Alejandro A. Schäffer

Publication Activity (10 Years)

Years Active: 1985-2022
Publications (10 Years): 12

Top Topics

Integer Linear Programming

Haplotype Inference

Top Venues

PLoS Comput. Biol.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

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)
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)
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) (2021)
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) (2021)
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) (2020)
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) (2020)
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) (2020)
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)
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) (2018)
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)
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) (2017)
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) (2016)
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) (2015)
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)
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 (2014)
Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
hybridization data from tumor cell populations. Bioinform. 29 (13) (2013)
Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer
Database indexing for production MegaBLAST searches. Bioinform. 24 (24) (2008)
Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer
Database indexing for production MegaBLAST searches. Bioinform. 24 (16) (2008)
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) (2007)
Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, Richa Agarwala
Improved BLAST searches using longer words for protein seeding. Bioinform. 23 (21) (2007)
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) (2006)
Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala
WindowMasker: window-based masker for sequenced genomes. Bioinform. 22 (2) (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. Bioinform. 21 (8) (2005)
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) (2000)
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) (2000)
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) (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)
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) (1999)
S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker
Approximation Algorithms for a Genetic Diagnostics Problem. J. Comput. Biol. 5 (1) (1998)
S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker
Approximation Algorithms for a Genetic Diagnostics Problem. WADS (1997)
Ramana M. Idury, Alejandro A. Schäffer
Multiple Matching of Parametrized Patterns. Theor. Comput. Sci. 154 (2) (1996)
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) (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)
Ramana M. Idury, Alejandro A. Schäffer
Multiple Matching of Rectangular Patterns Inf. Comput. 117 (1) (1995)
Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer
Optimal Edge Ranking of Trees in Polynomial Time. Algorithmica 13 (6) (1995)
Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer
Improved Dynamic Dictionary Matching Inf. Comput. 119 (2) (1995)
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) (1994)
Ramana M. Idury, Alejandro A. Schäffer
Multiple Matching of Parameterized Patterns. CPM (1994)
Ramana M. Idury, Alejandro A. Schäffer
Dynamic Dictionary Matching with Failure Functions. Theor. Comput. Sci. 131 (2) (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) (1994)
Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer
Improved Dynamic Dictionary Matching. SODA (1993)
Ramana M. Idury, Alejandro A. Schäffer
Triangulating Three-Colored Graphs in Linear Time and Linear Space. SIAM J. Discret. Math. 6 (2) (1993)
Ramana M. Idury, Alejandro A. Schäffer
Multiple matching of rectangular patterns. STOC (1993)
Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer
Optimal Edge Ranking of Trees in Polynomial Time. SODA (1993)
Alejandro A. Schäffer
A Faster Algorithm to Recognize Undirected Path Graphs. Discret. Appl. Math. 43 (2) (1993)
Ramana M. Idury, Alejandro A. Schäffer
Dynamic Dictionary Matching with Failure Functions (Extended Abstract). CPM (1992)
Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman
Markov Analysis of Multiple-Disk Prefetching for External Mergesort. ICPP (3) (1992)
Joan Feigenbaum, Alejandro A. Schäffer
Finding the prime factors of strong direct product graphs in polynomial time. Discret. Math. 109 (1-3) (1992)
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) (1991)
Alejandro A. Schäffer, Mihalis Yannakakis
Simple Local Search Problems That are Hard to Solve. SIAM J. Comput. 20 (1) (1991)
Alejandro A. Schäffer
Recognizing brittle graphs: remarks on a paper of Hoàng and Khouzam. Discret. Appl. Math. 31 (1) (1991)
Christos H. Papadimitriou, Alejandro A. Schäffer, Mihalis Yannakakis
On the Complexity of Local Search (Extended Abstract) STOC (1990)
David Peleg, Alejandro A. Schäffer
Time bounds on fault-tolerant broadcasting. Networks 19 (7) (1989)
Joseph Naor, Moni Naor, Alejandro A. Schäffer
Fast Parallel Algorithms for Chordal Graphs. SIAM J. Comput. 18 (2) (1989)
David Peleg, Alejandro A. Schäffer
Graph spanners. J. Graph Theory 13 (1) (1989)
Alejandro A. Schäffer
Optimal Node Ranking of Trees in Linear Time. Inf. Process. Lett. 33 (2) (1989)
Amos Fiat, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel
Storing and Searching a Multikey Table (Extended Abstract) STOC (1988)
Alejandro A. Schäffer
A Tighter Upper Bound on the Worst Case Behavior of Conway's Parallel Sorting Algorithm. J. Algorithms 9 (3) (1988)
Ramsey W. Haddad, Alejandro A. Schäffer
Recognizing Bellman-Ford-Orderable Graphs. SIAM J. Discret. Math. 1 (4) (1988)
Alejandro A. Schäffer, Christopher J. Van Wyk
Convex Hulls of Piecewise-Smooth Jordan Curves. J. Algorithms 8 (1) (1987)
Joseph Naor, Moni Naor, Alejandro A. Schäffer
Fast Parallel Algorithms for Chordal Graphs (Extended Abstract) STOC (1987)
Alejandro A. Schäffer
Shortest prefix strings containing all subset permutations. Discret. Math. 64 (2-3) (1987)
Joan Feigenbaum, Alejandro A. Schäffer
Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism. SIAM J. Comput. 15 (2) (1986)
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) (1985)