Alejandro A. Schäffer

According to our database, Alejandro A. Schäffer authored at least 58 papers between 1985 and 2022.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2022

Characterizing The Landscape Of Viral Expression In Cancer By Deep Learning.

Abdurrahman Elbasir, Ying Ye, Daniel E. Schäffer, Jayamanna Wickramasinghe, Xue Hao, Paul M. Lieberman, Quaid Morris, Rugang Zhang, Alejandro A. Schäffer, Noam Auslander

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

Ancestral haplotype reconstruction in endogamous populations using identity-by-descent.

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

PLoS Comput. Biol., 2021

Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation.

Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki

BMC Bioinform., 2021

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data.

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

Bioinform., 2021

2020

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data.

Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz

J. Comput. Biol., 2020

VADR: validation and annotation of virus sequence submissions to GenBank.

Alejandro A. Schäffer, Eneida Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi, Eric P. Nawrocki

BMC Bioinform., 2020

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem.

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

Bioinform., 2020

2018

VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening.

Alejandro A. Schäffer, Eric P. Nawrocki, Yoon Choi, Paul A. Kitts, Ilene Karsch-Mizrachi, Richard McVeigh

Bioinform., 2018

Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data.

Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Russell Schwartz

Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018

2017

Virus Variation Resource - improved response to emergent viral outbreaks.

Eneida Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister

Nucleic Acids Res., 2017

2016

Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study.

Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schäffer, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2016

2015

Inferring models of multiscale copy number evolution for single-tumor phylogenetics.

Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz

Bioinform., 2015

2014

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics.

Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz

PLoS Comput. Biol., 2014

PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD.

Edward Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D. Terwilliger, Alejandro A. Schäffer

BMC Bioinform., 2014

2013

Phylogenetic analysis of multiprobe fluorescence <i>in situ</i> hybridization data from tumor cell populations.

Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz

Bioinform., 2013

2008

Database indexing for production MegaBLAST searches.

Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer

Bioinform., 2008

2007

Improved BLAST searches using longer words for protein seeding.

Sergey A. Shiryev, Jason S. Papadopoulos, Alejandro A. Schäffer, Richa Agarwala

Bioinform., 2007

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control.

Alejandro A. Schäffer, Edward Stallknecht Rice, William J. Cook, Richa Agarwala

Bioinform., 2007

2006

A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences.

Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala

J. Comput. Biol., 2006

WindowMasker: window-based masker for sequenced genomes.

Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala

Bioinform., 2006

2005

A structure-based method for protein sequence alignment.

Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, Stephen H. Bryant

Bioinform., 2005

2000

Distance-Based Reconstruction of Tree Models for Oncogenesis.

Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer

J. Comput. Biol., 2000

Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations.

Richa Agarwala, Leslie G. Biesecker, Alejandro A. Schäffer

Discret. Appl. Math., 2000

1999

Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data.

Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Schäffer

J. Comput. Biol., 1999

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.

Alejandro A. Schäffer, Yuri I. Wolf, Chris P. Ponting, Eugene V. Koonin, L. Aravind, Stephen F. Altschul

Bioinform., 1999

1998

Approximation Algorithms for a Genetic Diagnostics Problem.

S. Rao Kosaraju, Alejandro A. Schäffer, Leslie G. Biesecker

J. Comput. Biol., 1998

1996

Multiple Matching of Parametrized Patterns.

Ramana M. Idury, Alejandro A. Schäffer

Theor. Comput. Sci., 1996

1995

Improved Dynamic Dictionary Matching

Amihood Amir, Martin Farach, Ramana M. Idury, Johannes A. La Poutré, Alejandro A. Schäffer

Inf. Comput., June, 1995

Multiple Matching of Rectangular Patterns

Ramana M. Idury, Alejandro A. Schäffer

Inf. Comput., February, 1995

Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment.

Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer

J. Comput. Biol., 1995

Optimal Edge Ranking of Trees in Polynomial Time.

Pilar de la Torre, Raymond Greenlaw, Alejandro A. Schäffer

Algorithmica, 1995

Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract).

Sandeep K. Gupta, John D. Kececioglu, Alejandro A. Schäffer

Proceedings of the Combinatorial Pattern Matching, 6th Annual Symposium, 1995

1994

Markov Analysis of Multiple-Disk Prefetching Strategies for External Merging.

Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman

Theor. Comput. Sci., 1994

Dynamic Dictionary Matching with Failure Functions.

Ramana M. Idury, Alejandro A. Schäffer

Theor. Comput. Sci., 1994

Faster Isometric Embedding in Products of Complete Graphs.

Franz Aurenhammer, Michael Formann, Ramana M. Idury, Alejandro A. Schäffer, Frank Wagner

Discret. Appl. Math., 1994

Multiple Matching of Parameterized Patterns.

Ramana M. Idury, Alejandro A. Schäffer

Proceedings of the Combinatorial Pattern Matching, 5th Annual Symposium, 1994

1993

Triangulating Three-Colored Graphs in Linear Time and Linear Space.

Ramana M. Idury, Alejandro A. Schäffer

SIAM J. Discret. Math., 1993

A Faster Algorithm to Recognize Undirected Path Graphs.

Alejandro A. Schäffer

Discret. Appl. Math., 1993

1992

Finding the prime factors of strong direct product graphs in polynomial time.

Joan Feigenbaum, Alejandro A. Schäffer

Discret. Math., 1992

Markov Analysis of Multiple-Disk Prefetching for External Mergesort.

Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman

Proceedings of the 1992 International Conference on Parallel Processing, 1992

Dynamic Dictionary Matching with Failure Functions (Extended Abstract).

Ramana M. Idury, Alejandro A. Schäffer

Proceedings of the Combinatorial Pattern Matching, Third Annual Symposium, 1992

1991

Simple Local Search Problems That are Hard to Solve.

Alejandro A. Schäffer, Mihalis Yannakakis

SIAM J. Comput., 1991

An Implicit Data Structure for Searching a Multikey Table in Logarithmic Time.

Amos Fiat, J. Ian Munro, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel

J. Comput. Syst. Sci., 1991

Recognizing brittle graphs: remarks on a paper of Hoàng and Khouzam.

Alejandro A. Schäffer

Discret. Appl. Math., 1991

1990

On the Complexity of Local Search (Extended Abstract)

Christos H. Papadimitriou, Alejandro A. Schäffer, Mihalis Yannakakis

Proceedings of the 22nd Annual ACM Symposium on Theory of Computing, 1990

1989

Fast Parallel Algorithms for Chordal Graphs.

Joseph Naor, Moni Naor, Alejandro A. Schäffer

SIAM J. Comput., 1989

Time bounds on fault-tolerant broadcasting.

David Peleg, Alejandro A. Schäffer

Networks, 1989

Graph spanners.

David Peleg, Alejandro A. Schäffer

J. Graph Theory, 1989

Optimal Node Ranking of Trees in Linear Time.

Alejandro A. Schäffer

Inf. Process. Lett., 1989

1988

Algorithmic problems on intersection graphs.

Alejandro A. Schäffer

PhD thesis, 1988

Recognizing Bellman-Ford-Orderable Graphs.

Ramsey W. Haddad, Alejandro A. Schäffer

SIAM J. Discret. Math., 1988

A Tighter Upper Bound on the Worst Case Behavior of Conway's Parallel Sorting Algorithm.

Alejandro A. Schäffer

J. Algorithms, 1988

Storing and Searching a Multikey Table (Extended Abstract)

Amos Fiat, Moni Naor, Alejandro A. Schäffer, Jeanette P. Schmidt, Alan Siegel

Proceedings of the 20th Annual ACM Symposium on Theory of Computing, 1988

1987

Convex Hulls of Piecewise-Smooth Jordan Curves.

Alejandro A. Schäffer, Christopher J. Van Wyk

J. Algorithms, 1987

Shortest prefix strings containing all subset permutations.

Alejandro A. Schäffer

Discret. Math., 1987

Fast Parallel Algorithms for Chordal Graphs (Extended Abstract)

Joseph Naor, Moni Naor, Alejandro A. Schäffer

Proceedings of the 19th Annual ACM Symposium on Theory of Computing, 1987

1986

Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism.

Joan Feigenbaum, Alejandro A. Schäffer

SIAM J. Comput., 1986

1985

A polynomial time algorithm for finding the prime factors of cartesian-product graphs.

Joan Feigenbaum, John Hershberger, Alejandro A. Schäffer

Discret. Appl. Math., 1985