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Your search keyword '"Stoye, Jens"' showing total 20 results
Start Over Author "Stoye, Jens" Publisher springer international publishing
20 results on '"Stoye, Jens"'

1. Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning

Author

Bonizzoni, Paola, De Felice, Clelia, Petescia, Alessia, Pirola, Yuri, Rizzi, Raffaella, Stoye, Jens, Zaccagnino, Rocco, Zizza, Rosalba, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Martín-Vide, Carlos, editor, Vega-Rodríguez, Miguel A., editor, and Wheeler, Travis, editor

Published
2021
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2. Computing the Rearrangement Distance of Natural Genomes

Author

Bohnenkämper, Leonard, Braga, Marília D. V., Doerr, Daniel, Stoye, Jens, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, and Schwartz, Russell, editor

Published
2020
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3. A Perspective on Comparative and Functional Genomics

Author

Doerr, Daniel, Stoye, Jens, Crippen, Gordon, Advisory Editor, Dress, Andreas, Editor-in-Chief, Giegerich, Robert, Editorial Board Member, Kelso, Janet, Editorial Board Member, Linial, Michal, Editor-in-Chief, Felsenstein, Joe, Advisory Editor, Troyanskaya, Olga, Editor-in-Chief, Gusfield, Dan, Advisory Editor, Myers, Gene, Editorial Board Member, Istrail, Sorin, Advisory Editor, Pevzner, Pavel, Editorial Board Member, Vingron, Martin, Editor-in-Chief, Lengauer, Thomas, Advisory Editor, McClure, Marcella, Advisory Editor, Nowak, Martin, Advisory Editor, Sankoff, David, Advisory Editor, Shamir, Ron, Advisory Editor, Steel, Mike, Advisory Editor, Stormo, Gary, Advisory Editor, Tavaré, Simon, Advisory Editor, Warnow, Tandy, Advisory Editor, and Welch, Lonnie, Advisory Editor

Published
2019
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5. Identifying Maximal Perfect Haplotype Blocks

Author

Cunha, Luís, Diekmann, Yoan, Kowada, Luis, Stoye, Jens, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, and Alves, Ronnie, editor

Published
2018
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6. Algorithms for Computing the Family-Free Genomic Similarity Under DCJ

Author

Rubert, Diego P., Medeiros, Gabriel L., Hoshino, Edna A., Braga, Marília D. V., Stoye, Jens, Martinez, Fábio V., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Meidanis, Joao, editor, and Nakhleh, Luay, editor

Published
2017
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7. Finding Teams in Graphs and Its Application to Spatial Gene Cluster Discovery

Author

Schulz, Tizian, Stoye, Jens, Doerr, Daniel, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Meidanis, Joao, editor, and Nakhleh, Luay, editor

Published
2017
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8. Dynamic Alignment-Free and Reference-Free Read Compression

Author

Holley, Guillaume, Wittler, Roland, Stoye, Jens, Hach, Faraz, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, and Sahinalp, S. Cenk, editor

Published
2017
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9. A Linear Time Approximation Algorithm for the DCJ Distance for Genomes with Bounded Number of Duplicates

Author

Rubert, Diego P., Feijão, Pedro, Braga, Marília D. V., Stoye, Jens, Martinez, Fábio V., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Frith, Martin, editor, and Storm Pedersen, Christian Nørgaard, editor

Published
2016
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10. New Genome Similarity Measures Based on Conserved Gene Adjacencies

Author

Kowada, Luis Antonio B., Doerr, Daniel, Dantas, Simone, Stoye, Jens, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Josef, Kittler, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, and Singh, Mona, editor

Published
2016
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12. Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

Author

Luhmann, Nina, Chauve, Cedric, Stoye, Jens, Wittler, Roland, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, and Campos, Sérgio, editor

Published
2014
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14. Restricted DCJ-Indel Model Revisited

Author

Braga, Marília D. V., Stoye, Jens, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Setubal, João C., editor, and Almeida, Nalvo F., editor

Published
2013
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19. A Perspective on Comparative and Functional Genomics

Author

Dörr, Daniel, Stoye, Jens, and Warnow, Tandy

Subjects
Hierarchy (mathematics), Perspective (graphical), Associated function, Computational biology, Ontology (information science), Biology, Genome, Functional genomics, Gene, Homologous gene
Abstract

Comparing genomes based on the order of genes provides insights into their evolutionary history and further allows to identify sets of genes with associated function. In the past two decades, many methods have been developed for identifying genomic regions that share homologous genes, which can be subsequently tested for functional associativity. As these methods are flexible by tolerating duplicate, missing, and intruding genes, we now study a case in which relationships between genes are established through a hierarchical relationship and thereby turn the problem of identifying regions with common functional associations inside out: We use a measure of dissimilarity between genes defined on a gene ontology hierarchy to identify collections of genomic regions with low functional dissimilarity.

Published
2019

20. Restricted DCJ-Indel Model Revisited

Author

Dias Vieira Braga, Marília, Stoye, Jens, Setubal, João C., and Almeida, Nalvo F.

Subjects
Combinatorics, Triangle inequality, Simple (abstract algebra), Open problem, Circular bacterial chromosome, Sorting, Join (topology), Time complexity, Upper and lower bounds, Mathematics
Abstract

The Double Cut and Join (DCJ) is a generic operation representing many rearrangements that can change the organization of a genome, but not its content. For comparing two genomes with unequal contents, in addition to DCJ operations, we have to allow insertions and deletions of DNA segments. The distance in the so-called general DCJ-indel model can be exactly computed, but allows circular chromosomes to be created at intermediate steps, even if the compared genomes are linear. In this case it is more plausible to consider the restricted DCJ-indel model, in which the reincorporation of a circular chromosome has to be done immediately after its creation. This model was studied recently by daaSilva et al.a(BMCaBioinformaticsa13, Suppl.a19, S14), but only an upper bound for the restricted DCJ-indel distance was provided. Here we solve an open problem posed in that paper and present a very simple proof showing that the distance, that can be computed in linear time, is always the same for both the general and the restricted DCJ-indel models. We also present a simpler algorithm for computing an optimal restricted DCJ-indel sorting scenario in O(n logn) time.

Published
2013

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