A polynomial time algorithm for finding the prime factors of cartesian-product graphs. - Joan Feigenbaum; John Hershberger 001; Alejandro A. Schäffer (Discret. Appl. Math., 1985)

Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism. - Joan Feigenbaum; Alejandro A. Schäffer (SIAM J. Comput., 1986)

Fast Parallel Algorithms for Chordal Graphs (Extended Abstract) - Joseph Naor; Moni Naor; Alejandro A. Schäffer (STOC, 1987)

Shortest prefix strings containing all subset permutations. - Alejandro A. Schäffer (Discret. Math., 1987)

Convex Hulls of Piecewise-Smooth Jordan Curves. - Alejandro A. Schäffer; Christopher J. Van Wyk (J. Algorithms, 1987)

Storing and Searching a Multikey Table (Extended Abstract) - Amos Fiat; Moni Naor; Alejandro A. Schäffer; Jeanette P. Schmidt; Alan Siegel (STOC, 1988)

A Tighter Upper Bound on the Worst Case Behavior of Conway's Parallel Sorting Algorithm. - Alejandro A. Schäffer (J. Algorithms, 1988)

Recognizing Bellman-Ford-Orderable Graphs. - Ramsey W. Haddad; Alejandro A. Schäffer (SIAM J. Discret. Math., 1988)

Algorithmic problems on intersection graphs. - Alejandro A. Schäffer (1988)

Optimal Node Ranking of Trees in Linear Time. - Alejandro A. Schäffer (Inf. Process. Lett., 1989)

Graph spanners. - David Peleg; Alejandro A. Schäffer (J. Graph Theory, 1989)

Time bounds on fault-tolerant broadcasting. - David Peleg; Alejandro A. Schäffer (Networks, 1989)

Fast Parallel Algorithms for Chordal Graphs. - Joseph Naor; Moni Naor; Alejandro A. Schäffer (SIAM J. Comput., 1989)

On the Complexity of Local Search (Extended Abstract) - Christos H. Papadimitriou; Alejandro A. Schäffer; Mihalis Yannakakis (STOC, 1990)

Recognizing brittle graphs: remarks on a paper of Hoàng and Khouzam. - Alejandro A. Schäffer (Discret. Appl. Math., 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)

Simple Local Search Problems That are Hard to Solve. - Alejandro A. Schäffer; Mihalis Yannakakis (SIAM J. Comput., 1991)

Dynamic Dictionary Matching with Failure Functions (Extended Abstract). - Ramana M. Idury; Alejandro A. Schäffer (CPM, 1992)

Markov Analysis of Multiple-Disk Prefetching for External Mergesort. - Vinay S. Pai; Alejandro A. Schäffer; Peter J. Varman (ICPP (3), 1992)

Finding the prime factors of strong direct product graphs in polynomial time. - Joan Feigenbaum; Alejandro A. Schäffer (Discret. Math., 1992)

A Faster Algorithm to Recognize Undirected Path Graphs. - Alejandro A. Schäffer (Discret. Appl. Math., 1993)

Triangulating Three-Colored Graphs in Linear Time and Linear Space. - Ramana M. Idury; Alejandro A. Schäffer (SIAM J. Discret. Math., 1993)

Multiple Matching of Parameterized Patterns. - Ramana M. Idury; Alejandro A. Schäffer (CPM, 1994)

Faster Isometric Embedding in Products of Complete Graphs. - Franz Aurenhammer; Michael Formann; Ramana M. Idury; Alejandro A. Schäffer; Frank Wagner 001 (Discret. Appl. Math., 1994)

Dynamic Dictionary Matching with Failure Functions. - Ramana M. Idury; Alejandro A. Schäffer (Theor. Comput. Sci., 1994)

Markov Analysis of Multiple-Disk Prefetching Strategies for External Merging. - Vinay S. Pai; Alejandro A. Schäffer; Peter J. Varman (Theor. Comput. Sci., 1994)

Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice (Extended Abstract). - Sandeep K. Gupta 002; John D. Kececioglu; Alejandro A. Schäffer (CPM, 1995)

Optimal Edge Ranking of Trees in Polynomial Time. - Pilar de la Torre; Raymond Greenlaw; Alejandro A. Schäffer (Algorithmica, 1995)

Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment. - Sandeep K. Gupta 002; John D. Kececioglu; Alejandro A. Schäffer (J. Comput. Biol., 1995)

Multiple Matching of Rectangular Patterns - Ramana M. Idury; Alejandro A. Schäffer (Inf. Comput., 1995)

Improved Dynamic Dictionary Matching - Amihood Amir; Martin Farach; Ramana M. Idury; Johannes A. La Poutré; Alejandro A. Schäffer (Inf. Comput., 1995)

Multiple Matching of Parametrized Patterns. - Ramana M. Idury; Alejandro A. Schäffer (Theor. Comput. Sci., 1996)

Approximation Algorithms for a Genetic Diagnostics Problem. - S. Rao Kosaraju; Alejandro A. Schäffer; Leslie G. Biesecker (J. Comput. Biol., 1998)

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)

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)

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)

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)

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)

WindowMasker: window-based masker for sequenced genomes. - Aleksandr Morgulis; E. Michael Gertz; Alejandro A. Schäffer; Richa Agarwala (Bioinform., 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)

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)

Improved BLAST searches using longer words for protein seeding. - Sergey A. Shiryev; Jason S. Papadopoulos; Alejandro A. Schäffer; Richa Agarwala (Bioinform., 2007)

Database indexing for production MegaBLAST searches. - Aleksandr Morgulis; George Coulouris; Yan Raytselis; Thomas L. Madden; Richa Agarwala; Alejandro A. Schäffer (Bioinform., 2008)

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. - Salim Akhter Chowdhury; Stanley Shackney; Kerstin Heselmeyer-Haddad; Thomas Ried; Alejandro A. Schäffer; Russell Schwartz (Bioinform., 2013)

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)

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)

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)

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)

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)

Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data. - Haoyun Lei; Bochuan Lyu; E. Michael Gertz; Alejandro A. Schäffer; Russell Schwartz (ICCABS, 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)

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; et al. (Bioinform., 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)

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 005; Guibo Li; Liqin Xu; Yong Hou; Michael Dean; Russell Schwartz (J. Comput. Biol., 2020)

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 005; Xulian Shi; et al. (Bioinform., 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)

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)

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 (BIBM, 2022)