Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affect... more Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datas... more TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logi... more MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logic are related by a series of inference permutations. It is also known as the word problem for *-autonomous categories. Previous work has shown the problem to be equivalent to a rewiring problem on proof nets, which are not canonical for full MLL due to the presence of the two units. Drawing from recent work on reconfiguration problems, in this paper it is shown that MLL proof equivalence is PSPACE-complete, using a reduction from Nondeterministic Constraint Logic. An important consequence of the result is that the existence of a satisfactory notion of proof nets for MLL with units is ruled out (under current complexity assumptions). The PSPACE-hardness result extends to equivalence of normal forms in MELL without units, where the weakening rule for the exponentials induces a similar rewiring problem.
A superpermutation on $n$ symbols is a string that contains each of the $n!$ permutations of the ... more A superpermutation on $n$ symbols is a string that contains each of the $n!$ permutations of the $n$ symbols as a contiguous substring. The shortest superpermutation on $n$ symbols was conjectured to have length $\sum_{i=1}^n i!$. The conjecture had been verified for $n \leq 5$. We disprove it by exhibiting an explicit counterexample for $n=6$. This counterexample was found by encoding the problem as an instance of the (asymmetric) Traveling Salesman Problem, and searching for a solution using a powerful heuristic solver.
A higher-dimensional analogue of Cayley's theorem is proved, and used to deduce a novel character... more A higher-dimensional analogue of Cayley's theorem is proved, and used to deduce a novel characterisation of the unit of a promonoidal category. This, and the other preceding work, is then used to give two characterisations of the categories that model the unitless fragment of intuitionistic multiplicative linear logic. Finally we consider the non-intuitionistic case, where the second characterisation in particular takes a surprisingly simple form.
We describe a notion of categorical model for unitless fragments of (multiplicative) linear logic... more We describe a notion of categorical model for unitless fragments of (multiplicative) linear logic. The basic definition uses promonoidal categories, and we also give an equivalent elementary axiomatisation.
Proceedings of the Joint Meeting of the Twenty-Third EACSL Annual Conference on Computer Science Logic (CSL) and the Twenty-Ninth Annual ACM/IEEE Symposium on Logic in Computer Science (LICS) - CSL-LICS '14, 2014
MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logi... more MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logic are related by a series of inference permutations. It is also known as the word problem for *-autonomous categories. Previous work has shown the problem to be equivalent to a rewiring problem on proof nets, which are not canonical for full MLL due to the presence of the two units. Drawing from recent work on reconfiguration problems, in this paper it is shown that MLL proof equivalence is PSPACE-complete, using a reduction from Nondeterministic Constraint Logic. An important consequence of the result is that the existence of a satisfactory notion of proof nets for MLL with units is ruled out (under current complexity assumptions).
If a compact closed category has finite products or finite coproducts then it in fact has finite ... more If a compact closed category has finite products or finite coproducts then it in fact has finite biproducts, and so is semi-additive.
GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and ... more GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the ge...
Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affect... more Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affect... more Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datas... more TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logi... more MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logic are related by a series of inference permutations. It is also known as the word problem for *-autonomous categories. Previous work has shown the problem to be equivalent to a rewiring problem on proof nets, which are not canonical for full MLL due to the presence of the two units. Drawing from recent work on reconfiguration problems, in this paper it is shown that MLL proof equivalence is PSPACE-complete, using a reduction from Nondeterministic Constraint Logic. An important consequence of the result is that the existence of a satisfactory notion of proof nets for MLL with units is ruled out (under current complexity assumptions). The PSPACE-hardness result extends to equivalence of normal forms in MELL without units, where the weakening rule for the exponentials induces a similar rewiring problem.
A superpermutation on $n$ symbols is a string that contains each of the $n!$ permutations of the ... more A superpermutation on $n$ symbols is a string that contains each of the $n!$ permutations of the $n$ symbols as a contiguous substring. The shortest superpermutation on $n$ symbols was conjectured to have length $\sum_{i=1}^n i!$. The conjecture had been verified for $n \leq 5$. We disprove it by exhibiting an explicit counterexample for $n=6$. This counterexample was found by encoding the problem as an instance of the (asymmetric) Traveling Salesman Problem, and searching for a solution using a powerful heuristic solver.
A higher-dimensional analogue of Cayley's theorem is proved, and used to deduce a novel character... more A higher-dimensional analogue of Cayley's theorem is proved, and used to deduce a novel characterisation of the unit of a promonoidal category. This, and the other preceding work, is then used to give two characterisations of the categories that model the unitless fragment of intuitionistic multiplicative linear logic. Finally we consider the non-intuitionistic case, where the second characterisation in particular takes a surprisingly simple form.
We describe a notion of categorical model for unitless fragments of (multiplicative) linear logic... more We describe a notion of categorical model for unitless fragments of (multiplicative) linear logic. The basic definition uses promonoidal categories, and we also give an equivalent elementary axiomatisation.
Proceedings of the Joint Meeting of the Twenty-Third EACSL Annual Conference on Computer Science Logic (CSL) and the Twenty-Ninth Annual ACM/IEEE Symposium on Logic in Computer Science (LICS) - CSL-LICS '14, 2014
MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logi... more MLL proof equivalence is the problem of deciding whether two proofs in multiplicative linear logic are related by a series of inference permutations. It is also known as the word problem for *-autonomous categories. Previous work has shown the problem to be equivalent to a rewiring problem on proof nets, which are not canonical for full MLL due to the presence of the two units. Drawing from recent work on reconfiguration problems, in this paper it is shown that MLL proof equivalence is PSPACE-complete, using a reduction from Nondeterministic Constraint Logic. An important consequence of the result is that the existence of a satisfactory notion of proof nets for MLL with units is ruled out (under current complexity assumptions).
If a compact closed category has finite products or finite coproducts then it in fact has finite ... more If a compact closed category has finite products or finite coproducts then it in fact has finite biproducts, and so is semi-additive.
GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and ... more GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the ge...
Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affect... more Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
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Papers by Robin Houston