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authorDouglas B. Rumbaugh <doug@douglasrumbaugh.com>2025-07-06 18:21:32 -0400
committerDouglas B. Rumbaugh <doug@douglasrumbaugh.com>2025-07-06 18:21:32 -0400
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@@ -2165,3 +2165,34 @@ keywords = {database systems, low-latency transactions, preemptive scheduling, u
biburl = {https://dblp.org/rec/conf/sigmod/IdreosZHKG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
+
+@article{kd-tree,
+ author = {Jon Louis Bentley},
+ title = {Multidimensional Binary Search Trees Used for Associative Searching},
+ journal = {Commun. {ACM}},
+ volume = {18},
+ number = {9},
+ pages = {509--517},
+ year = {1975},
+ url = {https://doi.org/10.1145/361002.361007},
+ doi = {10.1145/361002.361007},
+ timestamp = {Fri, 24 Mar 2023 16:31:07 +0100},
+ biburl = {https://dblp.org/rec/journals/cacm/Bentley75.bib},
+ bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@article{mantis,
+title = {Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index},
+journal = {Cell Systems},
+volume = {7},
+number = {2},
+pages = {201-207.e4},
+year = {2018},
+issn = {2405-4712},
+doi = {https://doi.org/10.1016/j.cels.2018.05.021},
+url = {https://www.sciencedirect.com/science/article/pii/S2405471218302394},
+author = {Prashant Pandey and Fatemeh Almodaresi and Michael A. Bender and Michael Ferdman and Rob Johnson and Rob Patro},
+keywords = {sequence search, RNA sequencing, de Bruijn graph, color equivalence classes, Mantis, experiment discovery, counting quotient filter, sequence Bloom tree, Bloom filter},
+abstract = {Summary
+Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches. In our evaluation, index construction with Mantis is 6× faster and yields a 20% smaller index than the state-of-the-art split sequence Bloom tree (SSBT). For queries, Mantis is 6–108× faster than SSBT and has no false-positives or -negatives. For example, Mantis was able to search for all 200,400 known human transcripts in an index of 2,652 RNA sequencing experiments in 82 min; SSBT took close to 4 days.}
+}