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REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets [article]

Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi
<span title="2020-03-30">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Then, REINDEER constructs and indexes monotigs, which in a nutshell are groups of k-mers of similar abundances. Availability: https://github.com/kamimrcht/REINDEER  ...  Motivation: In this work we present REINDEER, a novel computational method that performs indexing of sequences and records their abundances across a collection of datasets.  ...  Part of the experiments presented in this work were made possible thanks to the EBI computing resources and the Institut Pasteur cluster.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.03.29.014159">doi:10.1101/2020.03.29.014159</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2iw23c2ekfc5vm532ylmd4je3q">fatcat:2iw23c2ekfc5vm532ylmd4je3q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711201401/https://www.biorxiv.org/content/biorxiv/early/2020/03/30/2020.03.29.014159.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/13/1f/131fce92a6ad3782ecf0caa0f385e2e21328b012.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.03.29.014159"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Programme and abstracts - the 12th Nordic Reindeer/Reindeer Husbandry Research Conference, 11-13 March 2002, Kiruna, Sweden

Rolf Egil Haugerud (Editor in chief), Öje Danell, Birgitta Åhman (Issue editors)
<span title="2002-04-01">2002</span> <i title="UiT The Arctic University of Norway"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6uhkqz4urncl3dzbw3ia4ixuim" style="color: black;">Rangifer</a> </i> &nbsp;
In terms of food quality and quantity, the variation in time and space is very large. Within an area, the abundance of food may vary considerably within a time-span of hours.  ...  In longer term, phenological and successional changes in the vegetation add to the variation in food abundance and quality.  ...  One project is devoted to resource use and business economic optimizations of reindeer husbandry firms and reindeer herding districts in competition with other resource users.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7557/2.22.3.1616">doi:10.7557/2.22.3.1616</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6mk4bpntubftfewdyjcslfnijy">fatcat:6mk4bpntubftfewdyjcslfnijy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722201448/https://septentrio.uit.no/index.php/rangifer/article/download/1616/1518" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/28/62285418a6993354a7cefbc9cca1db92bdbea7a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7557/2.22.3.1616"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Programme and abstracts from the 16th Nordic Conference on Reindeer and Reindeer Husbandry Research, 16-18 November 2010, Tromsö, Norway

Rolf Egil Haugerud, Björn Hatteng, Berit M. Nystad Eskonsipo (Editors)
<span title="2010-11-01">2010</span> <i title="UiT The Arctic University of Norway"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6uhkqz4urncl3dzbw3ia4ixuim" style="color: black;">Rangifer</a> </i> &nbsp;
<p>The conference was organized by the Nordic Council for Reindeer Husbandry Research (NOR) and the Centre for Sami Studies (SESAM), University of Troms&oslash;.  ...  The 128 participants shared a well organized conference with 31 lectures and 19 posters at the University of Troms&oslash; 16-18 November 2010.</p>  ...  Acknowledgements This study is financed partly by The Norwegian Reindeer Administration Authorities, ''Development Fund of Reindeer Husbandry", and partly by Norut Tromsø, within the strategic institute  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7557/2.30.2.1092">doi:10.7557/2.30.2.1092</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nzbm6v5k6vejrawwvx3vijvjpu">fatcat:nzbm6v5k6vejrawwvx3vijvjpu</a> </span>
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MetaProFi: A protein-based Bloom filter for storing and querying sequence data for accurate identification of functionally relevant genetic variants [article]

Sanjay Kumar Srikakulam, Sebastian Keller, Fawaz Dabbaghie, Robert Bals, Olga V. Kalinina
<span title="2021-08-13">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We demonstrate the utility of MetaProFi by indexing UniProtKB datasets at organism- and at sequence-level in addition to the indexing of Tara Oceans dataset and the 2585 human RNA-seq experiments, showing  ...  Technological advances of next-generation sequencing present new computational challenges to develop methods to store and query these data in time- and memory-efficient ways.  ...  the Bloom filter matrix efficiently to index all the observed k-mers (presence/absence) for fast queries.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.08.12.456081">doi:10.1101/2021.08.12.456081</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f2amb2lqhnh57jr5nulfvxpzje">fatcat:f2amb2lqhnh57jr5nulfvxpzje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210817014004/https://www.biorxiv.org/content/biorxiv/early/2021/08/13/2021.08.12.456081.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8c/6f/8c6fb22e3ffdc62fcb5df3034f483469d6ed136d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.08.12.456081"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Data structures based on k-mers for querying large collections of sequencing datasets [article]

Camille Marchet, Christina Boucher, Simon J Puglisi, Paul Medvedev, Mikael Salson, Rayan Chikhi
<span title="2019-12-06">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Here we propose an accessible survey of these approaches, which are generally based on representing datasets as sets of k-mers.  ...  Towards this goal, in the last few years several computational approaches have been introduced to index and query large collections of datasets.  ...  The authors are grateful to Jan Holub for feedback on the BOSS section, and to Daniel Gautheret for his comments and corrections.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/866756">doi:10.1101/866756</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ietfkefjmzgkta274kaq5eoiwu">fatcat:ietfkefjmzgkta274kaq5eoiwu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106155925/https://www.biorxiv.org/content/biorxiv/early/2020/07/18/866756.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6e/09/6e09bdbbc7efb0a415f0dbcc97ecae4c42a7b050.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/866756"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Selected abstracts of "Bioinformatics: from Algorithms to Applications 2020" conference

<span title="2020-12-17">2020</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
O5 A rigorous approach to pairwise distance analysis of a protein family via multi-dimensional scaling and its application to the genealogy of squalene synthase paralogues of green algae Acknowledgments  ...  P8 Installing and searching BLAST databases in a data science framework Graham Alvare 1 , Abiel Roche-Lima 2 , Brian Fristensky 3* Acknowledgments This research was supported by the Russian Science  ...  REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. ISMB. 5 Bray, N.L., Pimentel, H., Melsted, P. and Pachter, L., 2016.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03838-2">doi:10.1186/s12859-020-03838-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33327929">pmid:33327929</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2t65jee32rgsnohhdwd7vbwj74">fatcat:2t65jee32rgsnohhdwd7vbwj74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201218114844/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03838-2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/f0/92f03c42851befa11a28cf4d2b2fd1b215f43790.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03838-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Dental calculus as a tool to study the evolution of the oral microbiome in mammals [article]

Jaelle C. Brealey, Henrique G. Leitão, Wenbo Xu, Love Dalén, Katerina Guschanski
<span title="2019-04-03">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Metagenomics sequencing of ancient dental calculus has provided valuable insights in humans, but few studies have attempted to characterise the dental calculus microbiome of non-human animals.  ...  With this new tool in hand, we can now study changes in microbiome composition and function as result of extrinsic and intrinsic processes in host history over millennia.  ...  Acknowledgements We thank Daniela Kalthoff and Emmanuel Gilissen for providing access to the mammalian museum  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/596791">doi:10.1101/596791</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/thnsjijffncxrnlmk2kfqsi6l4">fatcat:thnsjijffncxrnlmk2kfqsi6l4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190504133615/https://www.biorxiv.org/content/biorxiv/early/2019/04/03/596791.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/48/42/4842ab935b08471d76284da4792eaf87f17b970f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/596791"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

A big data approach to metagenomics for all-food-sequencing

Robin Kobus, José M. Abuín, André Müller, Sören Lukas Hellmann, Juan C. Pichel, Tomás F. Pena, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
<span title="2020-03-12">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
We introduce an alignment-free k-mer based method for detection and quantification of species composition in food and other complex biological matters.  ...  In comparison to the established tools CLARK, Kraken2, and Kraken2+Bracken it is superior in terms of false-positive rate and quantification accuracy.  ...  This allows us to employ databases that index large collections of reference genomes efficiently in terms of both construction times and memory consumption.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-3429-6">doi:10.1186/s12859-020-3429-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32164527">pmid:32164527</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sfkob5dcqrb2tfhm6ogjclmlxa">fatcat:sfkob5dcqrb2tfhm6ogjclmlxa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200316134412/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3429-6" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2a/ec/2aecfb273bbba03a46719a07787e8f3b12c8d468.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-3429-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Abstracts of posters

All Authors
<span title="2002-04-01">2002</span> <i title="UiT The Arctic University of Norway"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6uhkqz4urncl3dzbw3ia4ixuim" style="color: black;">Rangifer</a> </i> &nbsp;
Finns i alfabetisk ordning från sidan 55 -Are given in alphabetical order from page 55) A Fysiologi och veterinàrmedicin / Fysiologia, sairaudet ja terveys / Physiology and veterinary medicine 11 st/pres  ...  monimuotoisuus, y.m. / Climate, weather and biological diversity a.o.  ...  In this period we found a positive relation between the NAO winter-index and late autumn calf weights.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7557/2.22.3.1618">doi:10.7557/2.22.3.1618</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ildijoch4vcojncyxuoiv56nbe">fatcat:ildijoch4vcojncyxuoiv56nbe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720210013/https://septentrio.uit.no/index.php/rangifer/article/download/1618/1520" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/3c/ac3c45842b2f9a217453dd4d18cee21f59c82312.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7557/2.22.3.1618"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Multivariate Markovian Modeling of Tuberculosis: Forecast for the United States

Sara Debanne
<span title="">2000</span> <i title="Centers for Disease Control and Prevention (CDC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xfv7rdysezhxpa4oce7jejarnq" style="color: black;">Emerging Infectious Diseases</a> </i> &nbsp;
Public Health England, in collaboration with University of East Anglia, University of Oxford, and the Quadram Institute.  ...  We conducted high-throughput whole-genome sequencing using the Illumina NextSeq 500 system (Illumina, San Diego, CA, USA).  ...  Moose PrP is polymorphic at codon 109 (K/Q) and 209 (M/I), combined in 3 alleles: K 109 M 209 (observed in Europe and North America), Q 109 M 209 (observed in Europe), and K 109 I 209 (observed in North  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3201/eid0602.000207">doi:10.3201/eid0602.000207</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10756148">pmid:10756148</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2640843/">pmcid:PMC2640843</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/772hgyrffffprdrgyiwb7urehe">fatcat:772hgyrffffprdrgyiwb7urehe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191030013411/https://wwwnc.cdc.gov/eid/content/24/12/pdfs/v24-n12.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3201/eid0602.000207"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2640843" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

EMBnet.journal 19 Suppl. A

EMBnet Journal
<span title="2013-05-14">2013</span> <i title="EMBnet Stichting"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/safaaq4uondrvmmn5dstg3qpp4" style="color: black;">EMBnet journal</a> </i> &nbsp;
and Transcription factor binding. binding sites from Genome-Wide sequencing peaks sets. * Javier Santoyo: Challenges in whole exome sequencing to identify disease-causing variants in human rare diseases  ...  Supergenome. of viromes in veterinary and public health settings. * Ignacio Blanquer Blanquer: Supporting NGS pilelines in the cluod. * Luca Pireddu: Automated and traceable processing for large-scale  ...  The authors would also like to acknowledge support of Uppsala Genome Centre and UPPMAX for providing assistance in massive parallel sequencing and computational infrastructure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14806/ej.19.a.689">doi:10.14806/ej.19.a.689</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2xs4bsifarfipopojjerizk3ce">fatcat:2xs4bsifarfipopojjerizk3ce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220228220448/http://journal.embnet.org/index.php/embnetjournal/article/download/689/872" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/66/e4/66e4d60591ca10cef271a852709665c81a5c2ccb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14806/ej.19.a.689"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

BEYOND ANTIMICROBIALS - THE FUTUR OF GUT MICROBIOLOGY

<span title="">2002</span> <i title="EDP Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7vex3t5arfebjfcohm6c5eqdia" style="color: black;">Reproduction nutrition development (Print)</a> </i> &nbsp;
Screening for the presence of tet(W) in diverse ecosystems suggests that it may be as abundant as tet(M) in nature. tet(32) shares 76% amino acid sequence identity with tet(M) and only 68% identity with  ...  Oscillospiraspecific sequences were detected in a broad range of geographically distant ruminant species: North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer.  ...  Native electrophoresis combined with zymograms revealed the presence of CMC-ase and xylanase enzymes in protozoal protein.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1051/rnd/200242001">doi:10.1051/rnd/200242001</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/feyqt4gkyvgzvfok7vfdiujjji">fatcat:feyqt4gkyvgzvfok7vfdiujjji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719190657/https://rnd.edpsciences.org/articles/rnd/pdf/2002/01/rnd200242supl1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/64/c8641c30021bdc11329794020618e693f4248e24.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1051/rnd/200242001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences

Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, Knut Reinert, Universitätsbibliothek Der FU Berlin
<span title="2021-11-09">2021</span>
Raptor uses winnowing minimizers to define a set of representative k-mers, an extension of the interleaved Bloom filters (IBFs) as a set membership data structure and probabilistic thresholding for minimizers  ...  We present Raptor, a system for approximately searching many queries such as next-generation sequencing reads or transcripts in large collections of nucleotide sequences.  ...  ACKNOWLEDGMENTS The authors acknowledge the support of the de.NBI network for bioinformatics infrastructure, the Intel Se-qAn IPCC, the Max Planck Society and the IMPRS for Biology and Computation (BAC  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17169/refubium-32353">doi:10.17169/refubium-32353</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rpqil4j7q5bjfpr7frqw5alzmy">fatcat:rpqil4j7q5bjfpr7frqw5alzmy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220120025200/https://refubium.fu-berlin.de/bitstream/handle/fub188/32629/1-s2.0-S2589004221007501-main.pdf;jsessionid=D100F6DEA2A171DE4D57FFBF4FB4DD09?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/57/39/573972df8ff285e3c8bc1821f59d06650a1ab7fb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17169/refubium-32353"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Hantaviruses: A Global Disease Problem

Connie Schmaljohn
<span title="">1997</span> <i title="Centers for Disease Control and Prevention (CDC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xfv7rdysezhxpa4oce7jejarnq" style="color: black;">Emerging Infectious Diseases</a> </i> &nbsp;
His research focuses on molecular epidemiology and sequence analysis of adenoviruses and enteroviruses with next-generation and di-deoxy Sanger sequencing.  ...  Next-generation, whole-genome sequencing, and sequence data analyses was performed at the Wadsworth Center, NYSDOH.  ...  Patients D, G, K, and N who had acute phase peak antibody titers in the range of 80-160 only had <2fold declines in titer.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3201/eid0302.970202">doi:10.3201/eid0302.970202</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9204290">pmid:9204290</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2627612/">pmcid:PMC2627612</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6id5xpb4tvh7tghx6pjb22qruq">fatcat:6id5xpb4tvh7tghx6pjb22qruq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170718160703/https://wwwnc.cdc.gov/eid/pdfs/vol23no7_pdf-version.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3201/eid0302.970202"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2627612" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cryptococcus gattii

Vanbruseghem
<span title="">2010</span> <i title="Centers for Disease Control and Prevention (CDC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xfv7rdysezhxpa4oce7jejarnq" style="color: black;">Emerging Infectious Diseases</a> </i> &nbsp;
His research focuses on molecular epidemiology and sequence analysis of adenoviruses and enteroviruses with next-generation and di-deoxy Sanger sequencing.  ...  Next-generation, whole-genome sequencing, and sequence data analyses was performed at the Wadsworth Center, NYSDOH.  ...  Patients D, G, K, and N who had acute phase peak antibody titers in the range of 80-160 only had <2fold declines in titer.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3201/eid1602.999999">doi:10.3201/eid1602.999999</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gjt6pu65m5dcdbuccjiguxqlhq">fatcat:gjt6pu65m5dcdbuccjiguxqlhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170718160703/https://wwwnc.cdc.gov/eid/pdfs/vol23no7_pdf-version.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3201/eid1602.999999"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>
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