Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended
暂无分享,去创建一个
Alexandru I. Tomescu | Travis Gagie | Veli Mäkinen | Rayan Chikhi | Anna Kuosmanen | Topi Paavilainen
[1] Mohamed Ibrahim Abouelhoda,et al. A Chaining Algorithm for Mapping cDNA Sequences to Multiple Genomic Sequences , 2007, SPIRE.
[2] D. R. Fulkerson. Note on Dilworth’s decomposition theorem for partially ordered sets , 1956 .
[3] Eugene W. Myers,et al. Chaining multiple-alignment fragments in sub-quadratic time , 1995, SODA '95.
[4] Juha Kärkkäinen,et al. Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform , 2013, ESA.
[5] Veli Mäkinen,et al. Evaluating approaches to find exon chains based on long reads , 2016, bioRxiv.
[6] W. Marsden. I and J , 2012 .
[7] Jouni Sirén,et al. Indexing Variation Graphs , 2016, ALENEX.
[8] Claus-Peter Schnorr,et al. An Algorithm for Transitive Closure with Linear Expected Time , 1978, SIAM J. Comput..
[9] Mark de Berg,et al. Computational geometry: algorithms and applications , 1997 .
[10] David Eppstein,et al. Sparse dynamic programming I: linear cost functions , 1992, JACM.
[11] Haixu Tang,et al. Splicing graphs and EST assembly problem , 2002, ISMB.
[12] Alexandru I. Tomescu,et al. Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly , 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[13] Alexandru I. Tomescu,et al. Genome-Scale Algorithm Design: Genomics , 2015 .
[14] Pierre Peterlongo,et al. Read mapping on de Bruijn graphs , 2015, BMC Bioinformatics.
[15] Yangjun Chen,et al. An Efficient Algorithm for Answering Graph Reachability Queries , 2008, 2008 IEEE 24th International Conference on Data Engineering.
[16] Bernard De Baets,et al. Fast and Accurate cDNA Mapping and Splice Site Identification , 2014, BIOINFORMATICS.
[17] Benedict Paten,et al. A graph extension of the positional Burrows–Wheeler transform and its applications , 2017, Algorithms for Molecular Biology.
[18] Edith Cohen,et al. Reachability and distance queries via 2-hop labels , 2002, SODA '02.
[19] Gonzalo Navarro. Improved approximate pattern matching on hypertext , 2000, Theor. Comput. Sci..
[20] Alexandru I. Tomescu,et al. On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly , 2014, BMC Bioinformatics.
[21] Meng He,et al. Indexing Compressed Text , 2003 .
[22] Richard Durbin,et al. Extending reference assembly models , 2015, Genome Biology.
[23] Michael L. Fredman,et al. On computing the length of longest increasing subsequences , 1975, Discret. Math..
[24] Rob Patro,et al. Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.
[25] Moshe Lewenstein,et al. Pattern Matching in Hypertext , 1997, J. Algorithms.
[26] Veli Mäkinen,et al. Indexing Graphs for Path Queries with Applications in Genome Research , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[27] Ravindra K. Ahuja,et al. Network Flows: Theory, Algorithms, and Applications , 1993 .
[28] Stefan Felsner,et al. Recognition Algorithms for Orders of Small Width and Graphs of Small Dilworth Number , 2003, Order.
[29] Tetsuo Shibuya,et al. Match Chaining Algorithms for cDNA Mapping , 2003, WABI.
[30] Bernard De Baets,et al. A Long Fragment Aligner called ALFALFA , 2015, BMC Bioinformatics.
[31] Djamal Belazzougui,et al. Linear time construction of compressed text indices in compact space , 2014, STOC.
[32] Dong Kyue Kim,et al. String Matching in Hypertext , 1995, CPM.
[33] Richard M. Karp,et al. A n^5/2 Algorithm for Maximum Matchings in Bipartite Graphs , 1971, SWAT.
[34] James B. Orlin,et al. Max flows in O(nm) time, or better , 2013, STOC '13.
[35] Yangjun Chen,et al. On the Graph Decomposition , 2014, 2014 IEEE Fourth International Conference on Big Data and Cloud Computing.
[36] Pierre Peterlongo,et al. Read Mapping on de Bruijn graph , 2015, ArXiv.
[37] Vijay V. Vazirani,et al. Approximation Algorithms , 2001, Springer Berlin Heidelberg.
[38] Wing-Kai Hon,et al. Breaking a time-and-space barrier in constructing full-text indices , 2003, 44th Annual IEEE Symposium on Foundations of Computer Science, 2003. Proceedings..
[39] Robert E. Tarjan,et al. Scaling and related techniques for geometry problems , 1984, STOC '84.
[40] Yang Xiang,et al. Path-tree: An efficient reachability indexing scheme for large directed graphs , 2011, TODS.
[41] David Haussler,et al. A Flow Procedure for the Linearization of Genome Sequence Graphs , 2017, bioRxiv.
[42] H. V. Jagadish,et al. A compression technique to materialize transitive closure , 1990, TODS.
[43] Veli Mäkinen,et al. Normalized N50 assembly metric using gap-restricted co-linear chaining , 2022 .
[44] Eric Rivals,et al. YOC, A new strategy for pairwise alignment of collinear genomes , 2015, BMC Bioinformatics.
[45] Ulf Leser,et al. RRCA: Ultra-Fast Multiple In-species Genome Alignments , 2014, AlCoB.
[46] S. Louis Hakimi,et al. On Path Cover Problems in Digraphs and Applications to Program Testing , 1979, IEEE Transactions on Software Engineering.