Genome Res.

ISSN	1549-5469
ISSN-L	1088-9051
IUID	90a037e0136c42729eb2b4b7fc0111ff
Modified	2020-11-27T13:14:05.193Z
Created	2017-05-09T09:12:23.309Z

Year 2024

PubMed DOI Crossref

Visualization and analysis of medically relevant tandem repeats in nanopore sequencing of control cohorts with pathSTR.

De Coster W, Höijer I, Bruggeman I, ..., Ameur A, Rademakers R

Genome Res. 34 (11) 2074-2080 [2024-11-20; online 2024-11-20]

Clinical Genomics Uppsala [Technology development] NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]

PubMed DOI Crossref

Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps.

Bilgrav Saether K, Eisfeldt J, Bengtsson JD, ..., Carvalho CMB, Lindstrand A

Genome Res. 34 (11) 1785-1797 [2024-11-20; online 2024-11-20]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Stockholm [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing.

Eisfeldt J, Higginbotham EJ, Lenner F, ..., Scherer SW, Feuk L

Genome Res. 34 (11) 1763-1773 [2024-11-20; online 2024-11-20]

Bioinformatics Support for Computational Resources [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.

Eisfeldt J, Ameur A, Lenner F, ..., Feuk L, Lindstrand A

Genome Res. 34 (11) 1774-1784 [2024-11-20; online 2024-11-20]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Umeå [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]

PubMed DOI Crossref

Global compositional and functional states of the human gut microbiome in health and disease.

Lee S, Portlock T, Le Chatelier E, ..., Uhlen M, Shoaie S

Genome Res. 34 (6) 967-978 [2024-07-23; online 2024-07-23]

Bioinformatics Support for Computational Resources [Service]

Year 2023

PubMed DOI Crossref

Historical RNA expression profiles from the extinct Tasmanian tiger.

Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR

Genome Res. 33 (8) 1299-1316 [2023-08-00; online 2023-07-18]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2022

PubMed DOI Crossref

Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells.

Geng K, Merino LG, Wedemann L, ..., White RJ, Kutter C

Genome Res. 32 (10) 1876-1891 [2022-10-00; online 2022-09-30]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.

Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S

Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.

Viluma A, Flagstad Ø, Åkesson M, ..., Wabakken P, Ellegren H

Genome Res. 32 (3) 449-458 [2022-03-00; online 2022-02-08]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons.

Gao W, Gallardo-Dodd CJ, Kutter C

Genome Res. 32 (1) 97-110 [2022-01-00; online 2021-12-02]

Bioinformatics Support for Computational Resources [Service]

Year 2021

PubMed DOI Crossref

The Enterprise, a massive transposon carrying Spok meiotic drive genes.

Vogan AA, Ament-Velásquez SL, Bastiaans E, ..., Suh A, Johannesson H

Genome Res. 31 (5) 789-798 [2021-05-00; online 2021-04-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.

Kjellin J, Avesson L, Reimegård J, ..., Schaap P, Söderbom F

Genome Res. 31 (3) 436-447 [2021-03-00; online 2021-01-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Year 2020

PubMed DOI Crossref

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids.

Mugal CF, Wang M, Backström N, ..., Qvarnström A, Ellegren H

Genome Res. 30 (12) 1727-1739 [2020-12-00; online 2020-11-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Year 2019

PubMed DOI Crossref

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.

Wei W, Hennig BP, Wang J, ..., Steinmetz LM, Pelechano V

Genome Res. 29 (12) 1974-1984 [2019-12-00; online 2019-11-18]

Bioinformatics Support for Computational Resources [Service]

PubMed DOI Crossref

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

Pettersson ME, Rochus CM, Han F, ..., Folkvord A, Andersson L

Genome Res. - (-) - [2019-10-24; online 2019-10-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Year 2017

PubMed DOI Crossref

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Han F, Lamichhaney S, Grant BR, ..., Andersson L, Webster MT

Genome Res. 27 (6) 1004-1015 [2017-06-00; online 2017-04-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.

Weissensteiner MH, Pang AWC, Bunikis I, ..., Suh A, Wolf JBW

Genome Res. 27 (5) 697-708 [2017-05-00; online 2017-03-30]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]

Year 2016

PubMed DOI Crossref

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia.

Teppo S, Laukkanen S, Liuksiala T, ..., Heinäniemi M, Lohi O

Genome Res. 26 (11) 1468-1477 [2016-11-00; online 2016-09-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

PubMed DOI Crossref

Direct estimate of the rate of germline mutation in a bird.

Smeds L, Qvarnström A, Ellegren H

Genome Res. 26 (9) 1211-1218 [2016-09-00; online 2016-07-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.

Hagey DW, Zaouter C, Combeau G, ..., Huss M, Muhr J

Genome Res. 26 (7) 908-917 [2016-07-00; online 2016-05-02]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed DOI Crossref

nanoCAGE reveals 5' UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs.

Gandin V, Masvidal L, Hulea L, ..., Larsson O, Topisirovic I

Genome Res. 26 (5) 636-648 [2016-05-00; online 2016-03-18]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2015

PubMed DOI Crossref

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.

Burri R, Nater A, Kawakami T, ..., Török J, Ellegren H

Genome Res. 25 (11) 1656-1665 [2015-11-00; online 2015-09-09]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PubMed DOI Crossref

Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer.

Forsberg LA, Rasi C, Pekar G, ..., Tot T, Dumanski JP

Genome Res. 25 (10) 1521-1535 [2015-10-00; online 2015-10-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

PubMed DOI Crossref

A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin.

Svensson JP, Shukla M, Menendez-Benito V, ..., Allshire RC, Ekwall K

Genome Res. 25 (6) 872-883 [2015-06-00; online 2015-03-18]

Bioinformatics and Expression Analysis (BEA)

Year 2012

PubMed DOI Crossref

A-to-I editing of microRNAs in the mammalian brain increases during development.

Ekdahl Y, Farahani HS, Behm M, Lagergren J, Öhman M

Genome Res. 22 (8) 1477-1487 [2012-08-00; online 2012-05-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Year 2010

PubMed DOI Crossref

Characterization of the RNA content of chromatin.

Mondal T, Rasmussen M, Pandey GK, Isaksson A, Kanduri C

Genome Res. 20 (7) 899-907 [2010-07-00; online 2010-04-21]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

PubMed DOI Crossref

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Jolma A, Kivioja T, Toivonen J, ..., Ukkonen E, Taipale J

Genome Res. 20 (6) 861-873 [2010-06-00; online 2010-04-10]

Karolinska High Throughput Center (KHTC) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

PubMed DOI Crossref

The recombination landscape of the zebra finch Taeniopygia guttata genome.

Backström N, Forstmeier W, Schielzeth H, ..., Kempenaers B, Ellegren H

Genome Res. 20 (4) 485-495 [2010-04-00; online 2010-03-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

PubMed DOI Crossref

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution.

Völker M, Backström N, Skinner BM, ..., Ellegren H, Griffin DK

Genome Res. 20 (4) 503-511 [2010-04-00; online 2010-03-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure