{"entity": "researcher", "timestamp": "2026-10-05T20:48:48.559Z", "family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "affiliations": ["Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04"}}, "publications": [{"entity": "publication", "iuid": "062de5b535954abc89347c8dfaaaf44b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b"}}, "title": "Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.", "authors": [{"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Ye", "given": "Rosa", "initials": "R"}, {"family": "Knudsen", "given": "Bjarne", "initials": "B"}, {"family": "Simonsen", "given": "Martin", "initials": "M"}, {"family": "Turner", "given": "Benjamin", "initials": "B"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "Wu", "given": "Cheng-Cang", "initials": "CC"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-06-06", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "439", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between sequencing costs and assembly quality.\n\nIn order to sequence the genome of Norway spruce, which is of great size and complexity, we developed and applied a new technology based on the massive production, sequencing, and assembly of Fosmid pools (FP). The spruce chromosomes were sampled with ~40,000 bp Fosmid inserts to obtain around two-fold genome coverage, in parallel with traditional whole genome shotgun sequencing (WGS) of haploid and diploid genomes. Compared to the WGS results, the contiguity and quality of the FP assemblies were high, and they allowed us to fill WGS gaps resulting from repeats, low coverage, and allelic differences. The FP contig sets were further merged with WGS data using a novel software package GAM-NGS.\n\nBy exploiting FP technology, the first published assembly of a conifer genome was sequenced entirely with massively parallel sequencing. Here we provide a comprehensive report on the different features of the approach and the optimization of the process.We have made public the input data (FASTQ format) for the set of pools used in this study:ftp://congenie.org/congenie/Nystedt_2013/Assembly/ProcessedData/FosmidPools/.(alternatively accessible via http://congenie.org/downloads).The software used for running the assembly process is available at http://research.scilifelab.se/andrej_alexeyenko/downloads/fpools/.", "doi": "10.1186/1471-2164-15-439", "pmid": "24906298", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1471-2164-15-439"}, {"db": "pmc", "key": "PMC4070561"}], "notes": [], "created": "2017-05-04T14:56:29.797Z", "modified": "2021-07-08T13:26:08.069Z"}, {"entity": "publication", "iuid": "c403f99f84324b52bc5e13ce42920772", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c403f99f84324b52bc5e13ce42920772"}}, "title": "The Norway spruce genome sequence and conifer genome evolution.", "authors": [{"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Vicedomini", "given": "Riccardo", "initials": "R"}, {"family": "Sahlin", "given": "Kristoffer", "initials": "K"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Gramzow", "given": "Lydia", "initials": "L"}, {"family": "Holmberg", "given": "Kristina", "initials": "K"}, {"family": "H\u00e4llman", "given": "Jimmie", "initials": "J"}, {"family": "Keech", "given": "Olivier", "initials": "O"}, {"family": "Klasson", "given": "Lisa", "initials": "L"}, {"family": "Koriabine", "given": "Maxim", "initials": "M"}, {"family": "Kucukoglu", "given": "Melis", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Luthman", "given": "Johannes", "initials": "J"}, {"family": "Lysholm", "given": "Fredrik", "initials": "F"}, {"family": "Niittyl\u00e4", "given": "Totte", "initials": "T"}, {"family": "Olson", "given": "Ake", "initials": "A"}, {"family": "Rilakovic", "given": "Nemanja", "initials": "N"}, {"family": "Ritland", "given": "Carol", "initials": "C"}, {"family": "Rossell\u00f3", "given": "Josep A", "initials": "JA"}, {"family": "Sena", "given": "Juliana", "initials": "J"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Thei\u00dfen", "given": "G\u00fcnter", "initials": "G"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Vanneste", "given": "Kevin", "initials": "K"}, {"family": "Wu", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Zerbe", "given": "Philipp", "initials": "P"}, {"family": "Arvestad", "given": "Lars", "initials": "L"}, {"family": "Bhalerao", "given": "Rishikesh", "initials": "R"}, {"family": "Bohlmann", "given": "Joerg", "initials": "J"}, {"family": "Bousquet", "given": "Jean", "initials": "J"}, {"family": "Garcia Gil", "given": "Rosario", "initials": "R"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "MacKay", "given": "John", "initials": "J"}, {"family": "Morgante", "given": "Michele", "initials": "M"}, {"family": "Ritland", "given": "Kermit", "initials": "K"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Thompson", "given": "Stacey Lee", "initials": "SL"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2013-05-30", "journal": {"volume": "497", "issn": "1476-4687", "issue": "7451", "pages": "579-584", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.", "doi": "10.1038/nature12211", "pmid": "23698360", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "nature12211"}], "notes": [], "created": "2017-05-04T14:56:13.625Z", "modified": "2024-01-16T13:48:50.828Z"}, {"entity": "publication", "iuid": "09a4a465924d40dcb5efe40d27bef7f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09a4a465924d40dcb5efe40d27bef7f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09a4a465924d40dcb5efe40d27bef7f0"}}, "title": "Scalable transcriptome preparation for massive parallel sequencing.", "authors": [{"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Werne", "given": "Beata", "initials": "B"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2011-07-07", "journal": {"volume": "6", "issn": "1932-6203", "issue": "7", "pages": "e21910", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The tremendous output of massive parallel sequencing technologies requires automated robust and scalable sample preparation methods to fully exploit the new sequence capacity.\n\nIn this study, a method for automated library preparation of RNA prior to massively parallel sequencing is presented. The automated protocol uses precipitation onto carboxylic acid paramagnetic beads for purification and size selection of both RNA and DNA. The automated sample preparation was compared to the standard manual sample preparation.\n\nThe automated procedure was used to generate libraries for gene expression profiling on the Illumina HiSeq 2000 platform with the capacity of 12 samples per preparation with a significantly improved throughput compared to the standard manual preparation. The data analysis shows consistent gene expression profiles in terms of sensitivity and quantification of gene expression between the two library preparation methods.", "doi": "10.1371/journal.pone.0021910", "pmid": "21760920", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-00159"}, {"db": "pmc", "key": "PMC3131396"}], "notes": [], "created": "2017-05-04T14:57:26.789Z", "modified": "2021-07-08T13:26:08.080Z"}, {"entity": "publication", "iuid": "e40c4e4e3c504fe7987d32aa7e46b036", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e40c4e4e3c504fe7987d32aa7e46b036.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e40c4e4e3c504fe7987d32aa7e46b036"}}, "title": "Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.", "authors": [{"family": "Hedskog", "given": "Charlotte", "initials": "C"}, {"family": "Mild", "given": "Mattias", "initials": "M"}, {"family": "Jernberg", "given": "Johanna", "initials": "J"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Bratt", "given": "G\u00f6ran", "initials": "G"}, {"family": "Leitner", "given": "Thomas", "initials": "T"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Albert", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2010-07-07", "journal": {"volume": "5", "issn": "1932-6203", "issue": "7", "pages": "e11345", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Ultra-deep pyrosequencing (UDPS) allows identification of rare HIV-1 variants and minority drug resistance mutations, which are not detectable by standard sequencing.\n\nHere, UDPS was used to analyze the dynamics of HIV-1 genetic variation in reverse transcriptase (RT) (amino acids 180-220) in six individuals consecutively sampled before, during and after failing 3TC and AZT containing antiretroviral treatment. Optimized UDPS protocols and bioinformatic software were developed to generate, clean and analyze the data. The data cleaning strategy reduced the error rate of UDPS to an average of 0.05%, which is lower than previously reported. Consequently, the cut-off for detection of resistance mutations was very low. A median of 16,016 (range 2,406-35,401) sequence reads were obtained per sample, which allowed detection and quantification of minority resistance mutations at amino acid position 181, 184, 188, 190, 210, 215 and 219 in RT. In four of five pre-treatment samples low levels (0.07-0.09%) of the M184I mutation were observed. Other resistance mutations, except T215A and T215I were below the detection limit. During treatment failure, M184V replaced M184I and dominated the population in combination with T215Y, while wild-type variants were rarely detected. Resistant virus disappeared rapidly after treatment interruption and was undetectable as early as after 3 months. In most patients, drug resistant variants were replaced by wild-type variants identical to those present before treatment, suggesting rebound from latent reservoirs.\n\nWith this highly sensitive UDPS protocol preexisting drug resistance was infrequently observed; only M184I, T215A and T215I were detected at very low levels. Similarly, drug resistant variants in plasma quickly decreased to undetectable levels after treatment interruption. The study gives important insights into the dynamics of the HIV-1 quasispecies and is of relevance for future research and clinical use of the UDPS technology.", "doi": "10.1371/journal.pone.0011345", "pmid": "20628644", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC2898805"}], "notes": [], "created": "2017-05-04T14:57:14.378Z", "modified": "2021-07-08T13:26:08.381Z"}, {"entity": "publication", "iuid": "96615cb5b131417481f41f74a9157a2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96615cb5b131417481f41f74a9157a2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96615cb5b131417481f41f74a9157a2c"}}, "title": "Whole-genome resequencing reveals loci under selection during chicken domestication.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Zody", "given": "Michael C", "initials": "MC"}, {"family": "Eriksson", "given": "Jonas", "initials": "J"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Jiang", "given": "Lin", "initials": "L"}, {"family": "Ingman", "given": "Max", "initials": "M"}, {"family": "Sharpe", "given": "Ted", "initials": "T"}, {"family": "Ka", "given": "Sojeong", "initials": "S"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}, {"family": "Besnier", "given": "Francois", "initials": "F"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}, {"family": "Bed'hom", "given": "Bertrand", "initials": "B"}, {"family": "Tixier-Boichard", "given": "Mich\u00e8le", "initials": "M"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Siegel", "given": "Paul", "initials": "P"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2010-03-25", "journal": {"volume": "464", "issn": "1476-4687", "issue": "7288", "pages": "587-591", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.", "doi": "10.1038/nature08832", "pmid": "20220755", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "nature08832"}, {"db": "GENBANK", "key": "GU323512"}, {"db": "GENBANK", "key": "GU323513"}, {"db": "GENBANK", "key": "GU323514"}, {"db": "GENBANK", "key": "GU323515"}, {"db": "GENBANK", "key": "GU323516"}, {"db": "GENBANK", "key": "GU323517"}, {"db": "GENBANK", "key": "GU323518"}, {"db": "GENBANK", "key": "GU323519"}, {"db": "GENBANK", "key": "GU323520"}, {"db": "GENBANK", "key": "GU323521"}, {"db": "GENBANK", "key": "GU323522"}, {"db": "GENBANK", "key": "GU323523"}, {"db": "GENBANK", "key": "GU323524"}, {"db": "GENBANK", "key": "GU323525"}, {"db": "GENBANK", "key": "GU323526"}, {"db": "GENBANK", "key": "GU323527"}, {"db": "GENBANK", "key": "GU323528"}, {"db": "GENBANK", "key": "GU323529"}, {"db": "GENBANK", "key": "GU323530"}, {"db": "GENBANK", "key": "GU323531"}, {"db": "GENBANK", "key": "GU323532"}, {"db": "GENBANK", "key": "GU323533"}, {"db": "GENBANK", "key": "GU323534"}, {"db": "GENBANK", "key": "GU323535"}, {"db": "GENBANK", "key": "GU323536"}, {"db": "GENBANK", "key": "GU323537"}, {"db": "GENBANK", "key": "GU323538"}, {"db": "GENBANK", "key": "GU323539"}, {"db": "GENBANK", "key": "GU323540"}, {"db": "GENBANK", "key": "GU323541"}, {"db": "GENBANK", "key": "GU323542"}, {"db": "GENBANK", "key": "GU323543"}, {"db": "GENBANK", "key": "GU323544"}, {"db": "GENBANK", "key": "GU323545"}, {"db": "GENBANK", "key": "GU323546"}, {"db": "GENBANK", "key": "GU323547"}, {"db": "GENBANK", "key": "GU323548"}, {"db": "GENBANK", "key": "GU323549"}, {"db": "GENBANK", "key": "GU323550"}, {"db": "GENBANK", "key": "GU323551"}, {"db": "GENBANK", "key": "GU323552"}, {"db": "GENBANK", "key": "GU323553"}, {"db": "GENBANK", "key": "GU323554"}, {"db": "GENBANK", "key": "GU323555"}, {"db": "GENBANK", "key": "GU323556"}], "notes": [], "created": "2017-05-04T14:57:13.139Z", "modified": "2021-07-07T15:13:59.929Z"}]}