8 Search Results for "Mount, Stephen M."

Document
DOI: 10.4230/LIPIcs.STACS.2026.36
Time-Optimal Construction of String Synchronizing Sets

Authors: Jonas Ellert and Tomasz Kociumaka

Published in: LIPIcs, Volume 364, 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)

Abstract
A powerful design principle behind many modern string algorithms is local consistency: breaking the symmetry between string positions based on their small contexts so that matching fragments are handled consistently. Among the most influential instantiations of this principle are string synchronizing sets [Kempa & Kociumaka; STOC 2019]. A τ-synchronizing set of a string of length n is a set of O(n/τ) string positions, chosen using their length-2τ contexts, such that (outside of highly periodic regions) every block of τ consecutive positions contains at least one element of the set. Synchronizing sets have found dozens of applications in diverse settings, from quantum and dynamic algorithms to fully compressed computation. In the classic word RAM model, particularly for strings over small alphabets, they enabled faster solutions to core problems in data compression, text indexing, and string similarity. In this work, we show that any string T ∈ [0 .. σ)ⁿ can be preprocessed in O(n log σ / log n) time so that, for any given integer τ ∈ [1 .. n], a τ-synchronizing set of T can be constructed in O((n log τ)/(τ log n)) time. Both bounds are optimal in the word RAM model with machine word size w = Θ(log n), matching the information-theoretic minimum for the input and output sizes, respectively. Previously, constructing a τ-synchronizing set required O(n/τ) time after an O(n)-time preprocessing [Kociumaka, Radoszewski, Rytter, and Waleń; SICOMP 2024], or, in the restricted regime of τ < 0.2 log_σ n, without any preprocessing needed [Kempa & Kociumaka; STOC 2019]. A simple instantiation of our method outputs the synchronizing set as a sorted list in O(n/τ) time, or as a bitmask in O(n/log n) time. Our optimal construction produces a compact fully indexable dictionary, supporting select queries in O(1) time and rank queries in O(log ((log τ)/(log log n))) time. The latter complexity matches known unconditional cell-probe lower bounds for τ ≤ n^{1-Ω(1)}. To achieve this, we introduce a general framework for efficiently processing sparse integer sequences via a custom variable-length encoding. We also augment the optimal variant of van Emde Boas trees [Pătraşcu & Thorup; STOC 2006] with a deterministic linear-time construction. When the set is represented as a bitmask under our sparse encoding, the same guarantees for select and rank queries hold after preprocessing in time proportional to the size of our encoding (in words).
Cite as

Jonas Ellert and Tomasz Kociumaka. Time-Optimal Construction of String Synchronizing Sets. In 43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 364, pp. 36:1-36:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{ellert_et_al:LIPIcs.STACS.2026.36,
  author =	{Ellert, Jonas and Kociumaka, Tomasz},
  title =	{{Time-Optimal Construction of String Synchronizing Sets}},
  booktitle =	{43rd International Symposium on Theoretical Aspects of Computer Science (STACS 2026)},
  pages =	{36:1--36:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-412-3},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{364},
  editor =	{Mahajan, Meena and Manea, Florin and McIver, Annabelle and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2026.36},
  URN =		{urn:nbn:de:0030-drops-255258},
  doi =		{10.4230/LIPIcs.STACS.2026.36},
  annote =	{Keywords: synchronizing sets, local consistency, packed strings}
}
Document
DOI: 10.4230/OASIcs.ICPEC.2025.10
Standards-Based Grading in Undergraduate Courses for Technology Majors

Authors: Ruth Lamprecht, Jonathan McCurdy, Melanie Butler, Brian Heinold, and Daniel Salinas Duron

Published in: OASIcs, Volume 133, 6th International Computer Programming Education Conference (ICPEC 2025)

Abstract
This paper outlines the methods employed by several instructors within a single department to implement standards-based assessments. The authors began integrating standards across multiple courses in their computer science, cybersecurity, data science, and mathematics programs. This shift was driven by a desire to promote equity in grading and to address the growing influence of artificial intelligence, which can obscure a student’s true understanding. In this work, the authors examine the supporting research that guided their motivation and informed their implementation of various grading techniques. With an emphasis on courses involving technology, they also detail the processes they use to manage the new assessments, provide examples of assessment questions, and share key lessons learned in making this transition successful for both instructors and students. This work addresses a significant gap in the literature, as there appears to be a notable lack of resources on the application of standards-based grading in technical disciplines.
Cite as

Ruth Lamprecht, Jonathan McCurdy, Melanie Butler, Brian Heinold, and Daniel Salinas Duron. Standards-Based Grading in Undergraduate Courses for Technology Majors. In 6th International Computer Programming Education Conference (ICPEC 2025). Open Access Series in Informatics (OASIcs), Volume 133, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lamprecht_et_al:OASIcs.ICPEC.2025.10,
  author =	{Lamprecht, Ruth and McCurdy, Jonathan and Butler, Melanie and Heinold, Brian and Salinas Duron, Daniel},
  title =	{{Standards-Based Grading in Undergraduate Courses for Technology Majors}},
  booktitle =	{6th International Computer Programming Education Conference (ICPEC 2025)},
  pages =	{10:1--10:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-393-5},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{133},
  editor =	{Queir\'{o}s, Ricardo and Pinto, M\'{a}rio and Portela, Filipe and Sim\~{o}es, Alberto},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICPEC.2025.10},
  URN =		{urn:nbn:de:0030-drops-240408},
  doi =		{10.4230/OASIcs.ICPEC.2025.10},
  annote =	{Keywords: Alternative Grading, Standards-Based Grading, Computer Science}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.20
SimdMinimizers: Computing Random Minimizers, fast

Authors: Ragnar Groot Koerkamp and Igor Martayan

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
Motivation. Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular sketching technique and used in a wide variety of applications. They sample at least one out of every w consecutive k-mers. As DNA sequencers are getting more accurate, some applications can afford to use a larger w and hence sparser and smaller sketches. And as sketches get smaller, their analysis becomes faster, so the time spent sketching the full-sized input becomes more of a bottleneck. Methods. Our library simd-minimizers implements a random minimizer algorithm using SIMD instructions. It supports both AVX2 and NEON architectures. Its main novelty is two-fold. First, it splits the input into 8 chunks that are streamed over in parallel through all steps of the algorithm. This is enabled by using the completely deterministic two-stacks sliding window minimum algorithm, which seems not to have been used before for finding minimizers. Results. Our library is up to 6.8× faster than a scalar implementation of the rescan method when w = 5 is small, and 3.4× faster for larger w = 19. Computing canonical minimizers is less than 50% slower than computing forward minimizers, and over 15× faster than the existing implementation in the minimizer-iter crate. Our library finds all (canonical) minimizers of a 3.2 Gbp human genome in 5.2 (resp. 6.7) seconds.
Cite as

Ragnar Groot Koerkamp and Igor Martayan. SimdMinimizers: Computing Random Minimizers, fast. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.SEA.2025.20,
  author =	{Groot Koerkamp, Ragnar and Martayan, Igor},
  title =	{{SimdMinimizers: Computing Random Minimizers, fast}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{20:1--20:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.20},
  URN =		{urn:nbn:de:0030-drops-232581},
  doi =		{10.4230/LIPIcs.SEA.2025.20},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.4
U-Index: A Universal Indexing Framework for Matching Long Patterns

Authors: Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
Motivation. Text indexing is a fundamental and well-studied problem. Classic solutions to this problem either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index - to accelerate matching, e.g., the suffix array. The former solutions thus retain excellent compressed space, but are practically slow to construct and query. The latter approaches, instead, sacrifice space efficiency but are typically faster; for example, the suffix array takes much more space than the text itself for commonly used alphabets, like ASCII or DNA, but it is very fast to construct and query. Methods. In this paper, we show that efficient text indexing can be achieved using just a small extra space on top of the original text, provided that the query patterns are sufficiently long. More specifically, we develop a new indexing paradigm in which a sketch of a query pattern is first matched against a sketch of the text. Once candidate matches are retrieved, they are verified using the original text. This paradigm is thus universal in the sense that it allows us to use any solution to index the sketched text, like a suffix array, FM-index, or r-index. Results. We explore both the theory and the practice of this universal framework. With an extensive experimental analysis, we show that, surprisingly, universal indexes can be constructed much faster than their unsketched counterparts and take a fraction of the space, as a direct consequence of (i) having a lower bound on the length of patterns and (ii) working in sketch space. Furthermore, these data structures have the potential of retaining or even improving query time, because matching against the sketched text is faster and verifying candidates can be theoretically done in constant time per occurrence (or, in practice, by short and cache-friendly scans of the text). Finally, we discuss some important applications of this novel indexing paradigm to computational biology. We hypothesize that such indexes will be particularly effective when the queries are sufficiently long, and so we demonstrate applications in long-read mapping.
Cite as

Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis. U-Index: A Universal Indexing Framework for Matching Long Patterns. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ayad_et_al:LIPIcs.SEA.2025.4,
  author =	{Ayad, Lorraine A. K. and Fici, Gabriele and Groot Koerkamp, Ragnar and Loukides, Grigorios and Patro, Rob and Pibiri, Giulio Ermanno and Pissis, Solon P.},
  title =	{{U-Index: A Universal Indexing Framework for Matching Long Patterns}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{4:1--4:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.4},
  URN =		{urn:nbn:de:0030-drops-232420},
  doi =		{10.4230/LIPIcs.SEA.2025.4},
  annote =	{Keywords: Text Indexing, Sketching, Minimizers, Hashing}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.3
Pydrofoil: Accelerating Sail-Based Instruction Set Simulators

Authors: Carl Friedrich Bolz-Tereick, Luke Panayi, Ferdia McKeogh, Tom Spink, and Martin Berger

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
We present Pydrofoil, a multi-stage compiler that generates instruction set simulators (ISSs) from processor instruction set architectures (ISAs) expressed in the high-level, verification-oriented ISA specification language Sail. Pydrofoil achieves a > 230× speedup over the C-based ISS generated by Sail on our benchmarks, thanks to the following insights. (i) An ISS is effectively an interpreter loop, and tracing just-in-time (JIT) compilers have proven effective at accelerating those, albeit mostly for dynamically typed languages. (ii) ISS workloads are highly atypical, dominated by intensive bit manipulation operations. Conventional compiler optimisations for general-purpose programming languages have limited impact for speeding up such workloads. We develop suitable domain-specific optimisations. (iii) Neither tracing JIT compilers, nor ahead-of-time (AOT) compilation alone, even with domain-specific optimisations, suffice for the generation of performant ISSs. Pydrofoil therefore implements a hybrid approach, pairing an AOT compiler with a tracing JIT built on the meta-tracing PyPy framework. AOT and JIT use domain-specific optimisations. Our benchmarks demonstrate that combining AOT and JIT compilers provides significantly greater performance gains than using either compiler alone.
Cite as

Carl Friedrich Bolz-Tereick, Luke Panayi, Ferdia McKeogh, Tom Spink, and Martin Berger. Pydrofoil: Accelerating Sail-Based Instruction Set Simulators. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 3:1-3:31, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bolztereick_et_al:LIPIcs.ECOOP.2025.3,
  author =	{Bolz-Tereick, Carl Friedrich and Panayi, Luke and McKeogh, Ferdia and Spink, Tom and Berger, Martin},
  title =	{{Pydrofoil: Accelerating Sail-Based Instruction Set Simulators}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{3:1--3:31},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.3},
  URN =		{urn:nbn:de:0030-drops-232962},
  doi =		{10.4230/LIPIcs.ECOOP.2025.3},
  annote =	{Keywords: Instruction set architecture, processor, domain-specific language, just-in-time compilation, meta-tracing}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.25
Reusing Highly Optimized IR in Dynamic Compilation

Authors: Andrej Pečimúth, David Leopoldseder, and Petr Tůma

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
Virtual machines (VMs) with dynamic compilers typically specialize compiled code to the state of the running VM instance and thus cannot reuse the code between multiple runs of the same application. The JIT compiler must recompile the same methods for each run of the application separately, which can prolong the application’s warmup time. We propose a technique to reduce compilation time by reusing a highly optimized intermediate representation (IR). We achieve this by tracing compiler-interface calls during compilation. The validity of the specializations in the IR is verified during a replay stage, and the replay also facilitates the relocation of runtime object references. The IR is stored on a compilation server, which can compile it to machine code and provide the code to local or remote VM instances. We implemented a compilation server with IR caching for GraalVM, a high-performance production-grade Java Virtual Machine (JVM). We present an evaluation based on four industry-standard benchmark suites. In each suite, our approach reduces compilation time by 23.6% to 36.8% and warmup time by 13.1% to 21.2% on average while preserving peak application performance.
Cite as

Andrej Pečimúth, David Leopoldseder, and Petr Tůma. Reusing Highly Optimized IR in Dynamic Compilation. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 25:1-25:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{pecimuth_et_al:LIPIcs.ECOOP.2025.25,
  author =	{Pe\v{c}im\'{u}th, Andrej and Leopoldseder, David and T\r{u}ma, Petr},
  title =	{{Reusing Highly Optimized IR in Dynamic Compilation}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{25:1--25:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.25},
  URN =		{urn:nbn:de:0030-drops-233176},
  doi =		{10.4230/LIPIcs.ECOOP.2025.25},
  annote =	{Keywords: code reuse, compilation time, warmup, remote compilation, dynamic compilation, virtual machines}
}
Document
DOI: 10.4230/LIPIcs.SoCG.2025.27
Computing Oriented Spanners and Their Dilation

Authors: Kevin Buchin, Antonia Kalb, Anil Maheshwari, Saeed Odak, Carolin Rehs, Michiel Smid, and Sampson Wong

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
Given a point set P in a metric space and a real number t ≥ 1, an oriented t-spanner is an oriented graph G = (P, E), where for every pair of distinct points p and q in P, the shortest oriented closed walk in G that contains p and q is at most a factor t longer than the perimeter of the smallest triangle in P containing p and q. The oriented dilation of a graph G is the minimum t for which G is an oriented t-spanner. For arbitrary point sets of size n in ℝ^d, where d ≥ 2 is a constant, the only known oriented spanner construction is an oriented 2-spanner with binom(n,2) edges. Moreover, there exists a set P of four points in the plane, for which the oriented dilation is larger than 1.46, for any oriented graph on P. We present the first algorithm that computes, in Euclidean space, a sparse oriented spanner whose oriented dilation is bounded by a constant. More specifically, for any set of n points in ℝ^d, where d is a constant, we construct an oriented (2+ε)-spanner with 𝒪(n) edges in 𝒪(n log n) time and 𝒪(n) space. Our construction uses the well-separated pair decomposition and an algorithm that computes a (1+ε)-approximation of the minimum-perimeter triangle in P containing two given query points in 𝒪(log n) time. While our algorithm is based on first computing a suitable undirected graph and then orienting it, we show that, in general, computing the orientation of an undirected graph that minimises its oriented dilation is NP-hard, even for point sets in the Euclidean plane. We further prove that even if the oriented graph is already given, computing its oriented dilation is APSP-hard for points in a general metric space. We complement this result with an algorithm that approximates the oriented dilation of a given graph in subcubic time for point sets in ℝ^d, where d is a constant.
Cite as

Kevin Buchin, Antonia Kalb, Anil Maheshwari, Saeed Odak, Carolin Rehs, Michiel Smid, and Sampson Wong. Computing Oriented Spanners and Their Dilation. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 27:1-27:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{buchin_et_al:LIPIcs.SoCG.2025.27,
  author =	{Buchin, Kevin and Kalb, Antonia and Maheshwari, Anil and Odak, Saeed and Rehs, Carolin and Smid, Michiel and Wong, Sampson},
  title =	{{Computing Oriented Spanners and Their Dilation}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{27:1--27:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.27},
  URN =		{urn:nbn:de:0030-drops-231792},
  doi =		{10.4230/LIPIcs.SoCG.2025.27},
  annote =	{Keywords: spanner, oriented graph, dilation, orientation, well-separated pair decomposition, minimum-perimeter triangle}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.10
Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification

Authors: Mohamed K. Gunady, Steffen Cornwell, Stephen M. Mount, and Héctor Corrada Bravo

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Analysis of differential alternative splicing from RNA-seq data is complicated by the fact that many RNA-seq reads map to multiple transcripts, and that annotated transcripts from a given gene are often a small subset of many possible complete transcripts for that gene. Here we describe Yanagi, a tool which segments a transcriptome into disjoint regions to create a segments library from a complete transcriptome annotation that preserves all of its consecutive regions of a given length L while distinguishing annotated alternative splicing events in the transcriptome. In this paper, we formalize this concept of transcriptome segmentation and propose an efficient algorithm for generating segment libraries based on a length parameter dependent on specific RNA-Seq library construction. The resulting segment sequences can be used with pseudo-alignment tools to quantify expression at the segment level. We characterize the segment libraries for the reference transcriptomes of Drosophila melanogaster and Homo sapiens. Finally, we demonstrate the utility of quantification using a segment library based on an analysis of differential exon skipping in Drosophila melanogaster and Homo sapiens. The notion of transcript segmentation as introduced here and implemented in Yanagi will open the door for the application of lightweight, ultra-fast pseudo-alignment algorithms in a wide variety of analyses of transcription variation.
Cite as

Mohamed K. Gunady, Steffen Cornwell, Stephen M. Mount, and Héctor Corrada Bravo. Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{gunady_et_al:LIPIcs.WABI.2017.10,
  author =	{Gunady, Mohamed K. and Cornwell, Steffen and Mount, Stephen M. and Bravo, H\'{e}ctor Corrada},
  title =	{{Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{10:1--10:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.10},
  URN =		{urn:nbn:de:0030-drops-76487},
  doi =		{10.4230/LIPIcs.WABI.2017.10},
  annote =	{Keywords: RNA-Seq, Genome Sequencing, Kmer-based alignment, Transcriptome Quantification, Differential Alternative Splicing}
}
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