Alejandro A. Schäffer

发表

Markov Analysis of Multiple-Disk Prefetching for External Mergesort

Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman, 1992, ICPP.

Recognizing Bellman-Ford-Orderable Graphs

Alejandro A. Schäffer, Ramsey W. Haddad, 1988, SIAM J. Discret. Math..

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

Russell Schwartz, Alejandro A. Schäffer, Haoyun Lei, 2018, bioRxiv.

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

Russell Schwartz, Alejandro A. Schäffer, E. Michael Gertz, 2015, Bioinform..

VADR: validation and annotation of virus sequence submissions to GenBank

Alejandro A. Schäffer, Eric P. Nawrocki, Ilene Karsch-Mizrachi, 2020, BMC Bioinformatics.

A Faster Algorithm to Recognize Undirected Path Graphs

Alejandro A. Schäffer, A. Schäffer, 1993, Discret. Appl. Math..

Optimal edge ranking of trees in polynomial time

Alejandro A. Schäffer, Raymond Greenlaw, Pilar de la Torre, 1993, SODA '93.

Fast parallel algorithms for chordal graphs

Moni Naor, Joseph Naor, Alejandro A. Schäffer, 1987, STOC '87.

Virus Variation Resource – improved response to emergent viral outbreaks

Alejandro A. Schäffer, Yiming Bao, Eric P. Nawrocki, 2016, Nucleic Acids Res..

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

Russell Schwartz, Alejandro A. Schäffer, Liqin Xu, 2018, bioRxiv.

A structure-based method for protein sequence alignment

Alejandro A. Schäffer, Anna R. Panchenko, Stephen H. Bryant, 2005, Bioinform..

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

Alejandro A. Schäffer, 1988, J. Algorithms.

Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism

Joan Feigenbaum, Alejandro A. Schäffer, 1986, SIAM J. Comput..

Multiple matching of rectangular patterns

Alejandro A. Schäffer, Ramana M. Idury, 1993, STOC '93.

Time bounds on fault-tolerant broadcasting

Alejandro A. Schäffer, David Peleg, 1989, Networks.

Rh_tsp_map 3.0: End-to-end Radiation Hybrid Mapping with Improved Speed and Quality Control

William J. Cook, Alejandro A. Schäffer, Richa Agarwala, 2007, Bioinform..

Triangulating Three-Colored Graphs in Linear Time and Linear Space

Alejandro A. Schäffer, Ramana M. Idury, A. Schäffer, 1993, SIAM J. Discret. Math..

Database indexing for production MegaBLAST searches

Alejandro A. Schäffer, George Coulouris, Thomas L. Madden, 2008, Bioinform..

Strain level microbial detection and quantification with applications to single cell metagenomics

Alejandro A. Schäffer, Yuzhen Ye, Kaiyuan Zhu, 2020, bioRxiv.

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

Alejandro A. Schäffer, Richa Agarwala, Leslie G. Biesecker, 2000, SODA '99.

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

Joan Feigenbaum, Alejandro A. Schäffer, John Hershberger, 1985, Discret. Appl. Math..

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

Sandeep K. Gupta, Alejandro A. Schäffer, John D. Kececioglu, 1995, CPM.

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

Russell Schwartz, Alejandro A. Schäffer, Stanley Shackney, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

PhISCS-BnB: A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem

Funda Ergün, Alejandro A. Schäffer, Salem Malikic, 2020, bioRxiv.

Dynamic Dictionary Matching with Failure Functions

Alejandro A. Schäffer, Ramana M. Idury, A. Schäffer, 1994, Theor. Comput. Sci..

Approximation Algorithms for a Genetic Diagnostics Problem

Alejandro A. Schäffer, S. Rao Kosaraju, Leslie G. Biesecker, 1998, J. Comput. Biol..

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

Russell Schwartz, Alejandro A. Schäffer, Stanley Shackney, 2014, PLoS Comput. Biol..

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

Alejandro A. Schäffer, Richa Agarwala, E. Michael Gertz, 2006, J. Comput. Biol..

Shortest prefix strings containing all subset permutations

Alejandro A. Schäffer, 1987, Discret. Math..

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

Sandeep K. Gupta, Alejandro A. Schäffer, John D. Kececioglu, 1995, J. Comput. Biol..

Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data

Feng Jiang, Alejandro A. Schäffer, Christos H. Papadimitriou, 1999, J. Comput. Biol..

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

Alejandro A. Schäffer, Eric P. Nawrocki, Ilene Karsch-Mizrachi, 2018, Bioinform..

Simple Local Search Problems That are Hard to Solve

Mihalis Yannakakis, Alejandro A. Schäffer, M. Yannakakis, 1991, SIAM J. Comput..

Database indexing for production MegaBLAST searches

Alejandro A. Schäffer, George Coulouris, Thomas L. Madden, 2008, Bioinform..

PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD

Alejandro A. Schäffer, Charles Audet, Sébastien Le Digabel, 2014, BMC Bioinformatics.

Optimal Node Ranking of Trees in Linear Time

Alejandro A. Schäffer, A. Schäffer, 1989, Inf. Process. Lett..

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

Amos Fiat, Moni Naor, Jeanette P. Schmidt, 1991, J. Comput. Syst. Sci..

Markov Analysis of Multiple-Disk Prefetching Strategies for External Merging

Vinay S. Pai, Alejandro A. Schäffer, Peter J. Varman, 1994, Theor. Comput. Sci..

Storing and Searching a Multikey Table (Extended Abstract)

Amos Fiat, Moni Naor, Jeanette P. Schmidt, 1988, STOC 1988.

Graph spanners

Alejandro A. Schäffer, David Peleg, 1989, J. Graph Theory.

Faster Isometric Embedding in Products of Complete Graphs

Franz Aurenhammer, Alejandro A. Schäffer, Frank Wagner, 1994, Discret. Appl. Math..

Multiple Matching of Parametrized Patterns

Alejandro A. Schäffer, Ramana M. Idury, A. Schäffer, 1996, Theor. Comput. Sci..

Multiple Matching of Rectangular Patterns

Alejandro A. Schäffer, Ramana M. Idury, 1995, Inf. Comput..

Convex Hulls of Piecewise-Smooth Jordan Curves

Alejandro A. Schäffer, Christopher J. Van Wyk, 1987, J. Algorithms.

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

Russell Schwartz, Yong Hou, Alejandro A. Schäffer, 2019, RECOMB.

Distance-Based Reconstruction of Tree Models for Oncogenesis

Feng Jiang, Alejandro A. Schäffer, Christos H. Papadimitriou, 2000, J. Comput. Biol..

Approximation Algorithms for a Genetic Diagnostics Problem

Alejandro A. Schäffer, S. Rao Kosaraju, Leslie G. Biesecker, 1997, WADS.

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

Alejandro A. Schäffer, 1991, Discret. Appl. Math..

ON THE COMPLEXITY OF LOCAL SEARCH (Extended Abstract)

Mihalis Yannakakis, Alejandro A. Schäffer, Christos H. Papadimitriou, 1990, STOC 1990.

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

Russell Schwartz, Alejandro A. Schäffer, Stanley Shackney, 2013, Bioinform..

WindowMasker: window-based masker for sequenced genomes

Alejandro A. Schäffer, Richa Agarwala, E. Michael Gertz, 2006, Bioinform..

Dynamic Dictionary Matching with Failure Functions (Extended Abstract)

Alejandro A. Schäffer, Ramana M. Idury, 1992, CPM.

Fast Parallel Algorithms for Chordal Graphs* (Extended Abstract)

Moni Naor, Joseph Naor, Alejandro A. Schäffer, 1987, STOC 1987.

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

Alejandro A. Schäffer, L. Aravind, Chris P. Ponting, 1999, Bioinform..

Improved dynamic dictionary matching

Alejandro A. Schäffer, Amihood Amir, Martin Farach-Colton, 1995, SODA '93.

Improved BLAST searches using longer words for protein seeding

Alejandro A. Schäffer, Richa Agarwala, Jason S. Papadopoulos, 2007, Bioinform..

Storing and searching a multikey table

Amos Fiat, Moni Naor, Jeanette P. Schmidt, 1988, STOC '88.

On the complexity of local search

Mihalis Yannakakis, Alejandro A. Schäffer, Christos H. Papadimitriou, 1990, STOC '90.

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

Joan Feigenbaum, Alejandro A. Schäffer, J. Feigenbaum, 1992, Discret. Math..

Multiple Matching of Parameterized Patterns

Alejandro A. Schäffer, Ramana M. Idury, A. Schäffer, 1994, CPM.

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

Alejandro A. Schäffer, Eric P. Nawrocki, Ilene Karsch-Mizrachi, 2021, BMC Bioinform..

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

Russell Schwartz, Alejandro A. Schäffer, Liqin Xu, 2021, Bioinform..

A note on finding a strict saddlepoint

Subhash Suri, Alejandro A. Schäffer, Michael L. Fredman, 1991 .

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

Russell Schwartz, Alejandro A. Schäffer, Liqin Xu, 2020, bioRxiv.

Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees

Mathieu Lemire, Alejandro A. Schäffer, Daniel E. Weeks, 2011, Human Heredity.

PSEUDOMARKER: A Powerful Program for Joint Linkage and/or Linkage Disequilibrium Analysis on Mixtures of Singletons and Related Individuals

Alejandro A. Schäffer, Brian W. Lambert, Tero Hiekkalinna, 2011, Human Heredity.

A note on the chromatic number of the alternative negation of two graphs

Alejandro A. Schäffer, Ashok Subramanian, 1988 .

Computing the bump number with techniques from two-processor scheduling

Alejandro A. Schäffer, Barbara Simons, 1988 .

PSI-BLAST pseudocounts and the minimum description length principle

Alejandro A. Schäffer, Richa Agarwala, E. Michael Gertz, 2008, Nucleic acids research.

Mutant deoxynucleotide carrier is associated with congenital microcephaly

Alejandro A. Schäffer, Richa Agarwala, Izabela Makalowska, 2002, Nature Genetics.

Abstract 2895: Phylogenetic models of tumor progression from fluorescence in situ hybridization (FISH) data on many single cells of a solid tumor.

Russell Schwartz, Alejandro A. Schäffer, Darawalee Wangsa, 2013 .