A5069448726- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Parallel Computing and Optimization Techniques
- Logic, programming, and type systems
- Genetic diversity and population structure
- Species Distribution and Climate Change
- Semantic Web and Ontologies
- Distributed and Parallel Computing Systems
- Evolution and Paleontology Studies
- Formal Methods in Verification
- Embedded Systems Design Techniques
- Numerical Methods and Algorithms
- Homelessness and Social Issues
- Software Engineering Research
- Distributed systems and fault tolerance
- Digital Humanities and Scholarship
- Protist diversity and phylogeny
- Law, AI, and Intellectual Property
- Natural Language Processing Techniques
- IPv6, Mobility, Handover, Networks, Security
- Human Resource and Talent Management
- Robotics and Sensor-Based Localization
- Logic, Reasoning, and Knowledge
- Jury Decision Making Processes
Duke University
2015-2017
National Evolutionary Synthesis Center
2013-2015
Creative Commons
2007
Massachusetts Institute of Technology
1986-2005
Millennium Engineering and Integration (United States)
2004
Cornell University
1992-2003
University of Sussex
1997
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity homologous character data across disparately related currently renders direct inference untenable. To reconstruct comprehensive life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into phylogeny. We present draft containing 2.3 million tips-the Open Tree Life. Realization this required assembly two...
Orbit was an optimizing compiler for T, a dialect of Scheme. Its aggressive use CPS conversion, novel closure representations, and efficient code generation strategies made it the best Scheme at time many years to come. The design T directly spawned six PhD theses one Masters thesis, influenced other projects as well, including SML New Jersey.
Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing published phylogenetic trees into comprehensive summary trees. No single taxonomy met the nomenclatural needs project. Here we describe a system reproducibly combining several source taxonomies synthetic taxonomy, discuss challenges synthesis downstream projects.
Article Macros that work Share on Authors: William Clinger Department of Computer Science, University Oregon OregonView Profile , Jonathan Rees Artificial Intelligence Laboratory, Massachusetts Institute Technology, Cambridge, MA MAView Authors Info & Claims POPL '91: Proceedings the 18th ACM SIGPLAN-SIGACT symposium Principles programming languagesJanuary 1991 Pages 155–162https://doi.org/10.1145/99583.99607Online:03 January 1991Publication History 102citation1,489DownloadsMetricsTotal...
article Free Access Share on ORBIT: an optimizing compiler for scheme Authors: Norman Adams Tektronix Inc., Beaverton, OR ORView Profile , David Kranz Yale Univ., New Haven, CT CTView Richard Kelsey Jonathan Rees Massachusetts Institute of Technology, Cambridge, MA MAView Paul Hudak James Philbin Authors Info & Claims ACM SIGPLAN NoticesVolume 21Issue 7July 1986 pp 219–233https://doi.org/10.1145/13310.13333Online:01 July 1986Publication History 296citation1,152DownloadsMetricsTotal...
Translational research, the effort to couple results of basic research clinical applications, depends on ability effectively answer questions using information that spans multiple disciplines. The Semantic Web, with its emphasis combining standard representation languages, access via web protocols, and technologies leverage computation, such as in form inference distributable query, offers a social technological basis for assembling, integrating making available biomedical knowledge at Web...
The T project is an experiment in language design and implementation. Its purpose to test the thesis developed by Steele Sussman their series of papers about Scheme language: that may be used as basis for a practical programming exceptional expressive power; and, implementations could perform better than other Lisp systems, competitively with languages, such C Bliss, which are usually considered inherently more efficient on conventional machine architectures. We developing portable...
Abstract Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy reusability of statements. Furthermore, establishing mapping between tip labels used taxa single common taxonomy...
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity homologous character data across disparately related currently renders direct inference untenable. To reconstruct comprehensive life we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into phylogeny. We present draft containing 2.3 million tips -- Open Tree Life. Realization this required assembly two...
In this paper we describe syntactic closures. Syntactic closures address the scoping problems that arise when writing macros. We discuss some issues raised by introducing into macro expansion interface, and compare with other approaches. Included is a complete implementation.
As biological disciplines extend into the 'big data' world, they will need a names-based infrastructure to index and interconnect distributed data. The must have access all names of organisms if it is manage information. Those who compile lists species hold different views as intellectual property rights that apply lists. This creates uncertainty impedes development much-needed for sharing data in digital world. laws United States America European Union are consistent with position...
Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated congruency between existing trees by comparing relationships of 147 QfO reference organisms from six Tree Life (ToL)/species tree projects: The National Center Biotechnology Information (NCBI) taxonomy, Opentree Life, sequenced species/species ToL, 16S ribosomal RNA (rRNA) database, published...
We describe a small set of additions to Scheme support object-oriented programming, including form multiple inheritance. The extensions proposed are in keeping with the spirit language and consequently differ from Lisp-based object systems such as Flavors Common Lisp Object System. Our mesh neatly underlying system. motivate our design examples, then implementation techniques that yields efficiency comparable dynamic implementations considered be high performance. complete has an...
Abstract Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most sets use taxonomic names to identify taxa. Open Tree of Life is one such project, synthesizing published phylogenetic trees into comprehensive supertrees. No single taxonomy met the nomenclatural needs project. Here we describe a system reproducibly combining several source taxonomies synthetic taxonomy, discuss challenges synthesis downstream projects.
The authors have implemented a software environment that permits small mobile robot to be programmed using the Scheme programming language. supports incremental modifications running programs and interactive debugging distributed read-evaluate-print loop. separates essential onboard run-time system from development environment, which runs on separate workstation. takes advantage of workstation's large address space user environment. It is fully detachable, so can operate autonomously if...
We present a new computational method for identifying regulated pathway components in transcript profiling (TP) experiments by evaluating transcriptional activity the context of known biological pathways. construct graph representing thousands protein functional relationships integrating knowledge from public databases and review articles. use notion distance to define neighborhoods. The pathways perturbed an experiment are then identified as subgraph induced genes, referred centers, having...
Phylogenetic estimates from published studies can be archived using general platforms like Dryad or TreeBASE. Such services fulfill a crucial role in ensuring transparency and reproducibility phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy reusability of statements. Furthermore, establishing mapping between tip labels used taxa single common taxonomy dramatically improves ability other researchers reuse estimates....