---
_id: '3570'
abstract:
- lang: eng
text: Visualization of high-dimensional or large geometric data sets is inherently
difficult, so we experiment with the use of audio to display the shape and connectivity
of these data sets. Sonification is used as both an addition to and a substitution
for the visual display. We describe a new algorithm called wave traversal that
provides a necessary intermediate step to sonification of the data; it produces
an ordered sequence of subsets, called waves, that allows us to map the data to
time. In this paper we focus in detail on the mathematics of wave traversal, in
particular, how wave traversal can be used as a discrete Morse function.
article_processing_charge: No
author:
- first_name: Ulrike
full_name: Axen, Ulrike
last_name: Axen
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Axen U, Edelsbrunner H. Auditory Morse analysis of triangulated manifolds.
In: Mathematical Visualization. Springer; 1998:223-236. doi:10.1007/978-3-662-03567-2_17'
apa: Axen, U., & Edelsbrunner, H. (1998). Auditory Morse analysis of triangulated
manifolds. In Mathematical Visualization (pp. 223–236). Springer. https://doi.org/10.1007/978-3-662-03567-2_17
chicago: Axen, Ulrike, and Herbert Edelsbrunner. “Auditory Morse Analysis of Triangulated
Manifolds.” In Mathematical Visualization, 223–36. Springer, 1998. https://doi.org/10.1007/978-3-662-03567-2_17.
ieee: U. Axen and H. Edelsbrunner, “Auditory Morse analysis of triangulated manifolds,”
in Mathematical Visualization, Springer, 1998, pp. 223–236.
ista: 'Axen U, Edelsbrunner H. 1998.Auditory Morse analysis of triangulated manifolds.
In: Mathematical Visualization. , 223–236.'
mla: Axen, Ulrike, and Herbert Edelsbrunner. “Auditory Morse Analysis of Triangulated
Manifolds.” Mathematical Visualization, Springer, 1998, pp. 223–36, doi:10.1007/978-3-662-03567-2_17.
short: U. Axen, H. Edelsbrunner, in:, Mathematical Visualization, Springer, 1998,
pp. 223–236.
date_created: 2018-12-11T12:04:01Z
date_published: 1998-10-20T00:00:00Z
date_updated: 2022-08-29T12:47:32Z
day: '20'
doi: 10.1007/978-3-662-03567-2_17
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 223 - 236
publication: Mathematical Visualization
publication_identifier:
isbn:
- '9783662035672'
publication_status: published
publisher: Springer
publist_id: '2815'
quality_controlled: '1'
status: public
title: Auditory Morse analysis of triangulated manifolds
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1998'
...
---
_id: '3627'
abstract:
- lang: eng
text: When a favourable mutation sweeps to fixation, those genes initially linked
to it increase in frequency; on average, this reduces diversity in the surrounding
region of the genome. In the first analysis of this 'hitch-hiking' effect, Maynard-Smith
and Haigh followed the increase of the neutral allele that chanced to be associated
with the new mutation in the first generation, and assumed that the subsequent
increase was deterministic. Later analyses, based on either coalescence arguments,
or on diffusion equations for the mean and variance of allele frequency, have
also made one or both of these assumptions. In the early generations, stochastic
fluctuations in the frequency of the selected allele, and coalescence of neutral
lineages, can be accounted for correctly by following relationships between genes
conditional on the number of copies of the favourable allele. This analysis shows
that the hitch-hiking effect is increased because an allele that is destined to
fix tends to increase more rapidly than exponentially. However, the identity generated
by the selective sweep has the same form as in previous work, h[r/s] (2 Ns)(-2r/s),
where h[r/s] tends to 1 with tight linkage. This analysis is extended to samples
of many genes; then, genes may trace back to several families of lineages, each
related through a common ancestor early in the selective sweep. Simulations show
that the number and sizes of these families can (in principle) be used to make
separate estimates of r/s and Ns.
acknowledgement: S. P. Otto kindly supplied the simulation results shown in Fig. 1.
I would like to thank B. Charlesworth, A. Etheridge and S. P. Otto for their comments
on the manuscript. This work was supported by the Biotechnology and Biological Sciences
Research Council, and by the Darwin Trust of Edinburgh.
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The effect of hitch-hiking on neutral genealogies. Genetical
Research. 1998;72(2):123-133. doi:10.1017/S0016672398003462
apa: Barton, N. H. (1998). The effect of hitch-hiking on neutral genealogies. Genetical
Research. Cambridge University Press. https://doi.org/10.1017/S0016672398003462
chicago: Barton, Nicholas H. “The Effect of Hitch-Hiking on Neutral Genealogies.”
Genetical Research. Cambridge University Press, 1998. https://doi.org/10.1017/S0016672398003462.
ieee: N. H. Barton, “The effect of hitch-hiking on neutral genealogies,” Genetical
Research, vol. 72, no. 2. Cambridge University Press, pp. 123–133, 1998.
ista: Barton NH. 1998. The effect of hitch-hiking on neutral genealogies. Genetical
Research. 72(2), 123–133.
mla: Barton, Nicholas H. “The Effect of Hitch-Hiking on Neutral Genealogies.” Genetical
Research, vol. 72, no. 2, Cambridge University Press, 1998, pp. 123–33, doi:10.1017/S0016672398003462.
short: N.H. Barton, Genetical Research 72 (1998) 123–133.
date_created: 2018-12-11T12:04:19Z
date_published: 1998-10-01T00:00:00Z
date_updated: 2022-08-29T12:42:44Z
day: '01'
doi: 10.1017/S0016672398003462
extern: '1'
intvolume: ' 72'
issue: '2'
language:
- iso: eng
month: '10'
oa_version: None
page: 123 - 133
publication: Genetical Research
publication_identifier:
issn:
- 0016-6723
publication_status: published
publisher: Cambridge University Press
publist_id: '2756'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The effect of hitch-hiking on neutral genealogies
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 72
year: '1998'
...
---
_id: '3628'
abstract:
- lang: eng
text: 'Determining the way in which deleterious mutations interact in their effects
on fitness is crucial to numerous areas in population genetics and evolutionary
biology. For example, if each additional mutation leads to a greater decrease
in log fitness than the last (synergistic epistasis), then the evolution of sex
and recombination may be favored to facilitate the elimination of deleterious
mutations. However, there is a severe shortage of relevant data. Three relatively
simple experimental methods to test for epistasis between deleterious mutations
in haploid species have recently been proposed. These methods involve crossing
individuals and examining the mean and/or skew in log fitness of the offspring
and parents. The main aim of this paper is to formalize these methods, and determine
the most effective way in which tests for epistasis could be carried out. We show
that only one of these methods is likely to give useful results: crossing individuals
that have very different numbers of deleterious mutations, and comparing the mean
log fitness of the parents with that of their offspring. We also reconsider experimental
data collected on Chlamydomonas moewussi using two of the three methods. Finally,
we suggest how the test could be applied to diploid species.'
acknowledgement: We thank BRIAN CHARLESWORTH, ANDREW CLARK, LAURENCE HURST, PETER KEIGHTLEY,
ALEXEY KONDRASHOV, CURT LIVELY, MARGARET MACKINNON, KATRINA LYTHGOE, SALLY OTTO,
ANDREW READ and ARJAN DE VISSER for useful discussion and comments on the manuscript.
This work was supported by the Biotechnology and Biological Sciences Research Council.
article_processing_charge: No
article_type: original
author:
- first_name: Stuart
full_name: West, Stuart
last_name: West
- first_name: Andrew
full_name: Peters, Andrew
last_name: Peters
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: West S, Peters A, Barton NH. Testing for epistasis between deleterious mutations.
Genetics. 1998;149(1):435-444. doi:10.1093/genetics/149.1.435
apa: West, S., Peters, A., & Barton, N. H. (1998). Testing for epistasis between
deleterious mutations. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/149.1.435
chicago: West, Stuart, Andrew Peters, and Nicholas H Barton. “Testing for Epistasis
between Deleterious Mutations.” Genetics. Genetics Society of America,
1998. https://doi.org/10.1093/genetics/149.1.435.
ieee: S. West, A. Peters, and N. H. Barton, “Testing for epistasis between deleterious
mutations,” Genetics, vol. 149, no. 1. Genetics Society of America, pp.
435–444, 1998.
ista: West S, Peters A, Barton NH. 1998. Testing for epistasis between deleterious
mutations. Genetics. 149(1), 435–444.
mla: West, Stuart, et al. “Testing for Epistasis between Deleterious Mutations.”
Genetics, vol. 149, no. 1, Genetics Society of America, 1998, pp. 435–44,
doi:10.1093/genetics/149.1.435.
short: S. West, A. Peters, N.H. Barton, Genetics 149 (1998) 435–444.
date_created: 2018-12-11T12:04:19Z
date_published: 1998-05-01T00:00:00Z
date_updated: 2022-08-29T08:53:09Z
day: '01'
doi: 10.1093/genetics/149.1.435
extern: '1'
external_id:
pmid:
- '9584115'
intvolume: ' 149'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://academic.oup.com/genetics/article/149/1/435/6034229
month: '05'
oa: 1
oa_version: None
page: 435 - 444
pmid: 1
publication: Genetics
publication_identifier:
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
publist_id: '2755'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Testing for epistasis between deleterious mutations
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 149
year: '1998'
...
---
_id: '3629'
abstract:
- lang: eng
text: 'This paper demonstrates the effect of habitat heterogeneity and a habitat
preference on the genetic structure of a hybrid zone between the toads Bombina
bombina and B. variegata (Anura: Discoglossidae); 1613 toads from 85 sites across
a transect near Pešćenica, Croatia, were scored for five unlinked diagnostic allozyme
markers. These were found to be largely concordant. Aside from minor systematic
deviations, there was little variance in allele frequency among loci within sites.
Yet the allele frequencies did not follow a smooth cline, but formed a mosaic
in the center, such that neighboring sites could differ markedly in their enzyme
score. A detailed ecological survey revealed a correlation between this pattern
and habitat. In keeping with the typical breeding sites of the parental taxa,
B. bombina-like hybrids were found more often in ponds, whereas B. variegata-like
hybrids were more common in puddles. In addition, there was significant heterozygote
deficit (FIS) and strong linkage disequilibrium (R), both of which were stronger
on the B. bombina side of the transect, and stronger in puddles than ponds. Mark-recapture
data showed: (1) that the animals disperse beyond the scale of the habitat pattern;
(2) frequent turn-over of individuals within sites; and (3) nonrandom movement
between two sites of different habitat type. We conclude that an active habitat
preference must contribute to the observed association between marker alleles
and habitat. As a consequence, there is incomplete mixing of the two gene pools,
which could explain the high level of FIS and R. The asymmetry in these parameters
may reflect asymmetry in the preference or in the distribution of habitats across
the zone. We discuss the implications of habitat preference for the dynamics of
hybrid zones.'
acknowledgement: This work was supported by a NERC studentshipto CJM, by NERC grants
GR3/9353, GR3/8002, andGR9/1909A to NHB, and by KBN grant 193/P04/95/09to JMS.
We are grateful to J. W.Arntzen, L.Kruuk, R. G.Harrison, J. W.Sites, and an anonymous
reviewer for their comments on the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Catriona
full_name: Maccallum, Catriona
last_name: Maccallum
- first_name: Beate
full_name: Nürnberger, Beate
last_name: Nürnberger
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jacek
full_name: Szymura, Jacek
last_name: Szymura
citation:
ama: Maccallum C, Nürnberger B, Barton NH, Szymura J. Habitat preference in the
Bombina hybrid zone in Croatia. Evolution. 1998;52(1):227-239. doi:10.1111/j.1558-5646.1998.tb05156.x
apa: Maccallum, C., Nürnberger, B., Barton, N. H., & Szymura, J. (1998). Habitat
preference in the Bombina hybrid zone in Croatia. Evolution. Wiley-Blackwell.
https://doi.org/10.1111/j.1558-5646.1998.tb05156.x
chicago: Maccallum, Catriona, Beate Nürnberger, Nicholas H Barton, and Jacek Szymura.
“Habitat Preference in the Bombina Hybrid Zone in Croatia.” Evolution.
Wiley-Blackwell, 1998. https://doi.org/10.1111/j.1558-5646.1998.tb05156.x.
ieee: C. Maccallum, B. Nürnberger, N. H. Barton, and J. Szymura, “Habitat preference
in the Bombina hybrid zone in Croatia,” Evolution, vol. 52, no. 1. Wiley-Blackwell,
pp. 227–239, 1998.
ista: Maccallum C, Nürnberger B, Barton NH, Szymura J. 1998. Habitat preference
in the Bombina hybrid zone in Croatia. Evolution. 52(1), 227–239.
mla: Maccallum, Catriona, et al. “Habitat Preference in the Bombina Hybrid Zone
in Croatia.” Evolution, vol. 52, no. 1, Wiley-Blackwell, 1998, pp. 227–39,
doi:10.1111/j.1558-5646.1998.tb05156.x.
short: C. Maccallum, B. Nürnberger, N.H. Barton, J. Szymura, Evolution 52 (1998)
227–239.
date_created: 2018-12-11T12:04:20Z
date_published: 1998-02-01T00:00:00Z
date_updated: 2022-08-26T11:00:17Z
day: '01'
doi: 10.1111/j.1558-5646.1998.tb05156.x
extern: '1'
external_id:
pmid:
- '28568140'
intvolume: ' 52'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 227 - 239
pmid: 1
publication: Evolution
publication_identifier:
issn:
- 0014-3820
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2754'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Habitat preference in the Bombina hybrid zone in Croatia
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 52
year: '1998'
...
---
_id: '3926'
abstract:
- lang: eng
text: 'Two components of sexual selection in the lesser wax moth, Achroia grisella,
are clearly defined: females choose males based on characters of their ultrasonic
advertisement signals, and males display agonistic behaviour patterns in contests
over signalling stations. We conducted a series of laboratory trials to determine
whether successes in these two sexual selection arenas were related. Our trials
showed that winners in contests over signalling stations were characterized by
earlier initiation of both signalling and aggression. These characteristics may
indicate higher levels of ‘motivation,’ but it is unclear whether this level is
a fixed trait. There was no relationship, however, between any measure of a male''s
attractiveness to females and his success in winning competition trials. Thus,
inter- and intra-sexual selection may be acting on different, uncorrelated traits
in A. grisella.'
acknowledgement: We thank Robert MINCKI-EY for collecting A. griseh from infested
honeybee colonies and Yikweon J,4M;. Feng-You JIA, James MCLLOUGH and Kelly WILLAMS
for indispensable laboratory assistaiice. Analyses of the ultrasonic advertisement
signals was made possible by digital signal-processing programs written by Tom PETERS
and Ric ROGERO (both of the University of Kansas Instrumentation Development Laboratory)
and Martin CREMER. Marc BRANHAM and Klaus-Gerhardt HELLER offered valuable discussion
during the project and Yikweon JAG, Klaus REINHOLD and several anonymous referees
provided critical reviews of the manuscript. Financial support was provided by
US National Science Foundation grant IBN-9407162.
article_processing_charge: No
article_type: original
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Michael
full_name: Greenfield, Michael
last_name: Greenfield
citation:
ama: 'Cremer S, Greenfield M. Partitioning the components of sexual selection: attractiveness
and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera, Pyralidae).
Ethology. 1998;104(1):1-9. doi:10.1111/j.1439-0310.1998.tb00025.x'
apa: 'Cremer, S., & Greenfield, M. (1998). Partitioning the components of sexual
selection: attractiveness and agonistic behaviour in male wax moths, Achroia grisella
(Lepidoptera, Pyralidae). Ethology. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0310.1998.tb00025.x'
chicago: 'Cremer, Sylvia, and Michael Greenfield. “Partitioning the Components of
Sexual Selection: Attractiveness and Agonistic Behaviour in Male Wax Moths, Achroia
Grisella (Lepidoptera, Pyralidae).” Ethology. Wiley-Blackwell, 1998. https://doi.org/10.1111/j.1439-0310.1998.tb00025.x.'
ieee: 'S. Cremer and M. Greenfield, “Partitioning the components of sexual selection:
attractiveness and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera,
Pyralidae),” Ethology, vol. 104, no. 1. Wiley-Blackwell, pp. 1–9, 1998.'
ista: 'Cremer S, Greenfield M. 1998. Partitioning the components of sexual selection:
attractiveness and agonistic behaviour in male wax moths, Achroia grisella (Lepidoptera,
Pyralidae). Ethology. 104(1), 1–9.'
mla: 'Cremer, Sylvia, and Michael Greenfield. “Partitioning the Components of Sexual
Selection: Attractiveness and Agonistic Behaviour in Male Wax Moths, Achroia Grisella
(Lepidoptera, Pyralidae).” Ethology, vol. 104, no. 1, Wiley-Blackwell,
1998, pp. 1–9, doi:10.1111/j.1439-0310.1998.tb00025.x.'
short: S. Cremer, M. Greenfield, Ethology 104 (1998) 1–9.
date_created: 2018-12-11T12:05:56Z
date_published: 1998-01-01T00:00:00Z
date_updated: 2022-08-26T09:11:08Z
day: '01'
doi: 10.1111/j.1439-0310.1998.tb00025.x
extern: '1'
intvolume: ' 104'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 9
publication: Ethology
publication_identifier:
issn:
- 0044-3573
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2227'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Partitioning the components of sexual selection: attractiveness and agonistic
behaviour in male wax moths, Achroia grisella (Lepidoptera, Pyralidae)'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 104
year: '1998'
...
---
_id: '4011'
abstract:
- lang: eng
text: The size and shape of macromolecules such as proteins and nucleic acids play
an important role in their functions. Prior efforts to quantify these properties
have been based on various discretization or tessellation procedures involving
analytical or numerical computations. In this article, we present an analytically
exact method for computing the metric properties of macromolecules based on the
alpha shape theory. This method uses the duality between alpha complex and the
weighted Voronoi decomposition of a molecule. We describe the intuitive ideas
and concepts behind the alpha shape theory and the algorithm for computing areas
and volumes of macromolecules. We apply our method to compute areas and volumes
of a number of protein systems. We also discuss several difficulties commonly
encountered in molecular shape computations and outline methods to overcome these
problems. (C) 1998 Wiley-Liss, Inc.
acknowledgement: We thank Michael Facello for the torus area formula and suggestion
regarding computation of MS model from SA model. We thank Nataraj Akkiraju, Patrick
Moran, and Marcus Wagner for interesting discussionson the topic of this article
and for help in the generationof two- and three-dimensional illustrations. We thank
NSF Meta Center Allocation for providing computational resources. The software
VOLBL is available at:http://alpha.ncsa.uiuc.edu/alpha.
article_processing_charge: No
article_type: original
author:
- first_name: Jie
full_name: Liang, Jie
last_name: Liang
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Pamidighantam
full_name: Sudhakar, Pamidighantam
last_name: Sudhakar
- first_name: Shankar
full_name: Subramaniam, Shankar
last_name: Subramaniam
citation:
ama: 'Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. Analytical shape
computation of macromolecules: I. molecular area and volume through alpha shape.
Proteins: Structure, Function and Bioinformatics. 1998;33(1):1-17. doi:10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O'
apa: 'Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P., & Subramaniam, S. (1998).
Analytical shape computation of macromolecules: I. molecular area and volume through
alpha shape. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell.
https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O'
chicago: 'Liang, Jie, Herbert Edelsbrunner, Ping Fu, Pamidighantam Sudhakar, and
Shankar Subramaniam. “Analytical Shape Computation of Macromolecules: I. Molecular
Area and Volume through Alpha Shape.” Proteins: Structure, Function and Bioinformatics.
Wiley-Blackwell, 1998. https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O.'
ieee: 'J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, and S. Subramaniam, “Analytical
shape computation of macromolecules: I. molecular area and volume through alpha
shape,” Proteins: Structure, Function and Bioinformatics, vol. 33, no.
1. Wiley-Blackwell, pp. 1–17, 1998.'
ista: 'Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical
shape computation of macromolecules: I. molecular area and volume through alpha
shape. Proteins: Structure, Function and Bioinformatics. 33(1), 1–17.'
mla: 'Liang, Jie, et al. “Analytical Shape Computation of Macromolecules: I. Molecular
Area and Volume through Alpha Shape.” Proteins: Structure, Function and Bioinformatics,
vol. 33, no. 1, Wiley-Blackwell, 1998, pp. 1–17, doi:10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O.'
short: 'J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, S. Subramaniam, Proteins:
Structure, Function and Bioinformatics 33 (1998) 1–17.'
date_created: 2018-12-11T12:06:25Z
date_published: 1998-10-01T00:00:00Z
date_updated: 2022-08-25T13:32:59Z
day: '01'
doi: 10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O
extern: '1'
intvolume: ' 33'
issue: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 1 - 17
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_identifier:
issn:
- 0887-3585
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2112'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Analytical shape computation of macromolecules: I. molecular area and volume
through alpha shape'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 33
year: '1998'
...
---
_id: '4012'
abstract:
- lang: eng
text: The structures of proteins are well-packed, yet they contain numerous cavities
which play key roles in accommodating small molecules, or enabling conformational
changes. From high-resolution structures it is possible to identify these cavities.
We have developed a precise algorithm based on alpha shapes for measuring space-filling-based
molecular models (such as van der Waals, solvent accessible, and molecular surface
descriptions). We applied this method for accurate computation of the surface
area and volume of cavities in several proteins. In addition, all of the atoms/residues
Lining the cavities are identified, We use this method to study the structure
and the stability of proteins, as well as to locate cavities that could contain
structural water molecules in the proton transport pathway in the membrane protein
bacteriorhodopsin.
acknowledgement: The software for constructing weighted Delaunay complexes and the
alpha shape filters was written by Ernst Mücke and Michael Facello. We thank them
forcreating reliable and robust software so that wecan build on their results. The
authors thank NSF Meta Center Allocation for providing computational resources.
The software VOLBL is part of the standard distribution of the alpha shapes software,
andis available at http://alpha.ncsa.uiuc.edu/alpha.
article_processing_charge: No
article_type: original
author:
- first_name: Jie
full_name: Liang, Jie
last_name: Liang
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Pamidighantam
full_name: Sudhakar, Pamidighantam
last_name: Sudhakar
- first_name: Shankar
full_name: Subramaniam, Shankar
last_name: Subramaniam
citation:
ama: 'Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. Analytical shape
computation of macromolecules: II. Inaccessible cavities in proteins. Proteins:
Structure, Function and Bioinformatics. 1998;33(1):18-29. doi:10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H'
apa: 'Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P., & Subramaniam, S. (1998).
Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins.
Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H'
chicago: 'Liang, Jie, Herbert Edelsbrunner, Ping Fu, Pamidighantam Sudhakar, and
Shankar Subramaniam. “Analytical Shape Computation of Macromolecules: II. Inaccessible
Cavities in Proteins.” Proteins: Structure, Function and Bioinformatics.
Wiley-Blackwell, 1998. https://doi.org/10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H.'
ieee: 'J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, and S. Subramaniam, “Analytical
shape computation of macromolecules: II. Inaccessible cavities in proteins,” Proteins:
Structure, Function and Bioinformatics, vol. 33, no. 1. Wiley-Blackwell, pp.
18–29, 1998.'
ista: 'Liang J, Edelsbrunner H, Fu P, Sudhakar P, Subramaniam S. 1998. Analytical
shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins:
Structure, Function and Bioinformatics. 33(1), 18–29.'
mla: 'Liang, Jie, et al. “Analytical Shape Computation of Macromolecules: II. Inaccessible
Cavities in Proteins.” Proteins: Structure, Function and Bioinformatics,
vol. 33, no. 1, Wiley-Blackwell, 1998, pp. 18–29, doi:10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H.'
short: 'J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, S. Subramaniam, Proteins:
Structure, Function and Bioinformatics 33 (1998) 18–29.'
date_created: 2018-12-11T12:06:26Z
date_published: 1998-10-01T00:00:00Z
date_updated: 2022-08-25T13:35:41Z
day: '01'
doi: 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H
extern: '1'
intvolume: ' 33'
issue: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 18 - 29
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_identifier:
issn:
- 0887-3585
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2113'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Analytical shape computation of macromolecules: II. Inaccessible cavities
in proteins'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 33
year: '1998'
...
---
_id: '4013'
abstract:
- lang: eng
text: The shape of a protein is important for its functions, This includes the location
and size of identifiable regions in its complement space. We formally define pockets
as regions in the complement with limited accessibility from the outside. Pockets
can be efficiently constructed by an algorithm based on alpha complexes. The algorithm
is implemented and applied to proteins with known three-dimensional conformations.
1998 Published by Elsevier Science B.V. All rights reserved.
acknowledgement: 'The authors thank Ping Fu and Ernst Miicke for their contributions
to the alpha shapes software in which the pockets software is embedded. '
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Facello, Michael
last_name: Facello
- first_name: Jie
full_name: Liang, Jie
last_name: Liang
citation:
ama: Edelsbrunner H, Facello M, Liang J. On the definition and the construction
of pockets in macromolecules. Discrete Applied Mathematics. 1998;88(1-3):83-102.
doi:10.1016/S0166-218X(98)00067-5
apa: Edelsbrunner, H., Facello, M., & Liang, J. (1998). On the definition and
the construction of pockets in macromolecules. Discrete Applied Mathematics.
Elsevier. https://doi.org/10.1016/S0166-218X(98)00067-5
chicago: Edelsbrunner, Herbert, Michael Facello, and Jie Liang. “On the Definition
and the Construction of Pockets in Macromolecules.” Discrete Applied Mathematics.
Elsevier, 1998. https://doi.org/10.1016/S0166-218X(98)00067-5.
ieee: H. Edelsbrunner, M. Facello, and J. Liang, “On the definition and the construction
of pockets in macromolecules,” Discrete Applied Mathematics, vol. 88, no.
1–3. Elsevier, pp. 83–102, 1998.
ista: Edelsbrunner H, Facello M, Liang J. 1998. On the definition and the construction
of pockets in macromolecules. Discrete Applied Mathematics. 88(1–3), 83–102.
mla: Edelsbrunner, Herbert, et al. “On the Definition and the Construction of Pockets
in Macromolecules.” Discrete Applied Mathematics, vol. 88, no. 1–3, Elsevier,
1998, pp. 83–102, doi:10.1016/S0166-218X(98)00067-5.
short: H. Edelsbrunner, M. Facello, J. Liang, Discrete Applied Mathematics 88 (1998)
83–102.
date_created: 2018-12-11T12:06:26Z
date_published: 1998-11-09T00:00:00Z
date_updated: 2022-08-25T15:06:30Z
day: '09'
doi: 10.1016/S0166-218X(98)00067-5
extern: '1'
external_id:
pmid:
- '9390238'
intvolume: ' 88'
issue: 1-3
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/S0166218X98000675?via%3Dihub
month: '11'
oa: 1
oa_version: Published Version
page: 83 - 102
pmid: 1
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166-218X
publication_status: published
publisher: Elsevier
publist_id: '2114'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the definition and the construction of pockets in macromolecules
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 88
year: '1998'
...
---
_id: '4015'
abstract:
- lang: eng
text: The reconstruction of a shape or surface from a finite set of points is a
practically significant and theoretically challenging problem. This paper presents
a unified view of algorithmic solutions proposed in the computer science literature
that are based on the Delaunay complex of the points.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Shape reconstruction with Delaunay complex. In: Proceedingsof
the 3rd Latin American Symposium on Theoretical Informatics. Vol 1380. Springer;
1998:119-132. doi:10.1007/BFb0054315'
apa: 'Edelsbrunner, H. (1998). Shape reconstruction with Delaunay complex. In Proceedingsof
the 3rd Latin American Symposium on Theoretical Informatics (Vol. 1380, pp.
119–132). Campinas, Brazil: Springer. https://doi.org/10.1007/BFb0054315'
chicago: Edelsbrunner, Herbert. “Shape Reconstruction with Delaunay Complex.” In
Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics,
1380:119–32. Springer, 1998. https://doi.org/10.1007/BFb0054315.
ieee: H. Edelsbrunner, “Shape reconstruction with Delaunay complex,” in Proceedingsof
the 3rd Latin American Symposium on Theoretical Informatics, Campinas, Brazil,
1998, vol. 1380, pp. 119–132.
ista: 'Edelsbrunner H. 1998. Shape reconstruction with Delaunay complex. Proceedingsof
the 3rd Latin American Symposium on Theoretical Informatics. LATIN: Latin American
Symposium on Theoretical Informatics , LNCS, vol. 1380, 119–132.'
mla: Edelsbrunner, Herbert. “Shape Reconstruction with Delaunay Complex.” Proceedingsof
the 3rd Latin American Symposium on Theoretical Informatics, vol. 1380, Springer,
1998, pp. 119–32, doi:10.1007/BFb0054315.
short: H. Edelsbrunner, in:, Proceedingsof the 3rd Latin American Symposium on Theoretical
Informatics, Springer, 1998, pp. 119–132.
conference:
end_date: 1998-04-24
location: Campinas, Brazil
name: 'LATIN: Latin American Symposium on Theoretical Informatics '
start_date: 1998-04-20
date_created: 2018-12-11T12:06:27Z
date_published: 1998-03-25T00:00:00Z
date_updated: 2022-08-25T12:22:10Z
day: '25'
doi: 10.1007/BFb0054315
extern: '1'
intvolume: ' 1380'
language:
- iso: eng
month: '03'
oa_version: None
page: 119 - 132
publication: Proceedingsof the 3rd Latin American Symposium on Theoretical Informatics
publication_identifier:
isbn:
- '9783540642756'
publication_status: published
publisher: Springer
publist_id: '2109'
quality_controlled: '1'
status: public
title: Shape reconstruction with Delaunay complex
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 1380
year: '1998'
...
---
_id: '4016'
abstract:
- lang: eng
text: Geomagic Wrap™ is a commercially available software for reconstructing shapes
and surfaces from 3D scanning data. The data can be any arbitrary finite point
set in 3D, and there are no requirements on local density or organization in slices
etc. The software contains components for surface reconstruction, improvement,
and analysis, and it supports a variety of input and output formats that make
it compatible with scanning hardware and CAD and graphics software.
alternative_title:
- SPIE
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Facello, Michael
last_name: Facello
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
- first_name: Jiang
full_name: Qian, Jiang
last_name: Qian
- first_name: Dmitry
full_name: Nekhayev, Dmitry
last_name: Nekhayev
citation:
ama: 'Edelsbrunner H, Facello M, Fu P, Qian J, Nekhayev D. Wrapping 3D scanning
data. In: Vol 3313. SPIE; 1998:148-158. doi:10.1117/12.302448'
apa: Edelsbrunner, H., Facello, M., Fu, P., Qian, J., & Nekhayev, D. (1998).
Wrapping 3D scanning data (Vol. 3313, pp. 148–158). Presented at the Three-Dimensional
Image Capture and Applications, SPIE. https://doi.org/10.1117/12.302448
chicago: Edelsbrunner, Herbert, Michael Facello, Ping Fu, Jiang Qian, and Dmitry
Nekhayev. “Wrapping 3D Scanning Data,” 3313:148–58. SPIE, 1998. https://doi.org/10.1117/12.302448.
ieee: H. Edelsbrunner, M. Facello, P. Fu, J. Qian, and D. Nekhayev, “Wrapping 3D
scanning data,” presented at the Three-Dimensional Image Capture and Applications,
1998, vol. 3313, pp. 148–158.
ista: Edelsbrunner H, Facello M, Fu P, Qian J, Nekhayev D. 1998. Wrapping 3D scanning
data. Three-Dimensional Image Capture and Applications, SPIE, vol. 3313, 148–158.
mla: Edelsbrunner, Herbert, et al. Wrapping 3D Scanning Data. Vol. 3313,
SPIE, 1998, pp. 148–58, doi:10.1117/12.302448.
short: H. Edelsbrunner, M. Facello, P. Fu, J. Qian, D. Nekhayev, in:, SPIE, 1998,
pp. 148–158.
conference:
name: Three-Dimensional Image Capture and Applications
date_created: 2018-12-11T12:06:27Z
date_published: 1998-01-01T00:00:00Z
date_updated: 2022-08-25T12:37:01Z
day: '01'
doi: 10.1117/12.302448
extern: '1'
intvolume: ' 3313'
language:
- iso: eng
month: '01'
oa_version: None
page: 148 - 158
publication_status: published
publisher: SPIE
publist_id: '2110'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wrapping 3D scanning data
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 3313
year: '1998'
...
---
_id: '4017'
abstract:
- lang: eng
text: Identification and size characterization of surface pockets and occluded cavities
are initial steps in protein structure-based ligand design. A new program, CAST,
for automatically locating and measuring protein pockets and cavities, is based
on precise computational geometry methods, including alpha shape and discrete
flow theory. CAST identifies and measures pockets and pocket mouth openings, as
well as cavities. The program specifies the atoms lining pockets, pocket openings.
and buried cavities; the volume and area of pockets and cavities; and the area
and circumference of mouth openings. CAST analysis of over 100 proteins has been
carried out; proteins examined include a set of 51 monomeric enzyme-ligand structures,
several elastase-inhibitor complexes, the FK506 binding protein, 30 HIV-1 protease-inhibitor
complexes, and a number of small and large protein inhibitors, Medium-sized globular
proteins typically have 10-20 pockets/cavities. Most often, binding sites are
pockets with 1-2 mouth openings; much less frequently they are cavities. Ligand
binding pockets vary widely in size, most within the range 10(2)-10(3) Angstrom(3).
Statistical analysis reveals that the number of pockets and cavities is correlated
with protein size, but there is no correlation between the size of the protein
and the size of binding sites. Most frequently, the largest pocket/cavity is thp
active site, but there are a number of instructive exceptions. Ligand volume and
binding site volume are somewhat correlated when binding site volume is less than
or equal to 700 Angstrom(3), but the ligand seldom occupies the entire site. Auxiliary
pockets near the active site have been suggested as additional binding surface
for designed ligands (Mattos C ct al., 1993, Nat Struct Biol 1:55-58). Analysis
of elastase-inhibitor complexes suggests that CAST can identify ancillary pockets,
suitable for recruitment in ligand design strategies. Analysis of the FK506 binding
protein, and of compounds developed in SAR by NMR (Shuker SE et al.. 1996, Science
274:1531-1534), indicates that CAST pocket computation may provide a priori identification
of target proteins for Linked-fragment design. CAST analysis of 30 HIV-1 protease-inhibitor
complexes shows that the flexible active site pocket can vary over a range of
853-1,566 Angstrom(3), and that there are two pockets near or adjoining the active
site that may be recruited for ligand design.
article_processing_charge: No
article_type: original
author:
- first_name: Jie
full_name: Liang, Jie
last_name: Liang
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Clare
full_name: Woodward, Clare
last_name: Woodward
citation:
ama: 'Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities:
Measurement of binding site geometry and implications for ligand design. Protein
Science. 1998;7(9):1884-1897. doi:10.1002/pro.5560070905'
apa: 'Liang, J., Edelsbrunner, H., & Woodward, C. (1998). Anatomy of protein
pockets and cavities: Measurement of binding site geometry and implications for
ligand design. Protein Science. Wiley-Blackwell. https://doi.org/10.1002/pro.5560070905'
chicago: 'Liang, Jie, Herbert Edelsbrunner, and Clare Woodward. “Anatomy of Protein
Pockets and Cavities: Measurement of Binding Site Geometry and Implications for
Ligand Design.” Protein Science. Wiley-Blackwell, 1998. https://doi.org/10.1002/pro.5560070905.'
ieee: 'J. Liang, H. Edelsbrunner, and C. Woodward, “Anatomy of protein pockets and
cavities: Measurement of binding site geometry and implications for ligand design,”
Protein Science, vol. 7, no. 9. Wiley-Blackwell, pp. 1884–1897, 1998.'
ista: 'Liang J, Edelsbrunner H, Woodward C. 1998. Anatomy of protein pockets and
cavities: Measurement of binding site geometry and implications for ligand design.
Protein Science. 7(9), 1884–1897.'
mla: 'Liang, Jie, et al. “Anatomy of Protein Pockets and Cavities: Measurement of
Binding Site Geometry and Implications for Ligand Design.” Protein Science,
vol. 7, no. 9, Wiley-Blackwell, 1998, pp. 1884–97, doi:10.1002/pro.5560070905.'
short: J. Liang, H. Edelsbrunner, C. Woodward, Protein Science 7 (1998) 1884–1897.
date_created: 2018-12-11T12:06:27Z
date_published: 1998-09-01T00:00:00Z
date_updated: 2022-08-25T12:49:41Z
day: '01'
doi: 10.1002/pro.5560070905
extern: '1'
external_id:
pmid:
- '9761470 '
intvolume: ' 7'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144175/
month: '09'
oa: 1
oa_version: Published Version
page: 1884 - 1897
pmid: 1
publication: Protein Science
publication_identifier:
issn:
- 0961-8368
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2111'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Anatomy of protein pockets and cavities: Measurement of binding site geometry
and implications for ligand design'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 7
year: '1998'
...
---
_id: '4019'
abstract:
- lang: eng
text: 'The construction of shape spaces is studied from a mathematical and a computational
viewpoint. A program is outlined reducing the problem to four tasks: the representation
of geometry, the canonical deformation of geometry, the measuring of distance
in shape space, and the selection of base shapes. The technical part of this paper
focuses on the second task: the specification of a deformation mixing two or more
shapes in continuously, changing proportions.'
acknowledgement: This research is partially supported by the National Science Foundation
under grants CCR-96-19542 and CCR-97-12088, and by the Army Research O*ce under
grant DAAG55-98-1-0177.
article_processing_charge: No
author:
- first_name: Ho
full_name: Cheng, Ho
last_name: Cheng
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ping
full_name: Fu, Ping
last_name: Fu
citation:
ama: 'Cheng H, Edelsbrunner H, Fu P. Shape space from deformation. In: Proceedings
of the 6th Pacific Conference on Computer Graphics and Applications. IEEE;
1998:104-113. doi:10.1109/PCCGA.1998.732056'
apa: 'Cheng, H., Edelsbrunner, H., & Fu, P. (1998). Shape space from deformation.
In Proceedings of the 6th Pacific Conference on Computer Graphics and Applications
(pp. 104–113). Singapore: IEEE. https://doi.org/10.1109/PCCGA.1998.732056'
chicago: Cheng, Ho, Herbert Edelsbrunner, and Ping Fu. “Shape Space from Deformation.”
In Proceedings of the 6th Pacific Conference on Computer Graphics and Applications,
104–13. IEEE, 1998. https://doi.org/10.1109/PCCGA.1998.732056.
ieee: H. Cheng, H. Edelsbrunner, and P. Fu, “Shape space from deformation,” in Proceedings
of the 6th Pacific Conference on Computer Graphics and Applications, Singapore,
1998, pp. 104–113.
ista: 'Cheng H, Edelsbrunner H, Fu P. 1998. Shape space from deformation. Proceedings
of the 6th Pacific Conference on Computer Graphics and Applications. CGA: Conference
on Computer Graphics and Applications , 104–113.'
mla: Cheng, Ho, et al. “Shape Space from Deformation.” Proceedings of the 6th
Pacific Conference on Computer Graphics and Applications, IEEE, 1998, pp.
104–13, doi:10.1109/PCCGA.1998.732056.
short: H. Cheng, H. Edelsbrunner, P. Fu, in:, Proceedings of the 6th Pacific Conference
on Computer Graphics and Applications, IEEE, 1998, pp. 104–113.
conference:
end_date: 1998-10-29
location: Singapore
name: 'CGA: Conference on Computer Graphics and Applications '
start_date: 1998-10-26
date_created: 2018-12-11T12:06:28Z
date_published: 1998-10-01T00:00:00Z
date_updated: 2022-08-25T12:06:20Z
day: '01'
doi: 10.1109/PCCGA.1998.732056
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 104 - 113
publication: Proceedings of the 6th Pacific Conference on Computer Graphics and Applications
publication_identifier:
isbn:
- '0818686200'
publication_status: published
publisher: IEEE
publist_id: '2107'
quality_controlled: '1'
status: public
title: Shape space from deformation
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1998'
...
---
_id: '4020'
abstract:
- lang: eng
text: Space Filing diagrams are geometric models of molecular conformations in three-dimensional
space. Each atom is a location is space and a quantitative expression of influence
on the immediate surrounding. This paper surveys the basic types of space filling
diagrams with a focus on the dual alpha shape. Properties of those diagrams that
relate to questions of connectivity, size, shape and symmetry, and metamorphosis
are discussed.
article_processing_charge: No
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Geometry for modeling biomolecules. In: Robotics: The Algorithmic
Perspective. AK Peters; 1998:265-277.'
apa: 'Edelsbrunner, H. (1998). Geometry for modeling biomolecules. In Robotics:
The Algorithmic Perspective (pp. 265–277). AK Peters.'
chicago: 'Edelsbrunner, Herbert. “Geometry for Modeling Biomolecules.” In Robotics:
The Algorithmic Perspective, 265–77. AK Peters, 1998.'
ieee: 'H. Edelsbrunner, “Geometry for modeling biomolecules,” in Robotics: The
Algorithmic Perspective, AK Peters, 1998, pp. 265–277.'
ista: 'Edelsbrunner H. 1998.Geometry for modeling biomolecules. In: Robotics: The
Algorithmic Perspective. , 265–277.'
mla: 'Edelsbrunner, Herbert. “Geometry for Modeling Biomolecules.” Robotics:
The Algorithmic Perspective, AK Peters, 1998, pp. 265–77.'
short: 'H. Edelsbrunner, in:, Robotics: The Algorithmic Perspective, AK Peters,
1998, pp. 265–277.'
date_created: 2018-12-11T12:06:28Z
date_published: 1998-10-01T00:00:00Z
date_updated: 2022-08-25T12:12:04Z
day: '01'
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 265 - 277
publication: 'Robotics: The Algorithmic Perspective'
publication_identifier:
isbn:
- '9781568810812'
publication_status: published
publisher: AK Peters
publist_id: '2108'
quality_controlled: '1'
status: public
title: Geometry for modeling biomolecules
type: book_chapter
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '1998'
...
---
_id: '4280'
article_processing_charge: No
article_type: original
author:
- first_name: Mike
full_name: Ritchie, Mike
last_name: Ritchie
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Ritchie M, Barton NH. Hybrids and hybrid zones: Reply from M.G. Ritchie and
N.H. Barton. Trends in Ecology and Evolution. 1998;13(7):282-283. doi:10.1016/S0169-5347(98)01396-2'
apa: 'Ritchie, M., & Barton, N. H. (1998). Hybrids and hybrid zones: Reply from
M.G. Ritchie and N.H. Barton. Trends in Ecology and Evolution. Cell Press.
https://doi.org/10.1016/S0169-5347(98)01396-2'
chicago: 'Ritchie, Mike, and Nicholas H Barton. “Hybrids and Hybrid Zones: Reply
from M.G. Ritchie and N.H. Barton.” Trends in Ecology and Evolution. Cell
Press, 1998. https://doi.org/10.1016/S0169-5347(98)01396-2.'
ieee: 'M. Ritchie and N. H. Barton, “Hybrids and hybrid zones: Reply from M.G. Ritchie
and N.H. Barton,” Trends in Ecology and Evolution, vol. 13, no. 7. Cell
Press, pp. 282–283, 1998.'
ista: 'Ritchie M, Barton NH. 1998. Hybrids and hybrid zones: Reply from M.G. Ritchie
and N.H. Barton. Trends in Ecology and Evolution. 13(7), 282–283.'
mla: 'Ritchie, Mike, and Nicholas H. Barton. “Hybrids and Hybrid Zones: Reply from
M.G. Ritchie and N.H. Barton.” Trends in Ecology and Evolution, vol. 13,
no. 7, Cell Press, 1998, pp. 282–83, doi:10.1016/S0169-5347(98)01396-2.'
short: M. Ritchie, N.H. Barton, Trends in Ecology and Evolution 13 (1998) 282–283.
date_created: 2018-12-11T12:08:01Z
date_published: 1998-07-01T00:00:00Z
date_updated: 2022-08-25T11:56:08Z
day: '01'
doi: 10.1016/S0169-5347(98)01396-2
extern: '1'
external_id:
pmid:
- '21238302'
intvolume: ' 13'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 282 - 283
pmid: 1
publication: Trends in Ecology and Evolution
publication_identifier:
issn:
- 0169-5347
publication_status: published
publisher: Cell Press
publist_id: '1806'
quality_controlled: '1'
status: public
title: 'Hybrids and hybrid zones: Reply from M.G. Ritchie and N.H. Barton'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 13
year: '1998'
...
---
_id: '4281'
abstract:
- lang: eng
text: 'Most higher organisms reproduce sexually, despite the automatic reproductive
advantage experienced by asexual variants. This implies the operation of selective
forces that confer an advantage to sexuality and genetic recombination, at either
the population or individual level. The effect of sex and recombination in breaking
down negative correlations between favorable variants at different genetic loci,
which increases the efficiency of natural selection, is likely to be a major factor
favoring their evolution and maintenance. Various processes that can cause such
an effect have been studied theoretically. It has, however, so far proved hard
to discriminate among them empirically. '
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: Barton NH, Charlesworth B. Why sex and recombination? Science. 1998;281(5385):1986-1990.
doi:10.1126/science.281.5385.1986
apa: Barton, N. H., & Charlesworth, B. (1998). Why sex and recombination? Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.281.5385.1986
chicago: Barton, Nicholas H, and Brian Charlesworth. “Why Sex and Recombination?”
Science. American Association for the Advancement of Science, 1998. https://doi.org/10.1126/science.281.5385.1986.
ieee: N. H. Barton and B. Charlesworth, “Why sex and recombination?,” Science,
vol. 281, no. 5385. American Association for the Advancement of Science, pp. 1986–1990,
1998.
ista: Barton NH, Charlesworth B. 1998. Why sex and recombination? Science. 281(5385),
1986–1990.
mla: Barton, Nicholas H., and Brian Charlesworth. “Why Sex and Recombination?” Science,
vol. 281, no. 5385, American Association for the Advancement of Science, 1998,
pp. 1986–90, doi:10.1126/science.281.5385.1986.
short: N.H. Barton, B. Charlesworth, Science 281 (1998) 1986–1990.
date_created: 2018-12-11T12:08:01Z
date_published: 1998-09-25T00:00:00Z
date_updated: 2022-08-25T11:53:29Z
day: '25'
doi: 10.1126/science.281.5385.1986
extern: '1'
external_id:
pmid:
- '9748151'
intvolume: ' 281'
issue: '5385'
language:
- iso: eng
month: '09'
oa_version: None
page: 1986 - 1990
pmid: 1
publication: Science
publication_identifier:
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '1804'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Why sex and recombination?
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 281
year: '1998'
...
---
_id: '4282'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Genetics and analysis of quantitative traits. Genetical Research.
1998;72(1):73-73. doi:10.1017/S0016672398219732
apa: Barton, N. H. (1998). Genetics and analysis of quantitative traits. Genetical
Research. Cambridge University Press. https://doi.org/10.1017/S0016672398219732
chicago: Barton, Nicholas H. “Genetics and Analysis of Quantitative Traits.” Genetical
Research. Cambridge University Press, 1998. https://doi.org/10.1017/S0016672398219732.
ieee: N. H. Barton, “Genetics and analysis of quantitative traits,” Genetical
Research, vol. 72, no. 1. Cambridge University Press, pp. 73–73, 1998.
ista: Barton NH. 1998. Genetics and analysis of quantitative traits. Genetical Research.
72(1), 73–73.
mla: Barton, Nicholas H. “Genetics and Analysis of Quantitative Traits.” Genetical
Research, vol. 72, no. 1, Cambridge University Press, 1998, pp. 73–73, doi:10.1017/S0016672398219732.
short: N.H. Barton, Genetical Research 72 (1998) 73–73.
date_created: 2018-12-11T12:08:01Z
date_published: 1998-08-01T00:00:00Z
date_updated: 2022-08-24T13:36:46Z
day: '01'
doi: 10.1017/S0016672398219732
extern: '1'
intvolume: ' 72'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 73 - 73
publication: Genetical Research
publication_identifier:
issn:
- 0016-6723
publication_status: published
publisher: Cambridge University Press
publist_id: '1801'
status: public
title: Genetics and analysis of quantitative traits
type: review
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 72
year: '1998'
...
---
_id: '4283'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The geometry of adaptation. Nature. 1998;395(6704):751-752.
doi:10.1038/27338
apa: Barton, N. H. (1998). The geometry of adaptation. Nature. Nature Publishing
Group. https://doi.org/10.1038/27338
chicago: Barton, Nicholas H. “The Geometry of Adaptation.” Nature. Nature
Publishing Group, 1998. https://doi.org/10.1038/27338.
ieee: N. H. Barton, “The geometry of adaptation,” Nature, vol. 395, no. 6704.
Nature Publishing Group, pp. 751–752, 1998.
ista: Barton NH. 1998. The geometry of adaptation. Nature. 395(6704), 751–752.
mla: Barton, Nicholas H. “The Geometry of Adaptation.” Nature, vol. 395,
no. 6704, Nature Publishing Group, 1998, pp. 751–52, doi:10.1038/27338.
short: N.H. Barton, Nature 395 (1998) 751–752.
date_created: 2018-12-11T12:08:02Z
date_published: 1998-10-01T00:00:00Z
date_updated: 2022-08-24T13:50:49Z
day: '01'
doi: 10.1038/27338
extern: '1'
intvolume: ' 395'
issue: '6704'
language:
- iso: eng
month: '10'
oa_version: None
page: 751 - 752
publication: Nature
publication_identifier:
issn:
- 0028-0836
publication_status: published
publisher: Nature Publishing Group
publist_id: '1802'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The geometry of adaptation
type: review
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 395
year: '1998'
...
---
_id: '4408'
abstract:
- lang: eng
text: 'This paper presents a complete axiomatization of fully decidable propositional
real-time linear temporal logics with past: the Event Clock Logic (ECL) and the
Metric Interval Temporal Logic with past (MITL). The completeness proof consists
of an effective proof building procedure for ECL. From this result we obtain a
complete axiomatization of MITL by providing axioms translating MITL formulae
into ECL formulae, the two logics being equally expressive. Our proof is structured
to yield a similar axiomatization and procedure for interesting fragments of these
logics, such as the linear temporal logic of the real numbers (LTR).'
acknowledgement: This work is supported in part by the ONR YIP award N00014-95-1-0520,
by the NSF CAREER award CCR-9501708, by the NSF grant CCR-9504469, by the DARPA/NASA
grant NAG2-1214, by the ARO MURI grant DAAH-04-96-1-0341, by the SRC contract 97-DC-324.041,
the Belgian National Fund for Scientific Research (FNRS), the European Commission
under WGs Aspire and Fireworks, the Portuguese FCT, and by Belgacom.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
- first_name: Pierre
full_name: Schobbens, Pierre
last_name: Schobbens
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Raskin J, Schobbens P, Henzinger TA. Axioms for real-time logics. In: Proceedings
of the 9th Interantional Conference on Concurrency Theory. Vol 1466. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik; 1998:219-236. doi:10.1007/BFb0055625'
apa: 'Raskin, J., Schobbens, P., & Henzinger, T. A. (1998). Axioms for real-time
logics. In Proceedings of the 9th Interantional Conference on Concurrency Theory
(Vol. 1466, pp. 219–236). Nice, France: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.1007/BFb0055625'
chicago: Raskin, Jean, Pierre Schobbens, and Thomas A Henzinger. “Axioms for Real-Time
Logics.” In Proceedings of the 9th Interantional Conference on Concurrency
Theory, 1466:219–36. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 1998.
https://doi.org/10.1007/BFb0055625.
ieee: J. Raskin, P. Schobbens, and T. A. Henzinger, “Axioms for real-time logics,”
in Proceedings of the 9th Interantional Conference on Concurrency Theory,
Nice, France, 1998, vol. 1466, pp. 219–236.
ista: 'Raskin J, Schobbens P, Henzinger TA. 1998. Axioms for real-time logics. Proceedings
of the 9th Interantional Conference on Concurrency Theory. CONCUR: Concurrency
Theory, LNCS, vol. 1466, 219–236.'
mla: Raskin, Jean, et al. “Axioms for Real-Time Logics.” Proceedings of the 9th
Interantional Conference on Concurrency Theory, vol. 1466, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 1998, pp. 219–36, doi:10.1007/BFb0055625.
short: J. Raskin, P. Schobbens, T.A. Henzinger, in:, Proceedings of the 9th Interantional
Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
1998, pp. 219–236.
conference:
end_date: 1998-09-11
location: Nice, France
name: 'CONCUR: Concurrency Theory'
start_date: 1998-09-08
date_created: 2018-12-11T12:08:42Z
date_published: 1998-01-01T00:00:00Z
date_updated: 2022-08-24T12:15:17Z
day: '01'
doi: 10.1007/BFb0055625
extern: '1'
intvolume: ' 1466'
language:
- iso: eng
month: '01'
oa_version: None
page: 219 - 236
publication: Proceedings of the 9th Interantional Conference on Concurrency Theory
publication_identifier:
isbn:
- '9783540648963'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '323'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Axioms for real-time logics
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 1466
year: '1998'
...
---
_id: '4410'
abstract:
- lang: eng
text: "Rectangular automata are well suited for approximate modeling of continuous-discrete
systems. The exact analysis of these automata is feasible for small examples but
can encounter severe numerical problems for even medium-sized systems. This paper
presents an analysis algorithm that uses conservative overapproximation to avoid
these numerical problems. The algorithm is demonstrated on a simple benchmark
system consisting of two connected tanks.\r\nSupported by the German Research
Council (DFG) under grant Ko1430/3 in the special program KONDISK (‘Continuous-discrete
dynamics of technical systems’)."
acknowledgement: This research was supported in part by the ONR YIP award N00014-95-1-0520,
by the NSF CAREER award CCR-9501708, by the NSF grant CCR-9504469, by the DARPA/NASA
grant NAG2-1214, by the ARO MURI grant DAAH-04-96-1-0341, and by the SRC contract
97-DC-324.041.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Jörg
full_name: Preußig, Jörg
last_name: Preußig
- first_name: Stefan
full_name: Kowalewski, Stefan
last_name: Kowalewski
- first_name: Howard
full_name: Wong Toi, Howard
last_name: Wong Toi
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Preußig J, Kowalewski S, Wong Toi H, Henzinger TA. An algorithm for the approximative
analysis of rectangular automata. In: Proceedings of the 5th International
Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems. Vol
1486. Springer; 1998:228-240. doi:10.1007/BFb0055350'
apa: 'Preußig, J., Kowalewski, S., Wong Toi, H., & Henzinger, T. A. (1998).
An algorithm for the approximative analysis of rectangular automata. In Proceedings
of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant
Systems (Vol. 1486, pp. 228–240). Lyngby, Denmark: Springer. https://doi.org/10.1007/BFb0055350'
chicago: Preußig, Jörg, Stefan Kowalewski, Howard Wong Toi, and Thomas A Henzinger.
“An Algorithm for the Approximative Analysis of Rectangular Automata.” In Proceedings
of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant
Systems, 1486:228–40. Springer, 1998. https://doi.org/10.1007/BFb0055350.
ieee: J. Preußig, S. Kowalewski, H. Wong Toi, and T. A. Henzinger, “An algorithm
for the approximative analysis of rectangular automata,” in Proceedings of
the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant
Systems, Lyngby, Denmark, 1998, vol. 1486, pp. 228–240.
ista: 'Preußig J, Kowalewski S, Wong Toi H, Henzinger TA. 1998. An algorithm for
the approximative analysis of rectangular automata. Proceedings of the 5th International
Symposium on Formal Techniques in Real-Time and Fault-Tolerant Systems. FTRTFT:
Formal Techniques in Real-Time and Fault-Tolerant Systems, LNCS, vol. 1486, 228–240.'
mla: Preußig, Jörg, et al. “An Algorithm for the Approximative Analysis of Rectangular
Automata.” Proceedings of the 5th International Symposium on Formal Techniques
in Real-Time and Fault-Tolerant Systems, vol. 1486, Springer, 1998, pp. 228–40,
doi:10.1007/BFb0055350.
short: J. Preußig, S. Kowalewski, H. Wong Toi, T.A. Henzinger, in:, Proceedings
of the 5th International Symposium on Formal Techniques in Real-Time and Fault-Tolerant
Systems, Springer, 1998, pp. 228–240.
conference:
end_date: 1998-09-18
location: Lyngby, Denmark
name: 'FTRTFT: Formal Techniques in Real-Time and Fault-Tolerant Systems'
start_date: 1998-09-14
date_created: 2018-12-11T12:08:43Z
date_published: 1998-01-01T00:00:00Z
date_updated: 2022-08-24T12:01:57Z
day: '01'
doi: 10.1007/BFb0055350
extern: '1'
intvolume: ' 1486'
language:
- iso: eng
month: '01'
oa_version: None
page: 228 - 240
publication: Proceedings of the 5th International Symposium on Formal Techniques in
Real-Time and Fault-Tolerant Systems
publication_identifier:
isbn:
- '9783540650034'
publication_status: published
publisher: Springer
publist_id: '320'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An algorithm for the approximative analysis of rectangular automata
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 1486
year: '1998'
...
---
_id: '4429'
abstract:
- lang: eng
text: We study the reachability problem for hybrid automata. Automatic approaches,
which attempt to construct the reachable region by symbolic execution, often do
not terminate. In these cases, we require the user to guess the reachable region,
and we use a theorem prover (Pvs) to verify the guess. We classify hybrid automata
according to the theory in which their reachable region can be defined finitely.
This is the theory in which the prover needs to operate in order to verify the
guess. The approach is interesting, because an appropriate guess can often be
deduced by extrapolating from the first few steps of symbolic execution.
acknowledgement: "This research was supported in part by the ONR YIP award N00014-95-1-0520,
by the NSF CAREER award CCR-9501708, by the NSF grant CCR-9504469, by the AFOSR
contract F49620-93-1-0056, by the ARO MURI grant DAAH-04-96-1-0341, by the ARPA
grant NAG2-892, and by the SRC contract 95-DC-324.036.\r\nSupported by Lavoisier
grant of the French Foreign Affairs Ministry and by SRI."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vlad
full_name: Rusu, Vlad
last_name: Rusu
citation:
ama: 'Henzinger TA, Rusu V. Reachability verification for hybrid automata. In: Proceedings
of the 1st International Workshop on Hybrid Systems: Computation and Control.
Vol 1386. Springer; 1998:190-204. doi:10.1007/3-540-64358-3_40'
apa: 'Henzinger, T. A., & Rusu, V. (1998). Reachability verification for hybrid
automata. In Proceedings of the 1st International Workshop on Hybrid Systems:
Computation and Control (Vol. 1386, pp. 190–204). Berkely, CA, United States
of America: Springer. https://doi.org/10.1007/3-540-64358-3_40'
chicago: 'Henzinger, Thomas A, and Vlad Rusu. “Reachability Verification for Hybrid
Automata.” In Proceedings of the 1st International Workshop on Hybrid Systems:
Computation and Control, 1386:190–204. Springer, 1998. https://doi.org/10.1007/3-540-64358-3_40.'
ieee: 'T. A. Henzinger and V. Rusu, “Reachability verification for hybrid automata,”
in Proceedings of the 1st International Workshop on Hybrid Systems: Computation
and Control, Berkely, CA, United States of America, 1998, vol. 1386, pp. 190–204.'
ista: 'Henzinger TA, Rusu V. 1998. Reachability verification for hybrid automata.
Proceedings of the 1st International Workshop on Hybrid Systems: Computation and
Control. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 1386, 190–204.'
mla: 'Henzinger, Thomas A., and Vlad Rusu. “Reachability Verification for Hybrid
Automata.” Proceedings of the 1st International Workshop on Hybrid Systems:
Computation and Control, vol. 1386, Springer, 1998, pp. 190–204, doi:10.1007/3-540-64358-3_40.'
short: 'T.A. Henzinger, V. Rusu, in:, Proceedings of the 1st International Workshop
on Hybrid Systems: Computation and Control, Springer, 1998, pp. 190–204.'
conference:
end_date: 1998-04-15
location: Berkely, CA, United States of America
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 1998-04-13
date_created: 2018-12-11T12:08:48Z
date_published: 1998-01-01T00:00:00Z
date_updated: 2022-08-24T11:29:14Z
day: '01'
doi: 10.1007/3-540-64358-3_40
extern: '1'
intvolume: ' 1386'
language:
- iso: eng
month: '01'
oa_version: None
page: 190 - 204
publication: 'Proceedings of the 1st International Workshop on Hybrid Systems: Computation
and Control'
publication_identifier:
isbn:
- '9783540643586'
publication_status: published
publisher: Springer
publist_id: '299'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reachability verification for hybrid automata
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 1386
year: '1998'
...