Alejandro A. Schäffer

67 papers A* 7B 5Journal 51Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer. Bioinform. Xuan Cindy Li, Yuelin Liu, Alejandro A. Schäffer, Stephen M. Mount, S. Cenk Sahinalp
2025	J	`jnl`	Finding Multiple Optimal Solutions to an Integer Linear Program by Random Perturbations of Its Objective Function. Algorithms Noah Schulhof, Pattara Sukprasert, Eytan Ruppin, Samir Khuller, Alejandro A. Schäffer
2022	—	`conf`	Characterizing The Landscape Of Viral Expression In Cancer By Deep Learning. BIBM Abdurrahman Elbasir, Ying Ye, Daniel E. Schäffer, Jayamanna Wickramasinghe, Xue Hao, Paul M. Lieberman, Quaid Morris, Rugang Zhang, Alejandro A. Schäffer, Noam Auslander
2021	J	`jnl`	Ancestral haplotype reconstruction in endogamous populations using identity-by-descent. PLoS Comput. Biol. 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
2021	J	`jnl`	Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation. BMC Bioinform. Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki
2021	J	`jnl`	Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinform. 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
2020	J	`jnl`	PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem. Bioinform. 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
2020	J	`jnl`	Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. J. Comput. Biol. Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz
2020	J	`jnl`	VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinform. Alejandro A. Schäffer, Eneida Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi, Eric P. Nawrocki
2019	B	`conf`	Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. RECOMB Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz
2018	—	`conf`	Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data. ICCABS Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Russell Schwartz
2018	J	`jnl`	VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening. Bioinform. Alejandro A. Schäffer, Eric P. Nawrocki, Yoon Choi, Paul A. Kitts, Ilene Karsch-Mizrachi, Richard McVeigh
2017	J	`jnl`	Virus Variation Resource - improved response to emergent viral outbreaks. Nucleic Acids Res. Eneida Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister
2016	J	`jnl`	Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study. IEEE ACM Trans. Comput. Biol. Bioinform. Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schäffer, Russell Schwartz
2015	J	`jnl`	Inferring models of multiscale copy number evolution for single-tumor phylogenetics. Bioinform. Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
2014	J	`jnl`	Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics. PLoS Comput. Biol. Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
2014	J	`jnl`	PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD. BMC Bioinform. Edward Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D. Terwilliger, Alejandro A. Schäffer
2013	J	`jnl`	Phylogenetic analysis of multiprobe fluorescence Bioinform. Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
2008	J	`jnl`	Database indexing for production MegaBLAST searches. Bioinform. Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer
2008	J	`jnl`	Database indexing for production MegaBLAST searches. Bioinform. Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer
2007	J	`jnl`	Improved BLAST searches using longer words for protein seeding. Bioinform. Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, Richa Agarwala
2007	J	`jnl`	rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control. Bioinform. Alejandro A. Schäffer, Edward Stallknecht Rice, William J. Cook, Richa Agarwala
2006	J	`jnl`	A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences. J. Comput. Biol. Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala
2006	J	`jnl`	WindowMasker: window-based masker for sequenced genomes. Bioinform. Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala
2005	J	`jnl`	A structure-based method for protein sequence alignment. Bioinform. Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, Stephen H. Bryant
2000	J	`jnl`	Distance-Based Reconstruction of Tree Models for Oncogenesis. J. Comput. Biol. Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer
2000	J	`jnl`	Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations. Discret. Appl. Math. Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schäffer
1999	J	`jnl`	IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinform. Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul
1999	J	`jnl`	Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data. J. Comput. Biol. Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer
1999	A*	`conf`	Inverse Inbreeding Coefficient Problems with an Application to Linkage Analysis of Recessive Diseases in Inbred Populations. SODA Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schäffer
1998	J	`jnl`	Approximation Algorithms for a Genetic Diagnostics Problem. J. Comput. Biol. S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker
1997	B	`conf`	Approximation Algorithms for a Genetic Diagnostics Problem. WADS S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker
1996	J	`jnl`	Multiple Matching of Parametrized Patterns. Theor. Comput. Sci. Ramana M. Idury, Alejandro A. Schäffer
1995	J	`jnl`	Improved Dynamic Dictionary Matching Inf. Comput. Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer
1995	J	`jnl`	Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment. J. Comput. Biol. Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer
1995	B	`conf`	Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract). CPM Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer
1995	J	`jnl`	Multiple Matching of Rectangular Patterns Inf. Comput. Ramana M. Idury, Alejandro A. Schäffer
1995	J	`jnl`	Optimal Edge Ranking of Trees in Polynomial Time. Algorithmica Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer
1994	J	`jnl`	Dynamic Dictionary Matching with Failure Functions. Theor. Comput. Sci. Ramana M. Idury, Alejandro A. Schäffer
1994	J	`jnl`	Faster Isometric Embedding in Products of Complete Graphs. Discret. Appl. Math. Franz Aurenhammer, Michael Formann, Ramana M. Idury, Alejandro A. Schäffer, Frank Wagner
1994	J	`jnl`	Markov Analysis of Multiple-Disk Prefetching Strategies for External Merging. Theor. Comput. Sci. Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman
1994	B	`conf`	Multiple Matching of Parameterized Patterns. CPM Ramana M. Idury, Alejandro A. Schäffer
1993	J	`jnl`	A Faster Algorithm to Recognize Undirected Path Graphs. Discret. Appl. Math. Alejandro A. Schäffer
1993	A*	`conf`	Improved Dynamic Dictionary Matching. SODA Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer
1993	A*	`conf`	Multiple matching of rectangular patterns. STOC Ramana M. Idury, Alejandro A. Schäffer
1993	A*	`conf`	Optimal Edge Ranking of Trees in Polynomial Time. SODA Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer
1993	J	`jnl`	Triangulating Three-Colored Graphs in Linear Time and Linear Space. SIAM J. Discret. Math. Ramana M. Idury, Alejandro A. Schäffer
1992	B	`conf`	Dynamic Dictionary Matching with Failure Functions (Extended Abstract). CPM Ramana M. Idury, Alejandro A. Schäffer
1992	J	`jnl`	Finding the prime factors of strong direct product graphs in polynomial time. Discret. Math. Joan Feigenbaum, Alejandro A. Schäffer
1992	—	`conf`	Markov Analysis of Multiple-Disk Prefetching for External Mergesort. ICPP (3) Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman
1991	J	`jnl`	An Implicit Data Structure for Searching a Multikey Table in Logarithmic Time. J. Comput. Syst. Sci. Amos Fiat, J. Ian Munro, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel
1991	J	`jnl`	Recognizing brittle graphs: remarks on a paper of Hoàng and Khouzam. Discret. Appl. Math. Alejandro A. Schäffer
1991	J	`jnl`	Simple Local Search Problems That are Hard to Solve. SIAM J. Comput. Alejandro A. Schäffer, Mihalis Yannakakis
1990	A*	`conf`	On the Complexity of Local Search (Extended Abstract) STOC Christos H. Papadimitriou, Alejandro A. Schäffer, Mihalis Yannakakis
1989	J	`jnl`	Fast Parallel Algorithms for Chordal Graphs. SIAM J. Comput. Joseph Naor, Moni Naor, Alejandro A. Schäffer
1989	J	`jnl`	Graph spanners. J. Graph Theory David Peleg, Alejandro A. Schäffer
1989	J	`jnl`	Optimal Node Ranking of Trees in Linear Time. Inf. Process. Lett. Alejandro A. Schäffer
1989	J	`jnl`	Time bounds on fault-tolerant broadcasting. Networks David Peleg, Alejandro A. Schäffer
1988	J	`jnl`	A Tighter Upper Bound on the Worst Case Behavior of Conway's Parallel Sorting Algorithm. J. Algorithms Alejandro A. Schäffer
1988	—	`—`	Algorithmic problems on intersection graphs. Alejandro A. Schäffer
1988	J	`jnl`	Recognizing Bellman-Ford-Orderable Graphs. SIAM J. Discret. Math. Ramsey W. Haddad, Alejandro A. Schäffer
1988	A*	`conf`	Storing and Searching a Multikey Table (Extended Abstract) STOC Amos Fiat, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel
1987	J	`jnl`	Convex Hulls of Piecewise-Smooth Jordan Curves. J. Algorithms Alejandro A. Schäffer, Christopher J. Van Wyk
1987	A*	`conf`	Fast Parallel Algorithms for Chordal Graphs (Extended Abstract) STOC Joseph Naor, Moni Naor, Alejandro A. Schäffer
1987	J	`jnl`	Shortest prefix strings containing all subset permutations. Discret. Math. Alejandro A. Schäffer
1986	J	`jnl`	Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism. SIAM J. Comput. Joan Feigenbaum, Alejandro A. Schäffer
1985	J	`jnl`	A polynomial time algorithm for finding the prime factors of cartesian-product graphs. Discret. Appl. Math. Joan Feigenbaum, John Hershberger, Alejandro A. Schäffer