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Science (New York, N.Y.), Vol. 315, No. 5815. (23 February 2007), pp. 1126-1130.
by C. von Mering, P. Hugenholtz, J. Raes, et al.S. G. Tringe, T. Doerks, L. J. Jensen, N. Ward, P. Bork
posted by
29 people
chica
dutilh
michaelbarton
hwright
pkm
idoerg
sriesenfeld
skembel
kozo-ni
ana
nickluscombe
michC
bluto
agg19954
TaqSys
azazello
structural_bioinformatics
Bioinformatics
EBI-regulation
Microbial-Ecology
Thaverkamp
larsjuhljensen
rvgomes
mjetten
microbiology_nijmegen
jlgreen
Green Lab
iSEEM
djkt
AbstractThe taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also ... | |
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PLoS Comput Biol, Vol. 5, No. 4. (10 April 2009), e1000352.
posted by
17 people
bluto
dutilh
jfr
Orengo Group Journal Picks
CorinYeats
dayjm
taylor73
Thaverkamp
hpaces
sriesenfeld
APRegier
dswan
druvus
djkt
iSEEM
skembel
idoerg
AbstractNumerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them. ... | |
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Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i7-13.
by Daniel Dalevi, Natalia N. Ivanova, Konstantinos Mavromatis, et al.Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos C. Kyrpides, Victor M. Markowitz
posted by
7 people
gaosong0329
Thaverkamp
iSEEM
druvus
skembel
hpaces
neils
AbstractMotivation: A typical metagenome dataset generated using a 454 pyrosequencing platform consists of short reads sampled from the collective genome of a microbial community. The amount of sequence in such datasets is usually insufficient for assembly, and traditional gene prediction cannot be applied to unassembled short reads. As a result, analysis of such datasets usually involves comparisons in terms of relative abundances of various protein families. The latter requires assignment of individual reads to protein families, which is hindered by the ... | |
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Nature, Vol. 450, No. 7169., pp. 560-565.
by Falk Warnecke, Peter Luginbühl, Natalia Ivanova, et al.Majid Ghassemian, Toby H. Richardson, Justin T. Stege, Michelle Cayouette, Alice C. Mchardy, Gordana Djordjevic, Nahla Aboushadi, Rotem Sorek, Susannah G. Tringe, Mircea Podar, Hector G. Martin, Victor Kunin, Daniel Dalevi, Julita Madejska, Edward Kirton, Darren Platt, Ernest Szeto, Asaf Salamov, Kerrie Barry, Natalia Mikhailova, Nikos C. Kyrpides, Eric G. Matson, Elizabeth A. Ottesen, Xinning Zhang, Myriam Hernández, Catalina Murillo, Luis G. Acosta, Isidore Rigoutsos, Giselle Tamayo, Brian D. Green, Cathy Chang, Edward M. Rubin, Eric J. Mathur, Dan E. Robertson, Philip Hugenholtz, Jared R. Leadbetter
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Environmental Microbiology, Vol. 6, No. 9. (September 2004), pp. 938-947.
AbstractA basic problem of the metagenomic approach in microbial ecology is the assignment of genomic fragments to a certain species or taxonomic group, when suitable marker genes are absent. Currently, the (G + C)-content together with phylogenetic information and codon adaptation for functional genes is mostly used to assess the relationship of different fragments. These methods, however, can produce ambiguous results. In order to evaluate sequence-based methods for fragment identification, we extensively compared (G + C)-contents and tetranucleotide usage patterns of 9054 fosmid-sized genomic ... | |
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Nature Methods, Vol. 6, No. 9. (02 August 2009), pp. 673-676.
posted by
16 people
dutilh
elipapa
CorinYeats
idoerg
azazello
Orengo Group Journal Picks
robertrentzsch
dakelley
skembel
Thaverkamp
iSEEM
sharpton
Journal picks
jbhiatt
Mycology
stajich
AbstractMetagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made metagenomics easier, by making sequencing faster, and more difficult, by producing shorter reads than previous technologies. Classifying sequences from reads as short as 100 base pairs ... | |
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Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1118-1124.
by Tobias Rausch, Sergey Koren, Gennady Denisov, et al.David Weese, Anne-Katrin Emde, Andreas Doring, Knut Reinert
posted by
27 people
dutilh
jonilaserson
justinhjohnson
orzenil
humburg
jfr
azazello
hzoltan
cthachuk
GustavoLacerda
jasontsai
n00c
nuin
dakelley
skembel
Thaverkamp
reyez
TRHvidsten
iSEEM
djkt
Bioinformatics
hpaces
APRegier
pengchy
natstreet
druvus
darian
AbstractMotivation: Novel high-throughput sequencing technologies pose new algorithmic challenges in handling massive amounts of short-read, high-coverage data. A robust and versatile consensus tool is of particular interest for such data since a sound multi-read alignment is a prerequisite for variation analyses, accurate genome assemblies and insert sequencing. Results: A multi-read alignment algorithm for de novo or reference-guided genome assembly is presented. The program identifies segments shared by multiple reads and then aligns these segments using a consistency-enhanced alignment graph. On ... | |
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PLoS Comput Biol In PLoS Comput Biol, Vol. 4, No. 9. (26 September 2008), e1000186.
posted by
25 people
justinhjohnson
dutilh
skembel
n00c
operon
BergmanLab
michaelbarton
azazello
Thaverkamp
dakelley
sconlan
GustavoLacerda
treangen
natstreet
antonkratz
druvus
Papers recommended by the Roscoff Plankton Group
vaulot
iSEEM
djkt
microbiology_nijmegen
Katje
Mycology
stajich
semrich
AbstractRecent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa , strain PAb1, using very ... | |
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ISME J, Vol. 2, No. 11. (4 September 2008), pp. 1146-1156.
by Kelly C. Wrighton, Peter Agbo, Falk Warnecke, et al.Karrie A. Weber, Eoin L. Brodie, Todd Z. Desantis, Philip Hugenholtz, Gary L. Andersen, John D. Coates
posted by
2 people
Thaverkamp
bluto
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Genome Biology, Vol. 9, No. 12. (2008), R179.
posted by
20 people
cerca
GustavoLacerda
bertelsen
Thaverkamp
cgaugain
ptrobajo
jfr
bluto
sylvainforet
Bioinformatics - CRUK
Stew
Cortel
Roswell Cancer Crosstalk
Zephyrus
guhjy
neils
cmzmasek
fgibson
dullhunk
druvus
AbstractKEGG spider is a web-based tool for interpretation of experimentally derived gene lists in order to gain understanding of metabolism variations at a genomic level. KEGG spider implements a 'pathway-free' framework that overcomes a major bottleneck of enrichment analyses: it provides global models uniting genes from different metabolic pathways. Analyzing a number of experimentally derived gene lists, we demonstrate that KEGG spider provides deeper insights into metabolism variations in comparison to existing methods. ... | |
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Science, Vol. 320, No. 5879. (23 May 2008), pp. 1043-1045.
AbstractThe oceans harbor a tremendous diversity of marine microbes. Different functional groups of bacteria, archaea, and protists arise from this diversity to dominate various habitats and drive globally important biogeochemical cycles. Explanations for the distribution of microbial taxa and their associated activity often focus on resource availability and abiotic conditions. However, the continual reshaping of communities by mortality, allelopathy, symbiosis, and other processes shows that community interactions exert strong selective pressure on marine microbes. Deeper exploration of microbial interactions is now ... | |
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Proceedings of the National Academy of Sciences, Vol. 105, No. 7. (19 February 2008), pp. 2510-2515.
posted by
9 people
Scis0000002
mhiromi
Thaverkamp
operon
bluto
vaulot
Microbial-Ecology
Papers recommended by the Roscoff Plankton Group
tuoshi
AbstractCyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis, the evolution of which transformed the biology and geochemistry of Earth. The rapid increase in published genomic sequences of cyanobacteria provides the first opportunity to reconstruct events in the evolution of oxygenic photosynthesis on the scale of entire genomes. Here, we demonstrate the overall phylogenetic incongruence among 682 orthologous protein families from 13 genomes of cyanobacteria. However, using principal coordinates analysis, we discovered a core set of 323 genes with similar ... | |
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Appl. Environ. Microbiol., Vol. 74, No. 2. (15 January 2008), pp. 503-515.
posted by
2 people
bluto
Thaverkamp
AbstractThe Baltic Sea is one of the largest brackish environments on Earth. Despite extensive knowledge about food web interactions and pelagic ecosystem functioning, information about the bacterial community composition in the Baltic Sea is scarce. We hypothesized that due to the eutrophic low-salinity environment and the long water residence time (>5 years), the bacterioplankton community from the Baltic proper shows a native "brackish" composition influenced by both freshwater and marine phylotypes. The bacterial community composition in surface water (3-m depth) was ... | |
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Nature, Vol. 424, No. 6952. (28 August 2003), pp. 1047-1051.
posted by
3 people
bluto
Microbial-Ecology
Thaverkamp
AbstractProchlorococcus is the numerically dominant phototroph in the tropical and subtropical oceans, accounting for half of the photosynthetic biomass in some areas. Here we report the isolation of cyanophages that infect Prochlorococcus, and show that although some are host-strain-specific, others cross-infect with closely related marine Synechococcus as well as between high-light- and low-light-adapted Prochlorococcus isolates, suggesting a mechanism for horizontal gene transfer. High-light-adapted Prochlorococcus hosts yielded Podoviridae exclusively, which were extremely host-specific, whereas low-light-adapted Prochlorococcus and all strains of Synechococcus yielded ... | |
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PLoS Biol, Vol. 4, No. 8. (4 July 2006)
by Matthew B B. Sullivan, Debbie Lindell, Jessica A A. Lee, Luke R R. Thompson, Joseph P P. Bielawski, Sallie W W. Chisholm
posted by
4 people
AaronDarling
bluto
Microbial-Ecology
Thaverkamp
AbstractCyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this ... | |
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PLoS Biol, Vol. 3, No. 5. (May 2005)
posted by
3 people
bluto
Microbial-Ecology
Thaverkamp
AbstractThe oceanic cyanobacteria Prochlorococcus are globally important, ecologically diverse primary producers. It is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. Here we present an analysis of genomes from three Prochlorococcus phages: a podovirus and two myoviruses. The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4) phages. Using the existing phage taxonomic framework as a guideline, we ... | |
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Environmental Microbiology, Vol. 7, No. 10. (October 2005), pp. 1505-1513.
posted by
4 people
bluto
beatrizfernandez
Microbial-Ecology
Thaverkamp
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PLoS Comput Biol, Vol. 5, No. 12. (11 December 2009), e1000593.
by Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, et al.Robert A. Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer
posted by
11 people
FAB-lab
rvosa
gaosong0329
Thaverkamp
Orengo Group Journal Picks
CorinYeats
elipapa
Julien_Fayolle
neils
maren
kshameer
AbstractMetagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical ... | |
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BMC Bioinformatics, Vol. 9, No. 1. (19 September 2008), 386.
by F. Meyer, D. Paarmann, M. D'Souza, et al.R. Olson, E. M. Glass, M. Kubal, T. Paczian, A. Rodriguez, R. Stevens, A. Wilke, J. Wilkening, R. A. Edwards
posted by
12 people
gaosong0329
Orengo Group Journal Picks
CorinYeats
taylor73
idoerg
Thaverkamp
druvus
guhjy
operon
ojabado
nuin
neils
AbstractBACKGROUND:Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers.RESULTS:A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic ... | |
![]() An efficient parallel approach for identifying protein families in large-scale metagenomic data setsIn SC '08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing (2008), pp. 1-10.
posted by
3 people
Thaverkamp
iSEEM
skembel
AbstractMetagenomics is the study of environmental microbial communities using state-of-the-art genomic tools. Recent advancements in high-throughput technologies have enabled the accumulation of large volumes of metagenomic data that was until a couple of years back was deemed impractical for generation. A primary bottleneck, however, is in the lack of scalable algorithms and open source software for large-scale data processing. In this paper, we present the design and implementation of a novel parallel approach to identify protein families from large-scale metagenomic data. ... | |
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Nature, Vol. 459, No. 7244. (14 May 2009), pp. 207-212.
posted by
7 people
bmezmer
hwright
tomhebbron
skembel
Thaverkamp
iSEEM
djkt
AbstractMarine viruses affect Bacteria, Archaea and eukaryotic organisms and are major components of the marine food web. Most studies have focused on their role as predators and parasites, but many of the interactions between marine viruses and their hosts are much more complicated. A series of recent studies has shown that viruses have the ability to manipulate the life histories and evolution of their hosts in remarkable ways, challenging our understanding of this almost invisible world. ... | |
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Applied and environmental microbiology, Vol. 75, No. 7. (1 April 2009), pp. 2221-2229.
posted by
5 people
rec3141
iSEEM
skembel
Thaverkamp
EKotlarska
AbstractThe Sorcerer II Global Ocean Sampling (GOS) sequencing effort has vastly expanded the landscape of metagenomics, providing an opportunity to study the genetic potential of surface ocean water bacterioplankton on a global scale. Here we describe the habitat-based microbial diversity, both taxon evenness and taxon richness, for each GOS site and estimate genome characteristics of a typical free-living, surface ocean water bacterium. While Alphaproteobacteria and particularly SAR11 dominate the 0.1- to 0.8-mum size fraction of surface ocean water bacteria (43% and ... | |
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Trends in genetics : TIG, Vol. 24, No. 11. (24 November 2008), pp. 539-551.
posted by
14 people
kiekyon
maximilianh
Thaverkamp
orzenil
kshameer
carlk
guhjy
natstreet
druvus
treangen
skembel
gjuggler
dchughes
operon
AbstractOrthology is a key evolutionary concept in many areas of genomic research. It provides a framework for subjects as diverse as the evolution of genomes, gene functions, cellular networks and functional genome annotation. Although orthologous proteins usually perform equivalent functions in different species, establishing true orthologous relationships requires a phylogenetic approach, which combines both trees and graphs (networks) using reliable species phylogeny and available genomic data from more than two species, and an insight into the processes of molecular evolution. Here, ... | |
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Proceedings of the National Academy of Sciences, Vol. 105, No. 39. (30 September 2008), pp. 15076-15081.
by Catherine A. Lozupone, Micah Hamady, Brandi L. Cantarel, et al.Pedro M. Coutinho, Bernard Henrissat, Jeffrey I. Gordon, Rob Knight
Abstract10.1073/pnas.0807339105 The extreme variation in gene content among phylogenetically related microorganisms suggests that gene acquisition, expansion, and loss are important evolutionary forces for adaptation to new environments. Accordingly, phylogenetically disparate organisms that share a habitat may converge in gene content as they adapt to confront shared challenges. This response should be especially pronounced for functional genes that are important for survival in a particular habitat. We illustrate this principle by showing that the repertoires of two different types of carbohydrate-active enzymes, ... | |
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Environmental Microbiology, Vol. 0, No. 0. (0), pp. ???-???.
by Katrin Zwirglmaier, Ludwig Jardillier, Martin Ostrowski, et al.Sophie Mazard, Laurence Garczarek, Daniel Vaulot, Fabrice Not, Ramon Massana, Osvaldo Ulloa, Dave J. Scanlan
posted by
6 people
hwright
Stenuite
Microbial-Ecology
Thaverkamp
andrewirwin
Biological oceanography
AbstractSummary Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are important contributors to global primary production occupying a key position at the base of marine food webs. The genetically diverse nature of each genus is likely an important reason for their successful colonization of vast tracts of the world's oceans, a feature that has led to detailed analysis of the distribution of these genetic lineages at the local and ocean basin scale. Here, we extend these analyses to the global dimension, ... | |
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Appl Environ Microbiol, Vol. 72, No. 11. (November 2006), pp. 7193-7204.
posted by
4 people
hwright
Stenuite
Microbial-Ecology
Thaverkamp
AbstractMarine microbial communities often contain multiple closely related phylogenetic clades, but in many cases, it is still unclear what physiological traits differentiate these putative ecotypes. The numerically abundant marine cyanobacterium Synechococcus can be divided into at least 14 clades. In order to better understand ecotype differentiation in this genus, we assessed the diversity of a Synechococcus community from a well-mixed water column in the Sargasso Sea during March 2002, a time of year when this genus typically reaches its annual peak ... | |
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BMC Bioinformatics, Vol. 9, No. 1. (28 April 2008), 217.
posted by
13 people
dakelley
mpizbioinfo
elipapa
Thaverkamp
idoerg
druvus
alexl
mjetten
anammox
microbiology_nijmegen
stajich
Mycology
azazello
AbstractBACKGROUND:Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. In contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous sequencing reads. One of the aims of all metagenomic ... | |
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BMC Genomics, Vol. 9, No. 1. (08 February 2008), 75.
by Ramy Aziz, Daniela Bartels, Aaron Best, et al.Matthew DeJongh, Terrence Disz, Robert Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth Glass, Michael Kubal, Folker Meyer, Gary Olsen, Robert Olson, Andrei Osterman, Ross Overbeek, Leslie McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko
posted by
14 people
chica
karinlag
Waikato - Erebus
hexaquo
azazello
sgoetz
stefanorb
coela
Thaverkamp
barriot
druvus
JeremyZucker
klager
MetabolicModeling
AbstractBACKGROUND:The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.DESCRIPTION:We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an ... | |
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Genome Biology, Vol. 8, No. 3. (09 March 2007), R34.
posted by
14 people
darian
n00c
joule
Thaverkamp
hpaces
orzenil
GustavoLacerda
natstreet
druvus
stajich
azazello
Mycology
gatech-compgenomics
Neeperando
AbstractGenome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting assembly errors. Users can analyze all levels of an assembly along with summary statistics and assembly metrics, and are guided by a ranking component towards likely mis-assemblies. Hawkeye is freely available and released as part of the open source AMOS project http://amos.sourceforge.net/hawkeye. ... | |
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BMC Bioinformatics, Vol. 8, No. 1. (26 February 2007), 64.
posted by
8 people
GustavoLacerda
michaelbarton
n00c
druvus
azazello
Neeperando
Thaverkamp
eckart_bindewald
AbstractBACKGROUND:Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run.RESULTS:We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs ... | |
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Genome research, Vol. 12, No. 4. (1 April 2002), pp. 656-664.
posted by
41 people
azazello
rshe
dchughes
rdowell
LabDros
gwallau
druvus
aprasad
maria_hauser
n00c
sficklin
Thaverkamp
cpwardell
BergmanLab
daveGerrard
coela
daforerog
pwais
umit
mmartin
paszkows
operon
miguel
pcahan1
Ayest
indigoviolet
mtagaya
treangen
michC
djkt
timflutre
olympos
cjeans
wenhan
natstreet
antonkratz
EisenLab
yoanjacquemin
talponer
bozdagd
gpappas
AbstractAnalyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. ... | |
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PLoS ONE, Vol. 3, No. 10. (8 October 2008), e3373.
posted by
16 people
gaosong0329
michaelbarton
Mycology
stajich
jonilaserson
BergmanLab
polivares
idoerg
sriesenfeld
iSEEM
skembel
guhjy
azazello
hpaces
druvus
nuin
AbstractThe new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. ... | |
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Nature, Vol. 411, No. 6839. (14 June 2001), pp. 786-789.
posted by
8 people
hwright
microbiology_nijmegen
kinestetika
azazello
bluto
jdelcampo
beatrizfernandez
Microbial-Ecology
AbstractProteorhodopsin, a retinal-containing integral membrane protein that functions as a light-driven proton pump, was discovered in the genome of an uncultivated marine bacterium; however, the prevalence, expression and genetic variability of this protein in native marine microbial populations remain unknown. Here we report that photoactive proteorhodopsin is present in oceanic surface waters. We also provide evidence of an extensive family of globally distributed proteorhodopsin variants. The protein pigments comprising this rhodopsin family seem to be spectrally tuned to different habitats--absorbing light ... | |
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PLoS Biol, Vol. 4, No. 11. (7 November 2006), e368.
by Florent E. Angly, Ben Felts, Mya Breitbart, et al.Peter Salamon, Robert A. Edwards, Craig Carlson, Amy M. Chan, Matthew Haynes, Scott Kelley, Hong Liu, Joseph M. Mahaffy, Jennifer E. Mueller, Jim Nulton, Robert Olson, Rachel Parsons, Steve Rayhawk, Curtis A. Suttle, Forest Rohwer
AbstractViruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness� quality ... | |
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Proceedings of the National Academy of Sciences, Vol. 105, No. 10. (11 March 2008), pp. 3805-3810.
by Jorge Frias-Lopez, Yanmei Shi, Gene W. Tyson, et al.Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm, Edward F. DeLong
posted by
14 people
hwright
druvus
elbrodie
idoerg
bluto
skembel
mcox
tmmurali
vaulot
mjetten
microbiology_nijmegen
jlgreen
Green Lab
iSEEM
Abstract10.1073/pnas.0708897105 Metagenomics is expanding our knowledge of the gene content, functional significance, and genetic variability in natural microbial communities. Still, there exists limited information concerning the regulation and dynamics of genes in the environment. We report here global analysis of expressed genes in a naturally occurring microbial community. We first adapted RNA amplification technologies to produce large amounts of cDNA from small quantities of total microbial community RNA. The fidelity of the RNA amplification procedure was validated with cultures and ... | |
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Nucleic acids research, Vol. 36, No. Database issue. (11 January 2008), pp. D480-484.
by Minoru Kanehisa, Michihiro Araki, Susumu Goto, et al.Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi
posted by
36 people
cdsouthan
GustavoLacerda
bertelsen
dadiamah
ajsferreira
Thaverkamp
sjcockell
JeremyZucker
jperkins
vkwn
pablocarb
VGreiff
mqbphcw3
karinlag
robert85
peterli
jjray
schwartzjmc
ubcg08l
allysonlister
YukaH
Cortel
coela
daforerog
reyez
namunet
irenas
guhjy
raiyar
barriot
renatomilani
shung
hpaces
massivemayhem
natstreet
TheresaNiederberger
AbstractKEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target ... | |
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Genome Biology, Vol. 8 (06 December 2007), R259.
by Christophe Six, Jean-Claude Thomas, Laurence Garczarek, et al.Martin Ostrowski, Alexis Dufresne, Nicolas Blot, David J. Scanlan, Frederic Partensky
posted by
3 people
cjeans
Microbial-Ecology
Thaverkamp
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Freshwater Biology, Vol. 0, No. 0. (0), pp. ???-???.
by Aaike D. E. Wever, Koenraad Muylaert, Denis Langlet, et al.Laurent Alleman, Pierre J. E. A. N. Descy, L. U. C. Andre, Christine Cocquyt, W. I. M. Vyverman
posted by
4 people
Stenuite
Microbial-Ecology
Thaverkamp
andrewirwin
AbstractSummary 1. In order to evaluate limitation of different phytoplankton groups by inorganic nutrients, multiple nutrient enrichment bioassays using the addition of iron (Fe) and the combined addition of nitrogen and phosphorus (NP) were carried out in the north and the south of Lake Tanganyika during the rainy and dry seasons in 2003 and 2004. 2. Nutrient additions resulted in an increase in phytoplankton growth rate relative to control treatments in all experiments. HPLC pigment data and epifluorescence microscopy counts indicated ... | |
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PLoS ONE, Vol. 2, No. 12. (2007)
AbstractProchlorococcus and Synechococcus picocyanobacteria are dominant contributors to marine primary production over large areas of the ocean. Phytoplankton cells are entrained in the water column and are thus often exposed to rapid changes in irradiance within the upper mixed layer of the ocean. An upward fluctuation in irradiance can result in photosystem II photoinactivation exceeding counteracting repair rates through protein turnover, thereby leading to net photoinhibition of primary productivity, and potentially cell death. Here we show that the effective cross-section for ... | |
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FEMS Microbiology Ecology, Vol. 62, No. 1. (2007), pp. 64-77.
posted by
4 people
Stenuite
Microbial-Ecology
Thaverkamp
andrewirwin
AbstractAbstract The abundance and distribution of Synechococcus spp. in the autotrophic picoplankton of Lake Constance, were followed in the pelagic and littoral habitat by qPCR over 2 years. One genotype, represented by isolated phycoerythrin-rich strain BO 8807, showed a seasonal distribution pattern in both habitats. Before a stable thermal stratification, the maximum of both the Synechococcus population and genotype BO 8807 occurred at 15 or 20 m water depth in the pelagic habitat. During the summer stratification, when the absolute abundance ... | |
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BMC Bioinformatics, Vol. 9, No. 1. (2008)
posted by
3 people
Microbial-Ecology
Thaverkamp
guhjy
AbstractBACKGROUND:Different algorithms have been proposed to solve various versions of degenerate primer design problem. For one of the most general cases, multiple degenerate primer design problem, very few algorithms exist, none of them satisfying the criterion of designing low number of primers that cover high number of sequences. Besides, the present algorithms require high computation capacity and running time.RESULTS:PAMPS, the method presented in this work, usually results in a 30% reduction in the number of degenerate primers required to cover all ... | |
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Vol. 37, No. 2. (29 January 2010), pp. 151-152.
by Uri Alon
posted by
117 people
clairespahr
darian
Zotero en español
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hayato1234
aaltenburger
CulCog
shangyung
alexloh80
ddayjason
mordiano
jfrazee
roryobrate
PollardWall
tony_c
findroot
z3phyr
logics of knowledge
A_Olympia
uhale
tmmurali
ggailani
JeremyZucker
glynj
hollace
Semantic-Social-Networks
INK-SSCI-SCI@CiteuLike.org
INK-SSCI-SCI
JamesOrbinski
ezm_mada
ianwelch
gvdh
Mnourian
fbergmann
spores
ama600
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agy100
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cianan
vjekos
rodrigofaccioli
TKAB
LondonAnalytics
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tnhh
ingo
applebyb
edutars
cwr
cardiffuni
yyfwuhan
GustavoLacerda
lgevers
guillermina
matatk
marekrud
jfr
geoforester
jketterer
waltonjones
jtcribbs
rebeccamancy
chenmengjie87
VGreiff
martydaniel
xavig
tarasdo
rybal
ddahlem
VisionLab
kristina
herraiz
sby
andreassorge
timread
Drrjhancock
balabu
rettema
djproctor
UniQ
nbhammond
mcc19732001
leegs
silberbauer
Thaverkamp
fungal
iCeGS
GuillaumeFilteau
Boxus
gotrunc
ThomasMichelsen
rodney
loison
leonardo
pigironjoe
ricardoerikson
daveGerrard
FAB-lab
rvosa
schlady
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azwinkau
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druvus
Journal picks
dullhunk
AbstractMotivated group members experience a full sense of choice: of doing what one wants. Such behavior shows high performance, is enjoyable, and enhances innovation. This essay describes principles of building a motivated research group. ... | |
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Bioinformatics In Bioinformatics, Vol. 26, No. 3. (1 February 2010), pp. 401-402.
by Iain Milne, Micha Bayer, Linda Cardle, et al.Paul Shaw, Gordon Stephen, Frank Wright, David Marshall
posted by
14 people
fstrozzi
dakelley
torfinnnome
natstreet
zerojinx
pekrau
Bioinformatics
dswan
GustavoLacerda
darian
orzenil
n00c
Thaverkamp
druvus
AbstractSummary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, ... | |
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Bioinformatics In Bioinformatics, Vol. 26, No. 3. (1 February 2010), pp. 378-384.
AbstractMotivation: Gene Ontology (GO), the de facto standard for representing protein functional aspects, is being used beyond the primary goal for which it is designed: protein functional annotation. It is increasingly used to evaluate large sets of relationships between proteins, e.g. protein-protein interactions or mRNA co-expression, under the assumption that related proteins tend to have the same or similar GO terms. Nevertheless, this assumption only holds for terms representing functional groups with biological significance ( classes'), and not for the ones ... | |
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Nature, Vol. 462, No. 7271. (18 November 2009), pp. 252-252.
posted by
7 people
8_01
yuifu
arthegall
Thaverkamp
druvus
Journal picks
dullhunk
AbstractInformation-sharing resources are essential to biologists and deserve international support. ... | |
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PloS one In PLoS ONE, Vol. 4, No. 11. (11 November 2009), e7710.
by Nobuaki Kono, Kazuharu Arakawa, Ryu Ogawa, et al.Nobuhiro Kido, Kazuki Oshita, Keita Ikegami, Satoshi Tamaki, Masaru Tomita
posted by
11 people
guhjy
fgibson
perkeo
Thaverkamp
druvus
Journal picks
dullhunk
brianb
renatomilani
thomaskelder
neils
AbstractBACKGROUND: Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always ... | |
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Nature Methods, Vol. 6, No. 11s. (15 October 2009), pp. S6-S12.
posted by
26 people
farhat
gdv
jfr
orzenil
dquest
darian
MVEverett
GustavoLacerda
claire_jubin
n00c
idoerg
ajsferreira
pst
owenlancaster
Orengo Group Journal Picks
robertrentzsch
oannes74
Thaverkamp
jasontsai
natstreet
seb1
druvus
chvlyl
GeeSharpMinor
venancio
desany
AbstractThe most important first step in understanding next-generation sequencing data is the initial alignment or assembly that determines whether an experiment has succeeded and provides a first glimpse into the results. In parallel with the growth of new sequencing technologies, several algorithms that align or assemble the large data output of today's sequencing machines have been developed. We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools. ... | |
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BMC bioinformatics, Vol. 10, No. 1. (08 October 2009), 324.
by Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis, Fragiskos N. Kolisis
posted by
12 people
guhjy
bertelsen
tonamswish
Thaverkamp
Orengo Group Journal Picks
sillitoe
trogdor
druvus
ptrobajo
dullhunk
reyez
renatomilani
AbstractBACKGROUND: The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a ... | |
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Molecular Cell, Vol. 35, No. 6. (24 September 2009), pp. 726-728.
by Uri Alon
posted by
337 people
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kirchengast
darian
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MV_KUL
tellis
datom
erisen
eduardosl
cm1acb
6065002
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hollace
wiizane
krisl
RobertSOakes
sgsfak
ceeskan
birukou
wmdeneve
Mnourian
ama600
spores
diogomartins
leomoraes
ypjones
srimandayam
edutars
cardiffuni
ilyashl
geoforester
rabio
waltonjones
jtcribbs
rebeccamancy
rrbarb
konilovsky
ckcheng
yangjustinc
vprieto
xavig
noamross
Integrative_biology_behavior
aubinhon
VisionLab
UAB Human Behavioral Neuroscience
kristina
goborobo
herraiz
sby
andreassorge
lilianvt
christianholz
rettema
bayesian
djproctor
mcc19732001
tariqabdulla
nbhammond
fredclem
Thaverkamp
zhouyu
karimartins
mlee1
Adrira
GuillaumeFilteau
gotrunc
lq408
marub
ommachi
dianella
billhao
rodney
NIlz
isabelpinho
kamilkonowalik
azwinkau
junehlee
shangyung
haiku
lzavala
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binghe
lds2152
dutilh
arinbasu
moernerlab
samjlord
pjmaybank
phoenixzxl
yza0008228
plenum
mcartwri
pgardois
jodeleeuw
Philonski
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skywalkerus02
viren4388
timread
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WeiquanXu
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mittinatten
alun
maxweizhao
akuhn
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iturtle
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viktor21614
michaelbanks
yuifu
luzmagomezb
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gareth
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ZXMYST
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dejang
zahreddin
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kruyvanna
jmchen1011
dmeister
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snichols15
aprasad
nanonan
herrk
hyunjin4jc
alexandreconde
nellygidas
adailtulima
grahampoulter
kizzie
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icq242500260
guhjy
sama535
kangism
ajstuapt
Dijoe
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psique
flydream0428
acockfield
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rdinnage
phildeley
Kaihami
jirak
banus
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isp
Schopfel
ansobol
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eisdur
Borelli
icecrown
Shared Literature Resource of the Microbial Fitness Group - MPI Bremen
kinestetika
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davide_caldo
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thiagomanel
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greenmachine
8_01
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gjuggler
lp2
atlantis2360
gena
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Journal picks
cpeters
tux2000
jdoconnell
smichan
meriemelkaroui
leliavski
eudominguezmartin
janderz8
sdaehne
artaban421
cefa
gvdh
penneyft
welliegirl
bertelsen
thegoose
Brain-like research group
xawen
chriswillmott
nellapower
ishiken
andreff
claudiushauptmann
cermak
bmoores
karthikraman
applebyb
mordiano
Gorzomagnificent
Horduna
ajaymalik
mmwoodman
dbikard
toszko
mthomure
timflutre
cyounkin
marsl0am
jmzhuo
dmorti
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ibre
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Sergey_gerbek
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ddbb12
seneca
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mmborges
GeeSharpMinor
jjjpppfff
zhangfh
andreacapocci
melo_mcr
aaltenburger
iannis
jichok
josephjose
TorstenWaldminghaus
kshameer
rudalert
kvalyi
UWA Science Communication
duel_jetty
allaves
milab@yzu
rabit
fercosber
hax123
iskanbasal
livingthingdan
poojamaj
gonzalez
amynmoore
ramalldf
pvdg
sfalsharif
dill2009
singhsh
rogermug
aha
jarekadam
Jansen04
cgravlee
lkakinami
anuragsethi
flips
robfree
kaliczp
yyfwuhan
luciensamary
elsantosneto
mgaldino
daveGerrard
sandfire
tnhh
lesandrop
munzmarci
pdpcosta
Information Integration Architecture
mxro
wangngu
myriasofo
OliverHarriman
AnthonySoprano
robertlischke
R_C_Cordeiro
daforerog
operon
nandipati
wenhaosparty
jeffcrow
leocmcheung
fgibson
snakehsu
cisevol
BergmanLab
michaelbarton
dna
dullhunk
danilov
m_lew
abellogin
cxshang
grahamc
SantoshKalwar
Xusheng
leonardo
roys
benoitvalley
zchen75
darshan
druvus
Asclepius
Roswell Cancer Crosstalk
Zephyrus
songpku
aalibes
flieder
pedromts
AbstractChoosing good problems is essential for being a good scientist. But what is a good problem, and how do you choose one? The subject is not usually discussed explicitly within our profession. Scientists are expected to be smart enough to figure it out on their own and through the observation of their teachers. This lack of explicit discussion leaves a vacuum that can lead to approaches such as choosing problems that can give results that merit publication in valued journals, resulting ... | |
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Journal of molecular biology, Vol. 388, No. 2. (1 May 2009), pp. 390-414.
posted by
3 people
Thaverkamp
druvus
ptrobajo
AbstractMetabolic databases contain information about thousands of small molecules and reactions, which can be represented as networks. In the context of metabolic reconstruction, pathways can be inferred by searching optimal paths in such networks. A recurrent problem is the presence of pool metabolites (e.g., water, energy carriers, and cofactors), which are connected to hundreds of reactions, thus establishing irrelevant shortcuts between nodes of the network. One solution to this problem relies on weighted networks to penalize highly connected compounds. A more ... | |
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BMC genomics, Vol. 10, No. 1. (2009), 400.
AbstractBACKGROUND: New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling ... | |
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Genome research, Vol. 19, No. 11. (29 November 2009), pp. 2125-2132.
posted by
32 people
jfr
humburg
hzoltan
darian
dakelley
tonamswish
inesdesantiago
Thaverkamp
BergmanLab
idonaldson
heliopais
owhitney
GustavoLacerda
ngehlenborg
sandfire
fpattyn
xianjun
katholt
stubrown
orzenil
operon
guhjy
kongl
Mycology
stajich
n00c
torfinnnome
nuin
kshameer
neils
druvus
natstreet
AbstractSequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region ... | |
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PLoS ONE, Vol. 4, No. 7. (28 July 2009), e6323.
posted by
26 people
sujaikumar
RGRutledge
Mycology
stajich
justinhjohnson
meanerelk
torfinnnome
hzoltan
darian
debasis
mqbphcw3
stubrown
Thaverkamp
PabloMarin
jasontsai
Journal picks
ThomasDOtto
heliopais
guhjy
JLab
BergmanLab
cisevol
n00c
natstreet
druvus
jbhiatt
AbstractMassively parallel sequencing offers an enormous potential for expression profiling, in particular for interspecific comparisons. Currently, different platforms for massively parallel sequencing are available, which differ in read length and sequencing costs. The 454-technology offers the highest read length. The other sequencing technologies are more cost effective, on the expense of shorter reads. Reliable expression profiling by massively parallel sequencing depends crucially on the accuracy to which the reads could be mapped to the corresponding genes. ... | |
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Genome Research, Vol. 19, No. 8. (5 August 2009), pp. 1450-1454.
posted by
4 people
iSEEM
djkt
Thaverkamp
druvus
Abstract10.1101/gr.091785.109 Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the contribution of genetic drift to genome evolution is problematic because the usual methods, based on intraspecific polymorphisms, can be thwarted by difficulties in delineating species' boundaries. The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. ... | |
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BMC research notes, Vol. 2, No. 1. (16 July 2009), 138.
by Ingo Wassink, Han Rauwerda, Pieter B. Neerincx, et al.Paul E. van der Vet, Timo M. Breit, Jack A. Leunissen, Anton Nijholt
AbstractBACKGROUND: R is the statistical language commonly used by many life scientists in (omics) data analysis. At the same time, these complex analyses benefit from a workflow approach, such as used by the open source workflow management system Taverna. However, Taverna had limited support for R, because it supported just a few data types and only a single output. Also, there was no support for graphical output and persistent sessions. Altogether this made using R in Taverna impractical. FINDINGS: We have ... | |
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Bioinformatics, Vol. 25, No. 17. (1 September 2009), pp. 2271-2278.
by Victor M. Markowitz, Konstantinos Mavromatis, Natalia N. Ivanova, I-Min A. Chen, Ken Chu, Nikos C. Kyrpides
posted by
7 people
michaelbarton
pajanne
kiekyon
Thaverkamp
neils
natstreet
druvus
AbstractMotivation: A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. Results: We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. ... | |
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PLoS ONE, Vol. 4, No. 6. (4 June 2009), e5797.
by Iain Anderson, Luke E. Ulrich, Boguslaw Lupa, et al.Dwi Susanti, Iris Porat, Sean D. Hooper, Athanasios Lykidis, Magdalena Sieprawska-Lupa, Lakshmi Dharmarajan, Eugene Goltsman, Alla Lapidus, Elizabeth Saunders, Cliff Han, Miriam Land, Susan Lucas, Biswarup Mukhopadhyay, William B. Whitman, Carl Woese, James Bristow, Nikos Kyrpides
posted by
1 person
Thaverkamp
Abstract<sec> <title>Background</title> <p>Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens.</p> </sec><sec> <title>Methodology/Principal Findings</title> <p>In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, <italic>Methanocorpusculum labreanum</italic> Z and <italic>Methanoculleus marisnigri</italic> JR1, and compared them with the genome of a third, <italic>Methanospirillum hungatei</italic> JF-1. Similar to Class ... | |
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Genome Biology, Vol. 10, No. 6. (05 June 2009), R61.
by Shiri Freilich, Anat Kreimer, Elhanan Borenstein, et al.Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin
posted by
10 people
bovee
michaelbarton
seamudbug
Winzer
tomhebbron
Microbial-Ecology
Thaverkamp
druvus
iSEEM
jlgreen
AbstractBACKGROUND:The growth-rate of an organism is an important phenotypic trait, directly affecting its ability to survive in a given environment. Here we present the first large scale computational study of the association between ecological strategies and growth rate across 113 bacterial species, occupying a variety of metabolic habitats. Genomic data are used to reconstruct the species' metabolic networks and habitable metabolic environments. These reconstructions are then used to investigate the typical ecological strategies taken by organisms in terms of two basic ... | |
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Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 21. (26 May 2009), pp. 8605-8610.
posted by
2 people
michaelbarton
Thaverkamp
AbstractVariation in gene content has been hypothesized to be the primary mode of adaptive evolution in microorganisms; however, very little is known about the spatial and temporal distribution of variable genes. Through population-scale comparative genomics of 7 Sulfolobus islandicus genomes from 3 locations, we demonstrate the biogeographical structure of the pan-genome of this species, with no evidence of gene flow between geographically isolated populations. The evolutionary independence of each population allowed us to assess genome dynamics over very recent evolutionary time, ... | |
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BMC bioinformatics, Vol. 10, No. 1. (2009), 161.
posted by
19 people
tonamswish
heliopais
Thaverkamp
bertelsen
dipenps
sotacam
GustavoLacerda
guhjy
Bioinformatics
dswan
ptrobajo
VGreiff
thegoose
vinithepooh
kshameer
renatomilani
cassj
Mycology
stajich
AbstractBACKGROUND: Gene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has established major advantages over individual gene analyses, including greater robustness, sensitivity and biological relevance. However, previous GSA methods have limited usage as they cannot handle datasets of different sample sizes or experimental designs. RESULTS: To address these limitations, we present a new GSA method called Generally Applicable Gene-set Enrichment (GAGE). We successfully apply ... | |
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BMC Bioinformatics, Vol. 10, No. 1. (2009), 154.
by Jochen Blom, Stefan Albaum, Daniel Doppmeier, et al.Alfred Puhler, Frank J. Vorholter, Martha Zakrzewski, Alexander Goesmann
posted by
6 people
Thaverkamp
nuin
druvus
operon
Journal picks
AlexBateman
AbstractBACKGROUND:The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons.RESULTS:To support these studies EDGAR - "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" ... | |
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Journal of microbiological methods (11 May 2009)
posted by
2 people
Bioinformatics
Thaverkamp
AbstractMetagenomic studies bypass the requirement of a pure culture for analysis, focusing instead on the genetic information present in a given sample. Metagenomics have been applied to various studies, with objectives ranging from genome reconstruction, gene prospecting and ecology. However, the use of metagenomics in comparative studies has been constrained by sequencing costs and computational limitations. Efforts are underway to improve current sequencing methods and reduce the expense involved. We suggest an alternative approach - pretreatment of the sample of interest ... | |
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Nature, Vol. 459, No. 7244. (14 May 2009), pp. 166-167.
posted by
2 people
Microbial-Ecology
Thaverkamp
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Nature, Vol. 459, No. 7244. (14 May 2009), pp. 185-192.
posted by
4 people
wiktorj
omc11
Microbial-Ecology
Thaverkamp
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BMC genomics, Vol. 10, No. 1. (2009), 219.
by Eli Meyer, Galina V. Aglyamova, Shi Wang, et al.Jade Buchanan-Carter, David Abrego, John K. Colbourne, Bette L. Willis, Mikhail V. Matz
posted by
10 people
sujaikumar
transptomics
avilella
orzenil
mlog
jonilaserson
Mycology
stajich
Thaverkamp
idoerg
AbstractBACKGROUND: New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of ... | |
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Science, Vol. 324, No. 5924. (10 April 2009), pp. 268-272.
by Alexandra Z. Worden, Jae-Hyeok Lee, Thomas Mock, et al.Pierre Rouze, Melinda P. Simmons, Andrea L. Aerts, Andrew E. Allen, Marie L. Cuvelier, Evelyne Derelle, Meredith V. Everett, Elodie Foulon, Jane Grimwood, Heidrun Gundlach, Bernard Henrissat, Carolyn Napoli, Sarah M. McDonald, Micaela S. Parker, Stephane Rombauts, Aasf Salamov, Peter Von Dassow, Jonathan H. Badger, Pedro M. Coutinho, Elif Demir, Inna Dubchak, Chelle Gentemann, Wenche Eikrem, Jill E. Gready, Uwe John, William Lanier, Erika A. Lindquist, Susan Lucas, Klaus F. X. Mayer, Herve Moreau, Fabrice Not, Robert Otillar, Olivier Panaud, Jasmyn Pangilinan, Ian Paulsen, Benoit Piegu, Aaron Poliakov, Steven Robbens, Jeremy Schmutz, Eve Toulza, Tania Wyss, Alexander Zelensky, Kemin Zhou, E. Virginia Armbrust, Debashish Bhattacharya, Ursula W. Goodenough, Yves Van de Peer, Igor V. Grigoriev
posted by
3 people
dandaman
operon
Thaverkamp
AbstractPicoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their ... | |
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Nature Biotechnology, Vol. 27, No. 5. (01 May 2009), pp. 455-457.
posted by
43 people
robsyme
sandfire
viren4388
meanerelk
justinhjohnson
michaelbarton
frohike
agbiotec
burak
cthachuk
hzoltan
tonamswish
heliopais
giovenko
Bioinformatics
jfr
torfinnnome
daforerog
jonilaserson
Chinnaiyan Lab
mkiyer
Annab
darian
BergmanLab
polivares
SIMR bioinformatics
ghattem
kiekyon
n00c
GeeSharpMinor
guhjy
nuin
reyez
orzenil
Thaverkamp
natstreet
druvus
fenghezi
Bioinformatics - CRUK
Stew
inesdesantiago
idonaldson
neils
AbstractA new generation of DNA sequencers that can rapidly and inexpensively sequence billions of bases is transforming genomic science. These new machines are quickly becoming the technology of choice for whole-genome sequencing and for a variety of sequencing-based assays, including gene expression, DNA-protein interaction, human resequencing and RNA splicing studies. ... | |
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Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W435-440.
by Hong S. Ooi, Chia Y. Kwo, Michael Wildpaner, et al.Fernanda L. Sirota, Birgit Eisenhaber, Sebastian Maurer-Stroh, Wing C. Wong, Alexander Schleiffer, Frank Eisenhaber, Georg Schneider
posted by
6 people
nlapalu
Thaverkamp
druvus
dullhunk
guhjy
renatomilani
AbstractFunction prediction of proteins with computational sequence analysis requires the use of dozens of prediction tools with a bewildering range of input and output formats. Each of these tools focuses on a narrow aspect and researchers are having difficulty obtaining an integrated picture. ANNIE is the result of years of close interaction between computational biologists and computer scientists and automates an essential part of this sequence analytic process. It brings together over 20 function prediction algorithms that have proven sufficiently reliable ... | |
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BMC genomics, Vol. 10 (29 April 2009), 203.
posted by
5 people
sujaikumar
Mycology
stajich
Schmidtc
Thaverkamp
AbstractBACKGROUND: Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads. RESULTS: Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 ... | |
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Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 457-469.
posted by
3 people
operon
calderonv
Thaverkamp
AbstractNucleotide sequences of microbial genomes provide evidence that genes have been shared among organisms, a phenomenon known as lateral genetic transfer (LGT). Hypotheses about the importance of LGT in the evolution and diversification of microbes can be tested by analyzing the extensive quantities of sequence data now available. Some analysis methods identify genes with sequence features that differ from those of the surrounding genome, whereas other methods are based on inference and comparison of phylogenetic trees. A large-scale search for LGT ... | |
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Journal of bioinformatics and computational biology, Vol. 6, No. 6. (December 2008), pp. 1193-1211.
posted by
2 people
Nagy
Thaverkamp
AbstractShort-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational ... | |
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Methods in molecular biology (Clifton, N.J.), Vol. 395 (2007), pp. 17-34.
by D. Karolchik, G. Bejerano, A. S. Hinrichs, et al.R. M. Kuhn, W. Miller, K. R. Rosenbloom, A. S. Zweig, D. Haussler, W. J. Kent
posted by
1 person
Thaverkamp
AbstractComparative analysis of DNA sequence from multiple species can provide insights into the function and evolutionary processes that shape genomes. The University of California Santa Cruz (UCSC) Genome Bioinformatics group has developed several tools and methodologies in its study of comparative genomics, many of which have been incorporated into the UCSC Genome Browser (http://genome.ucsc.edu), an easy-to-use online tool for browsing genomic data and aligned annotation "tracks" in a single window. The comparative genomics annotations in the browser include pairwise alignments, which ... | |
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Genome Biology, Vol. 10, No. 4. (24 April 2009), R44.
posted by
5 people
jfr
greg
thomaskelder
guhjy
Thaverkamp
AbstractA method is proposed that finds enriched pathways relevant to a studied condition using the measured molecular data and also the structural information of the pathway viewed as a network of nodes and edges. Tests are performed using simulated data and genomic data sets and the method is compared to two existing approaches. The analysis provided demonstrates the method proposed is very competitive with the current approaches and also provides biologically relevant results. ... | |
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BMC Genomics, Vol. 10, No. 1. (2009), 166.
by Pierre E. Fournier, Khalid E. Karkouri, Quentin Leroy, et al.Catherine Robert, Bernadette Giumelli, Patricia Renesto, Cristina Socolovschi, Philippe Parola, Stephane Audic, Didier Raoult
posted by
2 people
Thaverkamp
druvus
AbstractBACKGROUND:The Rickettsia genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent R. prowazekii, which causes epidemic typhus and kills its arthropod host, to the mild pathogen R. africae, the agent of African tick-bite fever, which does not affect the fitness of its tick vector.RESULTS:We evaluated the clonality of R. africae in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 ... | |
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BMC microbiology, Vol. 2 (28 August 2002)
posted by
2 people
florisbuijzen
Thaverkamp
AbstractBACKGROUND: Microorganisms inhabiting subterranean oil fields have recently attracted much attention. Since intact groundwater can easily be obtained from the bottom of underground oil-storage cavities without contamination by surface water, studies on such oil-storage cavities are expected to provide valuable information to understand microbial ecology of subterranean oil fields. RESULTS: DNA was extracted from the groundwater obtained from an oil-storage cavity situated at Kuji in Iwate, Japan, and 16S rRNA gene (16S rDNA) fragments were amplified by PCR using combinations of ... | |
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Journal of microbiological methods, Vol. 53, No. 2. (May 2003), pp. 211-219.
posted by
1 person
Thaverkamp
AbstractDevelopment of fast and accurate methods for monitoring environmental microbial diversity is one of the great challenges in microbiology today. Oligonucleotide probes based on 16S rRNA sequences are widely used to identify bacteria in the environment. However, the successful development of a chip of immobilized 16S rRNA probes for identification of large numbers of species in a single hybridization step has not yet been reported. In reverse sample genome probing (RSGP), labelled total community DNA is hybridized to arrays in which ... | |
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Antonie van Leeuwenhoek, Vol. 77, No. 2. (February 2000), pp. 103-116.
posted by
1 person
Thaverkamp
AbstractAlthough the importance of bacterial activities in oil reservoirs was recognized a long time ago, our knowledge of the nature and diversity of bacteria growing in these ecosystems is still poor, and their metabolic activities in situ largely ignored. This paper reviews our current knowledge about these bacteria and emphasises the importance of the petrochemical and geochemical characteristics in understanding their presence in such environments. ... | |
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Extremophiles : life under extreme conditions, Vol. 12, No. 3. (May 2008), pp. 335-342.
posted by
1 person
Thaverkamp
AbstractBTX (benzene, toluene and xylene) degrading bacteria were isolated from Pacific Ocean sediment and nearshore surface water. In the seawater near a ferry dock, degrading bacteria of a relatively wide diversity were detected, including species of Pseudomonas, Rhodococcus, Exiguobacterium and Bacillus; while species of Bacillus only have been detected from the deep-sea sediment. Most of the isolates showed degradation to more than one compound. Generally better growth was obtained with p-xylene and ethylbenzene than with the other two. All the bacteria ... | |
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Bioscience, biotechnology, and biochemistry, Vol. 72, No. 5. (May 2008), pp. 1388-1393.
posted by
1 person
Thaverkamp
AbstractWe obtained DNA fragments encoding putative aminotransferases possibly involved in the biosynthesis of aminoglycoside antibiotics from deep-sea sediments of the northwest Pacific Ocean by nested PCR, and 34 individual genes (total 89 clones) were identified. About half of the deep-sea sequences showed similarity with genes of known aminoglycoside-producers, but others were deep-sea specific genes. Furthermore, we found that temperature-gradient gel electrophoresis (TGGE) can be an effective tool in the analysis of these DNA fragments. ... | |
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Marine drugs, Vol. 6, No. 1. (2008), pp. 12-24.
posted by
1 person
Thaverkamp
AbstractThe marine environment represents a largely untapped source for isolation of new microorganisms with potential to produce biologically active secondary metabolites. Among such microorganisms, Gram-positive actinomycete bacteria are of special interest, since they are known to produce chemically diverse compounds with a wide range of biological activities. We have set out to isolate and characterize actinomycete bacteria from the sediments in one of the largest Norwegian fjords, the Trondheim fjord, with respect to diversity and antibiotic-producing potential. Approximately 3,200 actinomycete bacteria ... | |
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Systematic and applied microbiology, Vol. 32, No. 1. (February 2009), pp. 17-26.
posted by
1 person
Thaverkamp
AbstractThis study is the first culture-independent report on the regional variability of bacterial diversity in oxic sediments from the unexplored southern Cretan margin (SCM). Three main deep basins (water column depths: 2670-3603m), located at the mouth of two submarine canyons (Samaria Gorge and Paximades Channel) and an adjacent slope system, as well as two shallow upper-slope stations (water column depths: 215 and 520m), were sampled. A total of 454 clones were sequenced and the bacterial richness, estimated through five clone libraries ... | |
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The ISME journal (12 March 2009)
by Sandra Schöttner, Friederike Hoffmann, Christian Wild, Hans Tore T. Rapp, Antje Boetius, Alban Ramette
posted by
1 person
Thaverkamp
AbstractThe discovery of large ecosystems of cold-water corals (CWC), stretching along continental margins in depths of hundreds to thousands of meters, has raised many questions regarding their ecology, biodiversity and relevance as deep-sea hard-ground habitat. This study represents the first investigation that explicitly targets bacterial diversity from distinct microbial habitats associated with the cosmopolitan reef-building coral Lophelia pertusa, and also compares natural (fjord) and controlled (aquarium) conditions. Coral skeleton surface, coral mucus, ambient seawater and reef sediments clearly showed habitat-specific differences ... | |
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Computational biology and chemistry, Vol. 33, No. 2. (April 2009), pp. 121-136.
by K. Scheibye-Alsing, S. Hoffmann, A. Frankel, et al.P. Jensen, P. F. Stadler, Y. Mang, N. Tommerup, M. J. Gilchrist, A-B B. Nygård, S. Cirera, C. B. Jørgensen, M. Fredholm, J. Gorodkin
posted by
11 people
xueliangwei
darian
GustavoLacerda
n00c
katholt
orzenil
guhjy
natstreet
Thaverkamp
robsyme
druvus
AbstractDespite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive ... | |
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Genome biology, Vol. 10, No. 4. (15 April 2009), R36.
posted by
8 people
barriot
johnwhitaker
michaelbarton
Microbial-Ecology
Thaverkamp
cmzmasek
neils
biomcgary
AbstractBACKGROUND: Metabolic networks are responsible for many essential cellular processes, and exhibit a high level of evolutionary conservation from bacteria to eukaryotes. If genes encoding metabolic enzymes are horizontally transferred and are advantageous, they are likely to become fixed. Horizontal gene transfer (HGT) has played a key role in prokaryotic evolution and its importance in eukaryotes is increasingly evident. High levels of endosymbiotic gene transfer (EGT) accompanied the establishment of plastids and mitochondria, and more recent events have allowed further acquisition ... | |
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Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1424-1425.
by You Jung Kim, Nikhil Teletia, Victor Ruotti, et al.Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson, Jignesh M. Patel
posted by
17 people
bsamal
Julien_Fayolle
Bioinformatics
jfr
mmartin
n00c
guhjy
nuin
idonaldson
Journal picks
AlexBateman
bmajoros
humburg
Thaverkamp
druvus
svenrahmann
djkt
AbstractSummary: We have developed a tool, called ProbeMatch, for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike most of the existing tools such as ELAND which only perform ungapped alignments allowing at most two mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to three errors including insertion, deletion and mismatch. To speedup sequence alignment, ProbeMatch uses gapped q-grams and q-grams of various patterns to identify target hits to a query sequence. This ... | |
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Current Opinion in Microbiology, Vol. 8, No. 5. (October 2005), pp. 564-571.
posted by
3 people
druvus
Thaverkamp
AaronDarling
AbstractGenomics influences multiple areas of microbiology, and thus affects key microbiological concepts. Recent reports that describe the large genome and unusual coding capacity of mimivirus, the minimized fungal genomes that contain elements of bacterial metabolism, and the 'signature' eukaryotic proteins in bacteria are introducing grey shades into the black-and-white distinctions between microbial domains. The concept of the 'universal' minimal genome is being challenged, and the ability of minimal genomes to support cellular complexity is under investigation. There have been intriguing insights ... | |
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PLoS Genet, Vol. 5, No. 3. (6 March 2009), e1000406.
posted by
3 people
diamantis
Thaverkamp
trfield
Abstract<title>Author Summary</title> <p>Adaptation by natural selection depends on the spread of novel beneficial mutations, and one of the most important challenges in our understanding of adaptation is to be able to predict how beneficial mutations impact fitness. Here, we investigate the underlying distribution of fitness effects of beneficial mutations that natural selection acts on during the evolution of antibiotic resistance in the opportunistic human pathogen <italic>P. aeruginosa</italic>. When the fitness of the wild type is high, most beneficial mutations have small ... | |
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In Advances in Applied Microbiology Volume 66, Vol. 66 (2009), pp. 141-251.
posted by
2 people
Thaverkamp
florisbuijzen
AbstractOur understanding of the phylogenetic diversity, metabolic capabilities, ecological roles, and community dynamics of oil reservoir microbial communities is far from complete. The lack of appreciation of the microbiology of oil reservoirs can lead to detrimental consequences such as souring or plugging. In contrast, knowledge of the microbiology of oil reservoirs can be used to enhance productivity and recovery efficiency. It is clear that (1) nitrate and/or nitrite addition controls H 2 S production, (2) oxygen injection stimulates hydrocarbon metabolism and ... | |
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Genome Research, Vol. 19, No. 6. (1 June 2009), pp. 1084-1092.
posted by
4 people
Journal picks
ppgardne
Thaverkamp
samgj
Abstract10.1101/gr.089714.108 Identification and characterization of functional elements in the noncoding regions of genomes is an elusive and time-consuming activity whose output does not keep up with the pace of genome sequencing. Hundreds of bacterial genomes lay unexploited in terms of noncoding sequence analysis, although they may conceal a wide diversity of novel RNA genes, riboswitches, or other regulatory elements. We describe a strategy that exploits the entirety of available bacterial genomes to classify all noncoding elements of a selected reference species ... | |
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BMB reports, Vol. 41, No. 11. (30 November 2008), pp. 757-764.
posted by
4 people
Thaverkamp
daforerog
shoshin
guhjy
AbstractThe genomic sequences of a huge number of species have been determined. Typically, these genome sequences and the associated annotation data are accessed through Internet-based genome browsers that offer a user-friendly interface. Intelligent use of the data should expedite biological knowledge discovery. Such activity is collectively called data mining and involves queries that can be simple, complex, and even combinational. Various tools have been developed to make genome data mining available to computational and experimental biologists alike. In this mini-review, some ... | |
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Journal of the Royal Society, Interface / the Royal Society, Vol. 6, No. 31. (6 February 2009), pp. 129-147.
posted by
7 people
operon
bertelsen
richardbickerton
Thaverkamp
druvus
dullhunk
guhjy
AbstractRecent years have seen a huge increase in the generation of genomic and proteomic data. This has been due to improvements in current biological methodologies, the development of new experimental techniques and the use of computers as support tools. All these raw data are useless if they cannot be properly analysed, annotated, stored and displayed. Consequently, a vast number of resources have been created to present the data to the wider community. Annotation tools and databases provide the means to disseminate ... | |
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PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000160.
posted by
23 people
GustavoLacerda
ucbcjbm
pansapiens
kiekyon
Thaverkamp
niallhaslam
daforerog
Zalanszabo
bpcusack
microbiology_nijmegen
Katje
joseph_x_zhou
taguchi
sjcockell
markchen
ptrobajo
chad_davis
druvus
mdstobbe
giovenko
nilanjanroy
reyez
GeeSharpMinor
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Bioinformatics (2008), pp. 125-139.
posted by
2 people
Thaverkamp
inesdesantiago
AbstractThe dynamic structure and functions of genomes are being revealed simultaneously with the progress of genome analyses. Evidence indicating genome regional characteristics (genome annotations in a broad sense) provide the basis for further analyses. Target listing and screening can be effectively performed in silico using such data. This chapter describes steps to obtain publicly available genome annotations or construct new annotations based on your own analyses, as well as an overview of the types of available genome annotations and corresponding resources. ... | |
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BMC Bioinformatics, Vol. 9, No. 1. (07 October 2008), 420.
by Daniel Frank
posted by
9 people
Papers recommended by the Roscoff Plankton Group
Microbial-Ecology
vaulot
iSEEM
jlgreen
Thaverkamp
treangen
ojabado
nuin
AbstractBACKGROUND:Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects.RESULTS:XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of ... | |
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BMC Bioinformatics, Vol. 9, No. 1. (07 October 2008), 419.
posted by
5 people
operon
Bioinformatics
Thaverkamp
cgaugain
barriot
AbstractBACKGROUND:The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. DarkHorse, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability ... | |
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Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 38. (23 September 2008), pp. 14254-14261.
posted by
10 people
sharpton
Thaverkamp
AaronDarling
ilyashl
druvus
operon
inesdesantiago
Mycology
stajich
stringertheory
AbstractWe formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most ... | |
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Cell, Vol. 99 (1999), pp. 133-141.
posted by
4 people
thegoose2
Thaverkamp
C. elegans / WormBase
tharris
AbstractWhile all known natural isolates of C. elegans contain multiple copies of the Tc1 transposon, which are active in the soma, Tc1 transposition is fully silenced in the germline of many strains. We mutagenized one such silenced strain and isolated mutants in which Tc1 had been activated in the germline ("mutators"). Interestingly, many other transposons of unrelated sequence had also become active. Most of these mutants are resistant to RNA interference (RNAi). We found one of the mutated genes, mut-7, to ... | |





