - [c1]Joseph Naor, Moni Naor, Alejandro A. Schäffer:
Fast Parallel Algorithms for Chordal Graphs (Extended Abstract). STOC 1987: 355-364 - 1986
- [j2]Joan Feigenbaum, Alejandro A. Schäffer:
Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism. SIAM J. Comput. 15(2): 619-627 (1986) - 1985
- [j1]Joan Feigenbaum, John Hershberger, Alejandro A. Schäffer:
A polynomial time algorithm for finding the prime factors of cartesian-product graphs. Discret. Appl. Math. 12(2): 123-138 (1985)
Coauthor Index
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