Swiss Institute of Bioinformatics

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1639 publications

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2021
Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer.
Cachot A., Bilous M., Liu Y.C., Li X., Saillard M., Cenerenti M., Rockinger G.A., Wyss T., Guillaume P., Schmidt J. et al., 2021/02. Science advances, 7 (9) pp. eabe3348. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7FDE10B2A046]
Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells.
Kanev K., Roelli P., Wu M., Wurmser C., Delorenzi M., Pfaffl M.W., Zehn D., 2021/01/25. Nature communications, 12 (1) p. 569. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_C79F07ADC7C7]
Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.
Sun C., Huang J., Wang Y., Zhao X., Su L., Thomas GWC, Zhao M., Zhang X., Jungreis I., Kellis M. et al., 2021/01/23. Molecular biology and evolution, 38 (2) pp. 486-501. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7245D0A9D57D]
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.
Altenhoff A.M., Train C.M., Gilbert K.J., Mediratta I., Mendes de Farias T., Moi D., Nevers Y., Radoykova H.S., Rossier V., Warwick Vesztrocy A. et al., 2021/01/08. Nucleic acids research, 49 (D1) pp. D373-D379. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A827EF929B38]
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.
Bastian F.B., Roux J., Niknejad A., Comte A., Fonseca Costa S.S., de Farias T.M., Moretti S., Parmentier G., Rech de Laval V., Rosikiewicz M. et al., 2021/01/08. Nucleic acids research, 49 (D1) pp. D831-D847. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_FD0CF4F734E7]
Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR.
Defosset A., Kress A., Nevers Y., Ripp R., Thompson J.D., Poch O., Lecompte O., 2021/01/07. Genome biology and evolution, 13 (1) pp. evaa248. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_33071923673C]
CIITA-Transduced Glioblastoma Cells Uncover a Rich Repertoire of Clinically Relevant Tumor-Associated HLA-II Antigens.
Forlani G., Michaux J., Pak H., Huber F., Marie Joseph E.L., Ramia E., Stevenson B.J., Linnebacher M., Accolla R.S., Bassani-Sternberg M., 2021. Molecular & cellular proteomics, 20 p. 100032. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_848F6AADEDBE]
 
Computer-Aided Drug Design for Cancer Therapy
Daina Antoine, Röhrig Ute F., Zoete Vincent, 2021. pp. 386-401 dans Systems Medicine, Elsevier.
[DOI][serval:BIB_7CB4A862858D]
 
Efficient phasing and imputation of low-coverage sequencing data using large reference panels
Rubinacci Simone, Ribeiro Diogo M., Hofmeister Robin J., Delaneau Olivier, 2021/01. Nature Genetics, 53 (1) pp. 120-126.
[DOI][Pmid][serval:BIB_179AAEAAD0F6]
 
Evolution or Revolution? Recommendations to Improve the Swiss Health Data Framework.
Martani A., Geneviève L.D., Egli S.M., Erard F., Wangmo T., Elger B.S., 2021. Frontiers in public health, 9 p. 668386. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_43F346B1465D]
 
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.
Litovchenko M., Meireles-Filho ACA, Frochaux M.V., Bevers RPJ, Prunotto A., Anduaga A.M., Hollis B., Gardeux V., Braman V.S., Russeil JMC et al., 2021/01. Science advances, 7 (5) pp. eabc3781. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_DD598AB6CFE4]
 
Function Analysis of MBF1, a Factor Involved in the Response to Amino Acid Starvation and Virulence in Candida albicans.
Amorim-Vaz S., Coste A.T., Tran VDT, Pagni M., Sanglard D., 2021. Frontiers in fungal biology, 2 p. 658899. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_854842775929]
Genome-wide association study identifies 48 common genetic variants associated with handedness.
Cuellar-Partida G., Tung J.Y., Eriksson N., Albrecht E., Aliev F., Andreassen O.A., Barroso I., Beckmann J.S., Boks M.P., Boomsma D.I. et al., 2021/01. Nature human behaviour, 5 (1) pp. 59-70. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E7424914D13E]
Guidelines for Biobanking of Bone Marrow Adipose Tissue and Related Cell Types: Report of the Biobanking Working Group of the International Bone Marrow Adiposity Society.
Lucas S., Tencerova M., von der Weid B., Andersen T.L., Attané C., Behler-Janbeck F., Cawthorn W.P., Ivaska K.K., Naveiras O., Podgorski I. et al., 2021. Frontiers in endocrinology, 12 p. 744527. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C15C8E462E06]
 
Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication
Begum Tina, Serrano-Serrano Martha Liliana, Robinson-Rechavi Marc, 2021. Methods Ecol Evol, 12 pp. 1875-1887. Peer-reviewed.
[DOI][serval:BIB_E6A0AF8DC9DE]
Pericytes regulate vascular immune homeostasis in the CNS.
Török O., Schreiner B., Schaffenrath J., Tsai H.C., Maheshwari U., Stifter S.A., Welsh C., Amorim A., Sridhar S., Utz S.G. et al., 2021. Proceedings of the National Academy of Sciences of the United States of America, 118 (10) pp. e2016587118. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_2E291B9300F3]
Querying knowledge graphs in natural language.
Liang S., Stockinger K., de Farias T.M., Anisimova M., Gil M., 2021. Journal of big data, 8 (3) pp. 1-23. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_673D6C6C570E]
Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction.
Pak H., Michaux J., Huber F., Chong C., Stevenson B.J., Müller M., Coukos G., Bassani-Sternberg M., 2021. Molecular & cellular proteomics, 20 p. 100080. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DCFCF966CE50]
 
Statistical mediation of the relationships between chronological age and lipoproteins by nonessential amino acids in healthy men.
Mallol R., Vallvé J.C., Solà R., Girona J., Bergmann S., Correig X., Rock E., Winklhofer-Roob B.M., Rehues P., Guardiola M. et al., 2021. Computational and structural biotechnology journal, 19 pp. 6169-6178. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_42131A1ECFEA]
Summary Visualizations of Gene Ontology Terms With GO-Figure!
Reijnders MJMF, Waterhouse R.M., 2021. Frontiers in bioinformatics, 1 p. 638255. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_488C95053B55]
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients.
Bibert S., Guex N., Lourenco J., Brahier T., Papadimitriou-Olivgeris M., Damonti L., Manuel O., Liechti R., Götz L., Tschopp J. et al., 2021. Frontiers in immunology, 12 p. 666163. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_91CEC9119F7E]
UCell: Robust and scalable single-cell gene signature scoring.
Andreatta M., Carmona S.J., 2021. Computational and structural biotechnology journal, 19 pp. 3796-3798. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_ADC3FAC598DC]
Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery.
Baumgaertner P., Sankar M., Herrera F.G, Benedetti F., Barras D., Thierry A.C., Dangaj D., Kandalaft L.E., Coukos G., Xenarios I. et al., 2021. Frontiers in immunology, 12 p. 633910. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E707FFE34C52]
2020
 
Exploring chromatin conformation and gene co-expression through graph embedding.
Varrone M., Nanni L., Ciriello G., Ceri S., 2020/12/30. Bioinformatics, 36 (Supplement_2) pp. i700-i708. Peer-reviewed.
[DOI][Pmid][serval:BIB_8E078623E130]
Whole-exome Sequencing for the Identification of Rare Variants in Primary Immunodeficiency Genes in Children With Sepsis: A Prospective, Population-based Cohort Study.
Borghesi A., Trück J., Asgari S., Sancho-Shimizu V., Agyeman PKA, Bellos E., Giannoni E., Stocker M., Posfay-Barbe K.M., Heininger U. et al., 2020/12/17. Clinical infectious diseases, 71 (10) pp. e614-e623. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D6F373E4D323]
 
Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products.
Ricart E., Pupin M., Müller M., Lisacek F., 2020/12/15. Analytical chemistry, 92 (24) pp. 15862-15871. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AE3479B45287]
A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor
Benton R., Dessimoz C., Moi D., 2020/12/04. eLife, 9 pp. e62507.
[URN][DOI][Pmid][serval:BIB_C2A3842B891D]
Single-cell transcriptomics allows novel insights into aging and circadian processes.
Fonseca Costa S.S., Robinson-Rechavi M., Ripperger J.A., 2020/12/04. Briefings in functional genomics, 19 (5-6) pp. 343-349. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0223DAE8F649]
Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest
Sparks Michael E., Bansal Raman, Benoit Joshua B., Blackburn Michael B., Chao Hsu, Chen Mengyao, Cheng Sammy, Childers Christopher, Dinh Huyen, Doddapaneni Harsha Vardhan et al., 2020/12. BMC Genomics, 21 (1) p. 227. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_EA867D964FB3]
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
Waterhouse Robert M., Aganezov Sergey, Anselmetti Yoann, Lee Jiyoung, Ruzzante Livio, Reijnders Maarten J. M. F., Feron Romain, Bérard Sèverine, George Phillip, Hahn Matthew W. et al., 2020/12. BMC Biology, 18 (1). Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_223C09C9C506]
Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups
Szucsich Nikolaus U., Bartel Daniela, Blanke Alexander, Böhm Alexander, Donath Alexander, Fukui Makiko, Grove Simon, Liu Shanlin, Macek Oliver, Machida Ryuichiro et al., 2020/12. BMC Evolutionary Biology, 20 (1) p. 144. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_F85F0DF2857A]
 
Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity.
Yaghootkar H., Zhang Y., Spracklen C.N., Karaderi T., Huang L.O., Bradfield J., Schurmann C., Fine R.S., Preuss M.H., Kutalik Z. et al., 2020/12. Diabetes, 69 (12) pp. 2806-2818. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_99AF60202BCB]
Genome-enabled insights into the biology of thrips as crop pests
Rotenberg Dorith, Baumann Aaron A., Ben-Mahmoud Sulley, Christiaens Olivier, Dermauw Wannes, Ioannidis Panagiotis, Jacobs Chris G. C., Vargas Jentzsch Iris M., Oliver Jonathan E., Poelchau Monica F. et al., 2020/12. BMC Biology, 18 (1). Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_FBC6CD523028]
 
Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors.
Bakker M.K., van der Spek RAA, van Rheenen W., Morel S., Bourcier R., Hostettler I.C., Alg V.S., van Eijk K.R., Koido M., Akiyama M. et al., 2020/12. Nature genetics, 52 (12) pp. 1303-1313. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9D97AC434D8D]
Greater topoclimatic control of above- versus below-ground communities.
Mod H.K., Scherrer D., Di Cola V., Broennimann O., Blandenier Q., Breiner F.T., Buri A., Goudet J., Guex N., Lara E. et al., 2020/12. Global change biology, 26 (12) pp. 6715-6728. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_858D58CF6336]
 
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes.
Bosi E., Marselli L., De Luca C., Suleiman M., Tesi M., Ibberson M., Eizirik D.L., Cnop M., Marchetti P., 2020/12. NAR genomics and bioinformatics, 2 (4) pp. lqaa097. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5F65528ED583]
 
Molecular homology between canine spontaneous oral squamous cell carcinomas and human head-and-neck squamous cell carcinomas reveals disease drivers and therapeutic vulnerabilities.
Guscetti F., Nassiri S., Beebe E., Rito Brandao I., Graf R., Markkanen E., 2020/12. Neoplasia, 22 (12) pp. 778-788. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6ADE166E2DDA]
Persistent or Transient Human β Cell Dysfunction Induced by Metabolic Stress: Specific Signatures and Shared Gene Expression with Type 2 Diabetes.
Marselli L., Piron A., Suleiman M., Colli M.L., Yi X., Khamis A., Carrat G.R., Rutter G.A., Bugliani M., Giusti L. et al., 2020/12/01. Cell reports, 33 (9) p. 108466. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EA019EC4C301]
 
Expert recommendation from the Swiss Amyloidosis Network (SAN) for systemic AL-amyloidosis.
Schwotzer R., Flammer A.J., Gerull S., Pabst T., Arosio P., Averaimo M., Bacher V.U., Bode P., Cavalli A., Concoluci A. et al., 2020/11/30. Swiss medical weekly, 150 pp. w20364. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BFDED8F49F10]
 
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test
Dylus David, Pillonel Trestan, Opota Onya, Wüthrich Daniel, Seth-Smith Helena M. B., Egli Adrian, Leo Stefano, Lazarevic Vladimir, Schrenzel Jacques, Laurent Sacha et al., 2020/11/24. Frontiers in Microbiology, 11. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_347E9A7AF57F]
A generalized Robinson-Foulds distance for labeled trees.
Briand S., Dessimoz C., El-Mabrouk N., Lafond M., Lobinska G., 2020/11/18. BMC genomics, 21 (Suppl 10) p. 779. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2A5CE76C7989]
HLA tapasin independence: broader peptide repertoire and HIV control.
Bashirova A.A., Viard M., Naranbhai V., Grifoni A., Garcia-Beltran W., Akdag M., Yuki Y., Gao X., O'hUigin C., Raghavan M. et al., 2020/11/10. Proceedings of the National Academy of Sciences of the United States of America, 117 (45) pp. 28232-28238. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_2878DD324F2A]
 
The FKBP4 Gene, Encoding a Regulator of the Androgen Receptor Signaling Pathway, Is a Novel Candidate Gene for Androgen Insensitivity Syndrome.
Ilaslan E., Markosyan R., Sproll P., Stevenson B.J., Sajek M., Sajek M.P., Hayrapetyan H., Sarkisian T., Livshits L., Nef S. et al., 2020/11/09. International journal of molecular sciences, 21 (21) p. 8403. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1F7615E822AD]
Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART.
Wan C., Bachmann N., Mitov V., Blanquart F., Céspedes S.P., Turk T., Neumann K., Beerenwinkel N., Bogojeska J., Fellay J. et al., 2020/11/02. Nature communications, 11 (1) p. 5542. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EC2E5183286F]
 
Biogeography of microbial bile acid transformations along the murine gut.
Marion S., Desharnais L., Studer N., Dong Y., Notter M.D., Poudel S., Menin L., Janowczyk A., Hettich R.L., Hapfelmeier S. et al., 2020/11. Journal of lipid research, 61 (11) pp. 1450-1463. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_10621EEB0CBD]
 
Discovering functional evolutionary dependencies in human cancers.
Mina M., Iyer A., Tavernari D., Raynaud F., Ciriello G., 2020/11. Nature genetics, 52 (11) pp. 1198-1207. Peer-reviewed.
[DOI][Pmid][serval:BIB_6F00D45D2EAD]
Genotype imputation using the Positional Burrows Wheeler Transform.
Rubinacci S., Delaneau O., Marchini J., 2020/11. PLoS genetics, 16 (11) pp. e1009049. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_89CBA5F9A38B]
Robust inference of positive selection on regulatory sequences in the human brain.
Liu J., Robinson-Rechavi M., 2020/11. Science advances, 6 (48) pp. eabc9863. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_805F3C22323C]
 
Structural dissimilarity from self drives neoepitope escape from immune tolerance.
Devlin J.R., Alonso J.A., Ayres C.M., Keller GLJ, Bobisse S., Vander Kooi C.W., Coukos G., Gfeller D., Harari A., Baker B.M., 2020/11. Nature chemical biology, 16 (11) pp. 1269-1276. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_186F0AD1C570]
Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.
Gleizes A., Laubscher F., Guex N., Iseli C., Junier T., Cordey S., Fellay J., Xenarios I., Kaiser L., Mercier P.L., 2020/11/01. Viruses, 12 (11) pp. E1248. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5E9093826570]
 
Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.
Wells D.K., van Buuren M.M., Dang K.K., Hubbard-Lucey V.M., Sheehan KCF, Campbell K.M., Lamb A., Ward J.P., Sidney J., Blazquez A.B. et al., 2020/10/29. Cell, 183 (3) pp. 818-834.e13. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F6095670EC38]
 
Mechanical forces drive ordered patterning of hair cells in the mammalian inner ear.
Cohen R., Amir-Zilberstein L., Hersch M., Woland S., Loza O., Taiber S., Matsuzaki F., Bergmann S., Avraham K.B., Sprinzak D., 2020/10/12. Nature communications, 11 (1) p. 5137. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F21C9C5B673D]
T-cell repertoire analysis and metrics of diversity and clonality.
Chiffelle J., Genolet R., Perez M.A., Coukos G., Zoete V., Harari A., 2020/10. Current opinion in biotechnology, 65 pp. 284-295. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_598F3EDCA20B]
 
Parallel and Scalable Precise Clustering
Byma Stuart, Dhasade Akash, Altenhoff Adrian, Dessimoz Christophe, Larus James R., 2020/09/30. dans Proceedings of the ACM International Conference on Parallel Architectures and Compilation Techniques, ACM.
[DOI][serval:BIB_D9BAD3B1327F]
Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo.
Liu J., Frochaux M., Gardeux V., Deplancke B., Robinson-Rechavi M., 2020/09/19. BMC biology, 18 (1) p. 129. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_076B6D0800A4]
The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System.
Chartoumpekis D.V., Ziros P.G., Georgakopoulos-Soares I., Smith AAT, Marques A.C., Ibberson M., A Kopp P., Habeos I., Trougakos I.P., Khoo NKH et al., 2020/09/18. Antioxidants, 9 (9) pp. E884. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F9FB94E92E22]
What Role Can Process Mining Play in Recurrent Clinical Guidelines Issues? A Position Paper.
Gatta R., Vallati M., Fernandez-Llatas C., Martinez-Millana A., Orini S., Sacchi L., Lenkowicz J., Marcos M., Munoz-Gama J., Cuendet M.A. et al., 2020/09/11. International journal of environmental research and public health, 17 (18) pp. E6616. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F0FD74FBD2EB]
A Single Metabolite which Modulates Lipid Metabolism Alters Hematopoietic Stem/Progenitor Cell Behavior and Promotes Lymphoid Reconstitution.
Giger S., Kovtonyuk L.V., Utz S.G., Ramosaj M., Kovacs W.J., Schmid E., Ioannidis V., Greter M., Manz M.G., Lutolf M.P. et al., 2020/09/08. Stem Cell Reports, 3 (15) pp. 566-576. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_4276557C90C9]
 
Extracellular matrix gene expression during arm regeneration in Amphiura filiformis.
Ferrario C., Czarkwiani A., Dylus D.V., Piovani L., Candia Carnevali M.D., Sugni M., Oliveri P., 2020/09. Cell and tissue research, 381 (3) pp. 411-426. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_68ED078D9A99]
 
Genetic comorbidity between major depression and cardio-metabolic traits, stratified by age at onset of major depression.
Hagenaars S.P., Coleman JRI, Choi S.W., Gaspar H., Adams M.J., Howard D.M., Hodgson K., Traylor M., Air T.M., Andlauer TFM et al., 2020/09. American journal of medical genetics. Part B, Neuropsychiatric genetics, 183 (6) pp. 309-330. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_26E359C96886]
Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b214-222 by combinatorial peptide library screening.
Bovay A., Zoete V., Rizkallah P.J., Beck K., Delbreil P., Speiser D.E., Cole D.K., Fuertes Marraco S.A., 2020/09. Molecular immunology, 125 pp. 43-50. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_46FDF2862443]
Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland.
Gauthier J., Pajkovic M., Neuenschwander S., Kaila L., Schmid S., Orlando L., Alvarez N., 2020/09. Molecular ecology resources, 20 (5) pp. 1191-1205. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9AFAA5147BB2]
 
The phylogenetic range of bacterial and viral pathogens of vertebrates.
Shaw L.P., Wang A.D., Dylus D., Meier M., Pogacnik G., Dessimoz C., Balloux F., 2020/09. Molecular ecology, 29 (17) pp. 3361-3379. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_70C79EA22DA5]
 
The Interleukin 22 Pathway Interacts with Mutant KRAS to Promote Poor Prognosis in Colon Cancer.
McCuaig S., Barras D., Mann E.H., Friedrich M., Bullers S.J., Janney A., Garner L.C., Domingo E., Koelzer V.H., Delorenzi M. et al., 2020/08/15. Clinical cancer research, 26 (16) pp. 4313-4325. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E0B299A0A2D6]
Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence.
Zile K., Dessimoz C., Wurm Y., Masel J., 2020/08/01. Genome biology and evolution, 12 (8) pp. 1355-1366. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FE830F452AA4]
 
Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial.
Jacob L., Witteveen A., Beumer I., Delahaye L., Wehkamp D., van den Akker J., Snel M., Chan B., Floore A., Bakx N. et al., 2020/07/27. Communications biology, 3 (1) p. 397. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_675A859CA6A3]
 
Pharmacological disruption of the Notch transcription factor complex.
Lehal R., Zaric J., Vigolo M., Urech C., Frismantas V., Zangger N., Cao L., Berger A., Chicote I., Loubéry S. et al., 2020/07/14. Proceedings of the National Academy of Sciences of the United States of America, 117 (28) pp. 16292-16301. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_53A51DDF8D0E]
 
Vacuolins and myosin VII are required for phagocytic uptake and phagosomal membrane recycling in Dictyostelium discoideum.
Bosmani C., Leuba F., Hanna N., Bach F., Burdet F., Pagni M., Hagedorn M., Soldati T., 2020/07/06. Journal of cell science, 133 (13). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9A192C83C96C]
The Quest for Orthologs benchmark service and consensus calls in 2020.
Altenhoff A.M., Garrayo-Ventas J., Cosentino S., Emms D., Glover N.M., Hernández-Plaza A., Nevers Y., Sundesha V., Szklarczyk D., Fernández J.M. et al., 2020/07/02. Nucleic acids research, 48 (W1) pp. W538-W545. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EBF2C2C4065D]
A framework to assess the quality and impact of bioinformatics training across ELIXIR.
Gurwitz K.T., Singh Gaur P., Bellis L.J., Larcombe L., Alloza E., Balint B.L., Botzki A., Dimec J., Dominguez Del Angel V., Fernandes P.L. et al., 2020/07. PLoS computational biology, 16 (7) pp. e1007976. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_3B57279FB31E]
Brain microRNAs among social and solitary bees
Kapheim Karen M., Jones Beryl M., Søvik Eirik, Stolle Eckart, Waterhouse Robert M., Bloch Guy, Ben-Shahar Yehuda, 2020/07. Royal Society Open Science, 7 (7) p. 200517. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8DDA13D635C7]
Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera.
Oeyen J.P., Baa-Puyoulet P., Benoit J.B., Beukeboom L.W., Bornberg-Bauer E., Buttstedt A., Calevro F., Cash E.I., Chao H., Charles H. et al., 2020/07/01. Genome biology and evolution, 12 (7) pp. 1099-1188. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_598EC53E0F48]
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.
Moi D., Kilchoer L., Aguilar P.S., Dessimoz C., 2020/07. PLoS computational biology, 16 (7) pp. e1007553. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_06AA547BD763]
 
Prognostic imaging biomarkers for diabetic kidney disease (iBEAt): study protocol.
Gooding K.M., Lienczewski C., Papale M., Koivuviita N., Maziarz M., Dutius Andersson A.M., Sharma K., Pontrelli P., Garcia Hernandez A., Bailey J. et al., 2020/06/29. BMC nephrology, 21 (1) p. 242. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E47EE58F640E]
Combined deletion of Glut1 and Glut3 impairs lung adenocarcinoma growth.
Contat C., Ancey P.B., Zangger N., Sabatino S., Pascual J., Escrig S., Jensen L., Goepfert C., Lanz B., Lepore M. et al., 2020/06/23. eLife, 9 pp. e53618. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_5C7C965ADC59]
 
Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term.
Volery M., Scherz V., Jakob W., Bandeira D., Deggim-Messmer V., Lauber-Biason A., Wildhaber J., Falquet L., Curtis N., Zimmermann P., 2020/06/23. BMJ open, 10 (6) pp. e036275. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_41FCE96DFE45]
Developmental plasticity shapes social traits and selection in a facultatively eusocial bee.
Kapheim K.M., Jones B.M., Pan H., Li C., Harpur B.A., Kent C.F., Zayed A., Ioannidis P., Waterhouse R.M., Kingwell C. et al., 2020/06/16. Proceedings of the National Academy of Sciences of the United States of America, 117 (24) pp. 13615-13625. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3840B8AA6FF6]
 
Contribution of exome sequencing to the identification of genes involved in the response to clopidogrel in cardiovascular patients.
Fontana P., Ibberson M., Stevenson B., Wigger L., Daali Y., Niknejad A., Mach F., Docquier M., Xenarios I., Cuisset T. et al., 2020/06. Journal of thrombosis and haemostasis, 18 (6) pp. 1425-1434. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_310A8D0307B7]
 
Framization of a Temperley-Lieb algebra of type B
Flores M., Goundaroulis D., 2020/06. Journal of Pure and Applied Algebra, 224 (6) p. 106273.
[DOI][WoS][serval:BIB_14F8FAA49034]
 
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer.
Lee H.O., Hong Y., Etlioglu H.E., Cho Y.B., Pomella V., Van den Bosch B., Vanhecke J., Verbandt S., Hong H., Min J.W. et al., 2020/06. Nature genetics, 52 (6) pp. 594-603. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_22A1CCCC429D]
 
Reducing the burden of hypoglycaemia in people with diabetes through increased understanding: design of the Hypoglycaemia REdefining SOLutions for better liVEs (Hypo-RESOLVE) project.
de Galan B.E., McCrimmon R.J., Ibberson M., Heller S.R., Choudhary P., Pouwer F., Speight J., Carlton J., Pieber T.R., Rosilio M. et al., 2020/06. Diabetic medicine, 37 (6) pp. 1066-1073. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_942699F55E73]
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.
Du K., Stöck M., Kneitz S., Klopp C., Woltering J.M., Adolfi M.C., Feron R., Prokopov D., Makunin A., Kichigin I. et al., 2020/06. Nature ecology & evolution, 4 (6) pp. 841-852. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E5D3059F527A]
 
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, Mendes de Farias T, Moretti S, Parmentier G, Rech de Laval V, Rosikiewicz M et al., 2020/05/29..
[DOI][serval:BIB_65A649E27A82]
 
Genomic Encryption of Digital Data Stored in Synthetic DNA
Grass Robert N., Heckel Reinhard, Dessimoz Christophe, Stark Wendelin J., 2020/05/25. Angewandte Chemie International Edition, 59 (22) pp. 8476-8480. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_43671755DDDE]
 
Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma.
Dheilly E., Battistello E., Katanayeva N., Sungalee S., Michaux J., Duns G., Wehrle S., Sordet-Dessimoz J., Mina M., Racle J. et al., 2020/05/11. Cancer cell, 37 (5) pp. 674-689.e12. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C0FB07A8B571]
 
Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study.
Ambrosini G., Vorontsov I., Penzar D., Groux R., Fornes O., Nikolaeva D.D., Ballester B., Grau J., Grosse I., Makeev V. et al., 2020/05/11. Genome biology, 21 (1) p. 114. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2246D7C89D46]
 
Biallelic variants in PSMB1 encoding the proteasome subunit β6 cause impairment of proteasome function, microcephaly, intellectual disability, developmental delay and short stature.
Ansar M., Ebstein F., Özkoç H., Paracha S.A., Iwaszkiewicz J., Gesemann M., Zoete V., Ranza E., Santoni F.A., Sarwar M.T. et al., 2020/05/08. Human molecular genetics, 29 (7) pp. 1132-1143. Peer-reviewed.
[DOI][Pmid][serval:BIB_7528AD86E93D]
 
Ten simple rules for making training materials FAIR.
Garcia L., Batut B., Burke M.L., Kuzak M., Psomopoulos F., Arcila R., Attwood T.K., Beard N., Carvalho-Silva D., Dimopoulos A.C. et al., 2020/05. PLoS computational biology, 16 (5) pp. e1007854. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AB51D5C92C0C]
UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis.
Tavridou E., Schmid-Siegert E., Fankhauser C., Ulm R., 2020/05. PLoS genetics, 16 (5) pp. e1008797. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F4BCB657A029]
 
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.
Drysdale R., Cook C.E., Petryszak R., Baillie-Gerritsen V., Barlow M., Gasteiger E., Gruhl F., Haas J., Lanfear J., Lopez R. et al., 2020/04/15. Bioinformatics, 36 (8) pp. 2636-2642. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_071A84C02DF9]
Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9.
Plank M., Perepelkina M., Müller M., Vaga S., Zou X., Bourgoint C., Berti M., Saarbach J., Haesendonckx S., Winssinger N. et al., 2020/04. Molecular & cellular proteomics, 19 (4) pp. 655-671. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4D0914B0B753]
 
Dairy consumption is associated with lower plasma dihydroceramides in women from the D.E.S.I.R. cohort.
Fumeron F., Nicolas A., Bastard J.P., Fellahi S., Wigger L., Ibberson M., Cruciani-Guglielmacci C., Le Stunff H., Velho G., Magnan C. et al., 2020/04. Diabetes & metabolism, 46 (2) pp. 144-149. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_895023AD89B5]
 
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region.
Dellicour S., Lemey P., Artois J., Lam T.T., Fusaro A., Monne I., Cattoli G., Kuznetsov D., Xenarios I., Dauphin G. et al., 2020/04/01. Bioinformatics, 36 (7) pp. 2098-2104. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_792965764CE2]
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Chen Qingyu, Britto Ramona, Erill Ivan, Jeffery Constance J., Liberzon Arthur, Magrane Michele, Onami Jun-ichi, Robinson-Rechavi Marc, Sponarova Jana, Zobel Justin et al., 2020/04/01. Genomics, Proteomics & Bioinformatics, 18 pp. 91-103. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_688EF9445320]
 
Differential stromal reprogramming in benign and malignant naturally occurring canine mammary tumours identifies disease-modulating stromal components.
Amini P., Nassiri S., Malbon A., Markkanen E., 2020/03/26. Scientific reports, 10 (1) p. 5506. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8B8484524FB7]
 
Antiangiogenic immunotherapy suppresses desmoplastic and chemoresistant intestinal tumors in mice.
Ragusa S., Prat-Luri B., González-Loyola A., Nassiri S., Squadrito M.L., Guichard A., Cavin S., Gjorevski N., Barras D., Marra G. et al., 2020/03/02. The Journal of clinical investigation, 130 (3) pp. 1199-1216. Peer-reviewed.
[DOI][Pmid][serval:BIB_C704575BD9D9]
 
Brain expansion in early hominins predicts carnivore extinctions in East Africa.
Faurby S., Silvestro D., Werdelin L., Antonelli A., 2020/03. Ecology letters, 23 (3) pp. 537-544. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8C60CDD7B0C0]
Functional integration of "undead" neurons in the olfactory system.
Prieto-Godino L.L., Silbering A.F., Khallaf M.A., Cruchet S., Bojkowska K., Pradervand S., Hansson B.S., Knaden M., Benton R., 2020/03. Science Advances, 6 (11) pp. eaaz7238. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_39A62FD7ACE6]
HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation.
Arora J., Pierini F., McLaren P.J., Carrington M., Fellay J., Lenz T.L., 2020/03/01. Molecular biology and evolution, 37 (3) pp. 639-650. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4A4E20C0A676]
Methods detecting rhythmic gene expression are biologically relevant only for strong signal
Laloum David, Robinson-Rechavi Marc, 2020/03. PLOS Computational Biology, 16 (3) pp. 1-23.
[URN][DOI][serval:BIB_C090B1967D37]
New genome assembly of the barn owl (Tyto alba alba).
Ducrest A.L., Neuenschwander S., Schmid-Siegert E., Pagni M., Train C., Dylus D., Nevers Y., Warwick Vesztrocy A., San-Jose L.M., Dupasquier M. et al., 2020/03. Ecology and evolution, 10 (5) pp. 2284-2298. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_83891497D9E8]
OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.
Dingerdissen H.M., Bastian F., Vijay-Shanker K., Robinson-Rechavi M., Bell A., Gogate N., Gupta S., Holmes E., Kahsay R., Keeney J. et al., 2020/03. JCO clinical cancer informatics, 4 pp. 210-220. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_BC34650B96ED]
 
Aberrant expression of PAR bZIP transcription factors is associated with epileptogenesis, focus on hepatic leukemia factor.
Rambousek L., Gschwind T., Lafourcade C., Paterna J.C., Dib L., Fritschy J.M., Fontana A., 2020/02/28. Scientific reports, 10 (1) p. 3760. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_18F0209D2C05]
Fisetin protects against cardiac cell death through reduction of ROS production and caspases activity.
Rodius S., de Klein N., Jeanty C., Sánchez-Iranzo H., Crespo I., Ibberson M., Xenarios I., Dittmar G., Mercader N., Niclou S.P. et al., 2020/02/19. Scientific reports, 10 (1) p. 2896. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_01B9FD89D57C]
 
Contribution of Genetic Background and Data Collection on Adverse Events of Anti-human Immunodeficiency Virus (HIV) Drugs (D:A:D) Clinical Risk Score to Chronic Kidney Disease in Swiss HIV-infected Persons With Normal Baseline Estimated Glomerular Filtration Rate.
Dietrich L.G., Barceló C., Thorball C.W., Ryom L., Burkhalter F., Hasse B., Furrer H., Weisser M., Steffen A., Bernasconi E. et al., 2020/02/14. Clinical infectious diseases, 70 (5) pp. 890-897. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CEFAD592E5CD]
FADS3 is a Δ14Z sphingoid base desaturase that contributes to gender differences in the human plasma sphingolipidome.
Karsai G., Lone M., Kutalik Z., Brenna J.T., Li H., Pan D., von Eckardstein A., Hornemann T., 2020/02/14. The Journal of biological chemistry, 295 (7) pp. 1889-1897. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4F9B98961C35]
 
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data.
Moreno-Mayar J.V., Korneliussen T.S., Dalal J., Renaud G., Albrechtsen A., Nielsen R., Malaspinas A.S., 2020/02/01. Bioinformatics, 36 (3) pp. 828-841. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1A2FB983348E]
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release.
Duroy P.O., Bosshard S., Schmid-Siegert E., Neuenschwander S., Arib G., Lemercier P., Masternak J., Roesch L., Buron F., Girod P.A. et al., 2020/02. Biotechnology and bioengineering, 117 (2) pp. 466-485. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3F6D075DCCE1]
Grid diagrams as tools to investigate knot spaces and topoisomerase-mediated simplification of DNA topology.
Barbensi A., Celoria D., Harrington H.A., Stasiak A., Buck D., 2020/02. Science advances, 6 (9) pp. eaay1458. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_AF311EE3A9EB]
Hemocyte-targeted gene expression in the female malaria mosquito using the hemolectin promoter from Drosophila
Pondeville Emilie, Puchot Nicolas, Parvy Jean-Philippe, Carissimo Guillaume, Poidevin Mickael, Waterhouse Robert M., Marois Eric, Bourgouin Catherine, 2020/02. Insect Biochemistry and Molecular Biology p. 103339. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_4B5F0B93AEE3]
 
Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands.
Solleder M., Guillaume P., Racle J., Michaux J., Pak H.S., Müller M., Coukos G., Bassani-Sternberg M., Gfeller D., 2020/02. Molecular & cellular proteomics, 19 (2) pp. 390-404. Peer-reviewed.
[DOI][Pmid][serval:BIB_0EBACC6764B1]
Gene content evolution in the arthropods.
Thomas GWC, Dohmen E., Hughes DST, Murali S.C., Poelchau M., Glastad K., Anstead C.A., Ayoub N.A., Batterham P., Bellair M. et al., 2020/01/23. Genome biology, 21 (1) p. 15. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9D49DA02380A]
Disulfide-Linked Peptides for Blocking BTLA/HVEM Binding.
Spodzieja M., Kuncewicz K., Sieradzan A., Karczyńska A., Iwaszkiewicz J., Cesson V., Węgrzyn K., Zhukov I., Maszota-Zieleniak M., Michielin O. et al., 2020/01/18. International journal of molecular sciences, 21 (2). Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_A28A31EE871C]
Enhanced genome assembly and a new official gene set for Tribolium castaneum.
Herndon N., Shelton J., Gerischer L., Ioannidis P., Ninova M., Dönitz J., Waterhouse R.M., Liang C., Damm C., Siemanowski J. et al., 2020/01/14. BMC genomics, 21 (1) p. 47. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4C7DA203B5FA]
Neutrophils suppress tumor-infiltrating T cells in colon cancer via matrix metalloproteinase-mediated activation of TGFβ.
Germann M., Zangger N., Sauvain M.O., Sempoux C., Bowler A.D., Wirapati P., Kandalaft L.E., Delorenzi M., Tejpar S., Coukos G. et al., 2020/01/09. EMBO molecular medicine, 12 (1) pp. e10681. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F06A8D6CE8D2]
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).
Orengo C., Velankar S., Wodak S., Zoete V., Bonvin AMJJ, Elofsson A., Feenstra K.A., Gerloff D.L., Hamelryck T., Hancock J.M. et al., 2020. F1000Research, 9. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_7E6BA5C7154A]
 
Biocuration - mapping resources and needs.
Holinski A., Burke M.L., Morgan S.L., McQuilton P., Palagi P.M., 2020. F1000Research, 9 pp. ELIXIR-1094. Peer-reviewed.
[DOI][Pmid][serval:BIB_5E47F5B26806]
Biogenesis of HLA Ligand Presentation in Immune Cells Upon Activation Reveals Changes in Peptide Length Preference.
Marino F., Semilietof A., Michaux J., Pak H.S., Coukos G., Müller M., Bassani-Sternberg M., 2020. Frontiers in immunology, 11 p. 1981. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E06D274ABF64]
Characterization of Insect Immune Systems from Genomic Data
Waterhouse Robert M., Lazzaro Brian P., Sackton Timothy B., 2020. pp. 3-34 dans Springer Protocols Handbooks, Springer US.
[URN][DOI][serval:BIB_D98447B4FB89]
 
Classifying dementia progression using microbial profiling of saliva.
Bathini P., Foucras S., Dupanloup I., Imeri H., Perna A., Berruex J.L., Doucey M.A., Annoni J.M., Auber Alberi L., 2020. Alzheimer's & dementia, 12 (1) pp. e12000. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D08E4B7845AF]
 
Clinical bioinformatics for microbial genomics and metagenomics: an ESCMID Postgraduate Technical Workshop.
Greub G., Palagi P.M., Dylus D., Egli A., Pillonel T., Rossen JWA, Seth-Smith HMB, Lebrand A., ESGMD Study Group, 2020. Microbes and infection, 22 (10) pp. 626-634. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_806389DCE25C]
Deciphering the transcriptomic landscape of tumor-infiltrating CD8 lymphocytes in B16 melanoma tumors with single-cell RNA-Seq
Carmona Santiago J., Siddiqui Imran, Bilous Mariia, Held Werner, Gfeller David, 2020/01/01. OncoImmunology, 9 (1) p. 1737369. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EDA6E7092CF7]
 
EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data.
Racle J., Gfeller D., 2020. Methods in molecular biology, 2120 pp. 233-248. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AF1B21C1943C]
How to build phylogenetic species trees with OMA.
Dylus D., Nevers Y., Altenhoff A.M., Gürtler A., Dessimoz C., Glover N.M., 2020. F1000Research, 9 p. 511. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_D8D72D90D99B]
Identifying orthologs with OMA: A primer.
Zahn-Zabal M., Dessimoz C., Glover N.M., 2020. F1000Research, 9 p. 27. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_B7D7E8705809]
 
Making the most of genomic data with OMA.
Glover N.M., 2020. F1000Research, 9 p. 665. Peer-reviewed.
[DOI][Pmid][serval:BIB_53B7923F0FB7]
Molecular Evolution and Gene Function
Robinson-Rechavi Marc, 2020. dans Phylogenetics in the Genomic Era, hal.inria.fr.
[URN][serval:BIB_BB2B81C3E623]
Multicenter analysis of sputum microbiota in tuberculosis patients.
Sala C., Benjak A., Goletti D., Banu S., Mazza-Stalder Jesica, Jaton K., Busso P., Remm S., Leleu M., Rougemont J. et al., 2020. PloS one, 15 (10) pp. e0240250. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E924DB344DCF]
 
Myeloid Cells Orchestrate Systemic Immunosuppression, Impairing the Efficacy of Immunotherapy against HPV<sup>+</sup> Cancers.
Galliverti G., Wullschleger S., Tichet M., Murugan D., Zangger N., Horton W., Korman A.J., Coussens L.M., Swartz M.A., Hanahan D., 2020/01. Cancer immunology research, 8 (1) pp. 131-145. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_04D464D7C6BB]
 
Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference
Fernández Rosa, Gabaldón Toni, Dessimoz Christophe, 2020. dans Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book.
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Predicting combinations of immunomodulators to enhance dendritic cell-based vaccination based on a hybrid experimental and computational platform.
Ahmed R., Crespo I., Tuyaerts S., Bekkar A., Graciotti M., Xenarios I., Kandalaft L.E., 2020. Computational and structural biotechnology journal, 18 pp. 2217-27. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2B3CB067B0E1]
The Expression Comparison Tool in Bgee
Robinson-Rechavi Marc, Rech de Laval Valentine, Bastian Frédéric B., Wollbrett Julien, Bgee Team, 2020. dans Phylogenetics in the Genomic Era, hal.inria.fr.
[URN][serval:BIB_D44AAAA828A2]
The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations.
Manni M., Simao F.A., Robertson H.M., Gabaglio M.A., Waterhouse R.M., Misof B., Niehuis O., Szucsich N.U., Zdobnov E.M., 2020/01/01. Genome biology and evolution, 12 (1) pp. 3534-3549. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A4812FEC4F0C]
 
The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing.
Parsa S., Ortega-Molina A., Ying H.Y., Jiang M., Teater M., Wang J., Zhao C., Reznik E., Pasion J.P., Kuo D. et al., 2020. Nature cancer, 1 pp. 653-664. Peer-reviewed.
[DOI][Pmid][serval:BIB_69CD135EB662]
The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix.
Bignucolo O., Bernèche S., 2020. Frontiers in molecular biosciences, 7 p. 162. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9F3F3B036C88]
2019
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.
Mudge J.M., Jungreis I., Hunt T., Gonzalez J.M., Wright J.C., Kay M., Davidson C., Fitzgerald S., Seal R., Tweedie S. et al., 2019/12. Genome research, 29 (12) pp. 2073-2087. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_24414116FADD]
Herpes simplex encephalitis in adult patients with MASP-2 deficiency.
Bibert S., Piret J., Quinodoz M., Collinet E., Zoete V., Michielin O., Menasria R., Meylan P., Bihl T., Erard V. et al., 2019/12. PLoS pathogens, 15 (12) pp. e1008168. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_568322E0BDD0]
Identifying gene function and module connections by the integration of multispecies expression compendia
Li Hao, Rukina Daria, David Fabrice P.A., Li Terytty Yang, Oh Chang-Myung, Gao Arwen W., Katsyuba Elena, Bou Sleiman Maroun, Komljenovic Andrea, Huang Qingyao et al., 2019/12. Genome Research, 29 (12) pp. 2034-2045. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_7B783B226A9E]
Systemic and central nervous system metabolic alterations in Alzheimer's disease
van der Velpen Vera, Teav Tony, Gallart-Ayala Héctor, Mehl Florence, Konz Ioana, Clark Christopher, Oikonomidi Aikaterini, Peyratout Gwendoline, Henry Hugues, Delorenzi Mauro et al., 2019/12. Alzheimer's Research & Therapy, 11 (1). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_901648E242CF]
CD56 as a marker of an ILC1-like population with NK cell properties that is functionally impaired in AML.
Salomé B., Gomez-Cadena A., Loyon R., Suffiotti M., Salvestrini V., Wyss T., Vanoni G., Ruan D.F., Rossi M., Tozzo A. et al., 2019/11/26. Blood advances, 3 (22) pp. 3674-3687. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4BC26C680B22]
 
Strong Enrichment of Aromatic and Sulfur-Containing Residues in Ligand-Protein Binding Sites.
El Hage K., Zoete V., 2019/11/25. Journal of chemical information and modeling, 59 (11) pp. 4921-4928. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8964B650737F]
Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma.
Tsantoulis P., Delorenzi M., Bièche I., Vacher S., Mariani P., Cassoux N., Houy A., Stern M.H., Roman-Roman S., Dietrich P.Y. et al., 2019/11/20. Scientific reports, 9 (1) p. 17178. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_B2ADA6C4E5AE]
 
DDR1 role in fibrosis and its pharmacological targeting.
Moll S., Desmoulière A., Moeller M.J., Pache J.C., Badi L., Arcadu F., Richter H., Satz A., Uhles S., Cavalli A. et al., 2019/11. Biochimica et biophysica acta. Molecular cell research, 1866 (11) p. 118474. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_25F81C67012D]
 
Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes.
Racle J., Michaux J., Rockinger G.A., Arnaud M., Bobisse S., Chong C., Guillaume P., Coukos G., Harari A., Jandus C. et al., 2019/11. Nature biotechnology, 37 (11) pp. 1283-1286. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D9A8D08A5BC6]
A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL
Sima Ana Claudia, Dessimoz Christophe, Stockinger Kurt, Zahn-Zabal Monique, Mendes de Farias Tarcisio, 2019/10/29. F1000Research, 8 p. 1822. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_EF5C14AC5C45]
 
Inhibition Mechanisms of Indoleamine 2,3-Dioxygenase 1 (IDO1).
Röhrig U.F., Reynaud A., Majjigapu S.R., Vogel P., Pojer F., Zoete V., 2019/10/10. Journal of medicinal chemistry, 62 (19) pp. 8784-8795. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D8CCFFB94292]
 
1-Deoxydihydroceramide causes anoxic death by impairing chaperonin-mediated protein folding.
Hannich J.T., Haribowo A.G., Gentina S., Paillard M., Gomez L., Pillot B., Thibault H., Abegg D., Guex N., Zumbuehl A. et al., 2019/10. Nature metabolism, 1 (10) pp. 996-1008. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_62B2442C63AD]
 
Advances and Applications in the Quest for Orthologs.
Glover N., Dessimoz C., Ebersberger I., Forslund S.K., Gabaldón T., Huerta-Cepas J., Martin M.J., Muffato M., Patricio M., Pereira C. et al., 2019/10/01. Molecular biology and evolution, 36 (10) pp. 2157-2164. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A36FE75880A9]
Interoperable and scalable data analysis with microservices: applications in metabolomics.
Emami Khoonsari P., Moreno P., Bergmann S., Burman J., Capuccini M., Carone M., Cascante M., de Atauri P., Foguet C., Gonzalez-Beltran A.N. et al., 2019/10/01. Bioinformatics, 35 (19) pp. 3752-3760. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_2E01B5B0EEB9]
Predicting the Occurrence of Variants in RAG1 and RAG2.
Lawless D., Lango Allen H., Thaventhiran J., NIHR BioResource-Rare Diseases Consortium, Hodel F., Anwar R., Fellay J., Walter J.E., Savic S., 2019/10. Journal of clinical immunology, 39 (7) pp. 688-701. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8B2685C9BC41]
Application of the SwissDrugDesign Online Resources in Virtual Screening.
Daina A., Zoete V., 2019/09/18. International journal of molecular sciences, 20 (18) p. 4612. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B934FE45EAA7]
Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae
Matthey Noémie, Stutzmann Sandrine, Stoudmann Candice, Guex Nicolas, Iseli Christian, Blokesch Melanie, 2019/09/03. eLife, 8.
[URN][DOI][WoS][Pmid][serval:BIB_A98B4B2C6A99]
Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes.
Attardo G.M., Abd-Alla AMM, Acosta-Serrano A., Allen J.E., Bateta R., Benoit J.B., Bourtzis K., Caers J., Caljon G., Christensen M.B. et al., 2019/09/02. Genome biology, 20 (1) p. 187. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C423F727BB77]
 
Metabolically phenotyped pancreatectomized patients as living donors for the study of islets in health and diabetes.
Barovic M., Distler M., Schöniger E., Radisch N., Aust D., Weitz J., Ibberson M., Schulte A.M., Solimena M., 2019/09. Molecular metabolism, 27S (Suppl) pp. S1-S6. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_143F41D4B1F2]
Nuclear Orthologs Derived from Whole Genome Sequencing Indicate Cryptic Diversity in the Bemisia tabaci (Insecta: Aleyrodidae) Complex of Whiteflies
de Moya Robert S., Brown Judith K., Sweet Andrew D., Walden Kimberly K. O., Paredes-Montero Jorge R., Waterhouse Robert M., Johnson Kevin P., 2019/08/29. Diversity, 11 (9) p. 151. Peer-reviewed.
[URN][DOI][WoS][serval:BIB_AB703B52B49A]
Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.
Schvartzman J.B., Hernández P., Krimer D.B., Dorier J., Stasiak A., 2019/08/22. Nucleic acids research, 47 (14) pp. 7182-7198. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_55CCC896580F]
A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancreatic Adenocarcinoma—A Proof of Antigen Discovery Feasibility in Three Patients
Bassani-Sternberg Michal, Digklia Antonia, Huber Florian, Wagner Dorothea, Sempoux Christine, Stevenson Brian J., Thierry Anne-Christine, Michaux Justine, Pak HuiSong, Racle Julien et al., 2019/08/08. Frontiers in Immunology, 10 p. 1832. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0144F5D289B5]
 
A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure.
Sung Y.J., de Las Fuentes L., Winkler T.W., Chasman D.I., Bentley A.R., Kraja A.T., Ntalla I., Warren H.R., Guo X., Schwander K. et al., 2019/08/01. Human molecular genetics, 28 (15) pp. 2615-2633. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_95271BD54B2D]
Deciphering the complexity of human non-coding promoter-proximal transcriptome.
Mapelli S.N., Napoli S., Pisignano G., Garcia-Escudero R., Carbone G.M., Catapano C.V., 2019/08/01. Bioinformatics, 35 (15) pp. 2529-2534. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3084C6B239C8]
 
Epigenetic Control of Mitochondrial Fission Enables Self-Renewal of Stem-like Tumor Cells in Human Prostate Cancer
Civenni Gianluca, Bosotti Roberto, Timpanaro Andrea, Vàzquez Ramiro, Merulla Jessica, Pandit Shusil, Rossi Simona, Albino Domenico, Allegrini Sara, Mitra Abhishek et al., 2019/08. Cell Metabolism, 30 (2) pp. 303-318.e6. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_160F9BD5E05B]
Fostering improved human islet research: a European perspective.
Marchetti P., Schulte A.M., Marselli L., Schoniger E., Bugliani M., Kramer W., Overbergh L., Ullrich S., Gloyn A.L., Ibberson M. et al., 2019/08. Diabetologia, 62 (8) pp. 1514-1516. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4EAABE7C8EB6]
 
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.
Koopmans F., van Nierop P., Andres-Alonso M., Byrnes A., Cijsouw T., Coba M.P., Cornelisse L.N., Farrell R.J., Goldschmidt H.L., Howrigan D.P. et al., 2019/07/17. Neuron, 103 (2) pp. 217-234.e4. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_09976E2B9E69]
Expression and Immunostaining Analyses Suggest that Pneumocystis Primary Homothallism Involves Trophic Cells Displaying Both Plus and Minus Pheromone Receptors.
Luraschi A., Richard S., Almeida JMGCF, Pagni M., Cushion M.T., Hauser P.M., 2019/07/09. mBio, 10 (4). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B682BB46A683]
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules.
Daina A., Michielin O., Zoete V., 2019/07/02. Nucleic acids research, 47 (W1) pp. W357-W364. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_37625953AF4B]
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.
Tran VDT, Moretti S., Coste A.T., Amorim-Vaz S., Sanglard D., Pagni M., 2019/07/01. Bioinformatics, 35 (13) pp. 2258-2266. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3E96F1A1B541]
Cross-species functional modules link proteostasis to human normal aging.
Komljenovic A., Li H., Sorrentino V., Kutalik Z., Auwerx J., Robinson-Rechavi M., 2019/07. PLoS computational biology, 15 (7) pp. e1007162. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DB3E6C72F674]
OMA standalone: orthology inference among public and custom genomes and transcriptomes.
Altenhoff A.M., Levy J., Zarowiecki M., Tomiczek B., Warwick Vesztrocy A., Dalquen D.A., Müller S., Telford M.J., Glover N.M., Dylus D. et al., 2019/07. Genome research, 29 (7) pp. 1152-1163. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D405BD0232C3]
 
Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.
Turcot V., Lu Y., Highland H.M., Schurmann C., Justice A.E., Fine R.S., Bradfield J.P., Esko T., Giri A., Graff M. et al., 2019/07..
[DOI][WoS][Pmid][serval:BIB_B20E27C014A7]
 
RasGRP1 is a potential biomarker to stratify anti-EGFR therapy response in colorectal cancer.
Gbenedio O.M., Bonnans C., Grun D., Wang C.Y., Hatch A.J., Mahoney M.R., Barras D., Matli M., Miao Y., Garcia K.C. et al., 2019/06/25. JCI insight, 5 pp. e127552. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_3AFCE6869632]
HCF-2 inhibits cell proliferation and activates differentiation-gene expression programs.
Gudkova D., Dergai O., Praz V., Herr W., 2019/06/20. Nucleic acids research, 47 (11) pp. 5792-5808. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_2BB8B41DAB1A]
In Silico Transcriptomic Analysis of Wound-Healing-Associated Genes in Malignant Pleural Mesothelioma.
Rouka E., Beltsios E., Goundaroulis D., Vavougios G.D., Solenov E.I., Hatzoglou C., Gourgoulianis K.I., Zarogiannis S.G., 2019/06/12. Medicina, 55 (6). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_15280742A3C7]
 
Cooperation between Constitutive and Inducible Chemokines Enables T Cell Engraftment and Immune Attack in Solid Tumors.
Dangaj D., Bruand M., Grimm A.J., Ronet C., Barras D., Duttagupta P.A., Lanitis E., Duraiswamy J., Tanyi J.L., Benencia F. et al., 2019/06/10. Cancer cell, 35 (6) pp. 885-900.e10. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_95C8776874F3]
 
Proteomics Standards Initiative Extended FASTA Format.
Binz P.A., Shofstahl J., Vizcaíno J.A., Barsnes H., Chalkley R.J., Menschaert G., Alpi E., Clauser K., Eng J.K., Lane L. et al., 2019/06/07. Journal of proteome research, 18 (6) pp. 2686-2692. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C8C33CCB2A98]
 
Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features.
Ansar M., Ullah F., Paracha S.A., Adams D.J., Lai A., Pais L., Iwaszkiewicz J., Millan F., Sarwar M.T., Agha Z. et al., 2019/06/06. American journal of human genetics, 104 (6) pp. 1073-1087. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_29D795794213]
 
Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.
Philippe H., Poustka A.J., Chiodin M., Hoff K.J., Dessimoz C., Tomiczek B., Schiffer P.H., Müller S., Domman D., Horn M. et al., 2019/06/03. Current biology, 29 (11) pp. 1818-1826.e6. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_43B8702FAD67]
 
A catalog of genetic loci associated with kidney function from analyses of a million individuals.
Wuttke M., Li Y., Li M., Sieber K.B., Feitosa M.F., Gorski M., Tin A., Wang L., Chu A.Y., Hoppmann A. et al., 2019/06. Nature genetics, 51 (6) pp. 957-972. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9B3824B99372]
Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.
Davydov I.I., Salamin N., Robinson-Rechavi M., 2019/06/01. Molecular biology and evolution, 36 (6) pp. 1316-1332. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FF45CD1C1260]
Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes.
Khamis A., Canouil M., Siddiq A., Crouch H., Falchi M., Bulow M.V., Ehehalt F., Marselli L., Distler M., Richter D. et al., 2019/06. Molecular metabolism, 24 pp. 98-107. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5EA2C0408F1C]
Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error.
Vasilikopoulos A., Balke M., Beutel R.G., Donath A., Podsiadlowski L., Pflug J.M., Waterhouse R.M., Meusemann K., Peters R.S., Escalona H.E. et al., 2019/06. Molecular phylogenetics and evolution, 135 pp. 270-285. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_065CBB336649]
Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles.
Seppey M., Ioannidis P., Emerson B.C., Pitteloud C., Robinson-Rechavi M., Roux J., Escalona H.E., McKenna D.D., Misof B., Shin S. et al., 2019/05/17. Genome biology, 20 (1) p. 98. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4EC401109BAD]
 
Correction for Minocha et al., "Rapid Recapitulation of Nonalcoholic Steatohepatitis upon Loss of Host Cell Factor 1 Function in Mouse Hepatocytes".
Minocha S., Villeneuve D., Praz V., Moret C., Lopes M., Pinatel D., Rib L., Guex N., Herr W., 2019/05/15. Molecular and cellular biology, 39 (10). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8E933260533C]
From Normal to Obesity and Back: The Associations between Mitochondrial DNA Copy Number, Gender, and Body Mass Index.
Skuratovskaia D., Litvinova L., Vulf M., Zatolokin P., Popadin K., Mazunin I., 2019/05/09. Cells, 8 (5). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7EDAE94D3A97]
ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.
Shamanskiy V.A., Timonina V.N., Popadin K.Y., Gunbin K.V., 2019/05/08. BMC genomics, 20 (Suppl 3) p. 295. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BC9CD4F6FECD]
 
Chromatin three-dimensional interactions mediate genetic effects on gene expression.
Delaneau O., Zazhytska M., Borel C., Giannuzzi G., Rey G., Howald C., Kumar S., Ongen H., Popadin K., Marbach D. et al., 2019/05/03. Science, 364 (6439). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_266A5EFF0381]
A likelihood method for estimating present-day human contamination in ancient DNA samples using low-depth haploid chromosome data
Moreno-Mayar J. Víctor, Korneliussen Thorfinn Sand, Albrechtsen Anders, Dalal Jyoti, Renaud Gabriel, Nielsen Rasmus, Malaspinas Anna-Sapfo, 2019/05..
[URN][DOI][serval:BIB_84C6FA3621CE]
Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.
Deforges J., Reis R.S., Jacquet P., Sheppard S., Gadekar V.P., Hart-Smith G., Tanzer A., Hofacker I.L., Iseli C., Xenarios I. et al., 2019/05. Plant physiology, 180 (1) pp. 305-322. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F14F93B19301]
 
Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish.
Salis P., Lorin T., Lewis V., Rey C., Marcionetti A., Escande M.L., Roux N., Besseau L., Salamin N., Sémon M. et al., 2019/05. Pigment cell & melanoma research, 32 (3) pp. 391-402. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_70242B18941A]
 
Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5.
Ellegaard K.M., Brochet S., Bonilla-Rosso G., Emery O., Glover N., Hadadi N., Jaron K.S., van der Meer J.R., Robinson-Rechavi M., Sentchilo V. et al., 2019/05. Molecular ecology, 28 (9) pp. 2224-2237. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_37C4AFA6D4D6]
Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors.
Warrington N.M., Beaumont R.N., Horikoshi M., Day F.R., Helgeland Ø., Laurin C., Bacelis J., Peng S., Hao K., Feenstra B. et al., 2019/05. Nature genetics, 51 (5) pp. 804-814. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_56910884CABD]
DynaStI: A Dynamic Retention Time Database for Steroidomics.
Codesido S., Randazzo G.M., Lehmann F., González-Ruiz V., García A., Xenarios I., Liechti R., Bridge A., Boccard J., Rudaz S., 2019/04/30. Metabolites, 9 (5) p. 85. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_025EBCF708FD]
Navigating in vitro bioactivity data by investigating available resources using model compounds.
Ilmjärv S., Augsburger F., Bolleman J.T., Liechti R., Bridge A.J., Sandström J., Jaquet V., Xenarios I., Krause K.H., 2019/04/29. Scientific data, 6 (1) p. 45. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_55F187AAC00A]
Genetic studies of accelerometer-based sleep measures yield new insights into human sleep behaviour.
Jones S.E., van Hees V.T., Mazzotti D.R., Marques-Vidal P., Sabia S., van der Spek A., Dashti H.S., Engmann J., Kocevska D., Tyrrell J. et al., 2019/04/05. Nature communications, 10 (1) p. 1585. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_689ECE78C085]
Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.
Panfilio K.A., Vargas Jentzsch I.M., Benoit J.B., Erezyilmaz D., Suzuki Y., Colella S., Robertson H.M., Poelchau M.F., Waterhouse R.M., Ioannidis P. et al., 2019/04/02. Genome biology, 20 (1) p. 64. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1F5349B51FC7]
 
Going Beyond the Sequences: TCR Binding Patterns at the Service of Cancer Detection.
Zoete V., Coukos G., 2019/04/01. Cancer research, 79 (7) pp. 1299-1301. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B6A2460E1FCA]
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.
Piližota I., Train C.M., Altenhoff A., Redestig H., Dessimoz C., 2019/04/01. Bioinformatics, 35 (7) pp. 1159-1166. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6469004280EE]
 
Publisher Correction: Uncoupling protein 2 reprograms the tumor microenvironment to support the anti-tumor immune cycle.
Cheng W.C., Tsui Y.C., Ragusa S., Koelzer V.H., Mina M., Franco F., Läubli H., Tschumi B., Speiser D., Romero P. et al., 2019/04..
[DOI][WoS][Pmid][serval:BIB_2453C5C48240]
 
Biallelic variants in FBXL3 cause intellectual disability, delayed motor development and short stature.
Ansar M., Paracha S.A., Serretti A., Sarwar M.T., Khan J., Ranza E., Falconnet E., Iwaszkiewicz J., Shah S.F., Qaisar A.A. et al., 2019/03/15. Human molecular genetics, 28 (6) pp. 972-979. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CC3DB25E32E9]
Circulating CD56<sup>bright</sup> NK cells inversely correlate with survival of melanoma patients.
de Jonge K., Ebering A., Nassiri S., Maby-El Hajjami H., Ouertatani-Sakouhi H., Baumgaertner P., Speiser D.E., 2019/03/14. Scientific reports, 9 (1) p. 4487. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_07410EEFFC5B]
 
Simultaneous Bayesian inference of phylogeny and molecular coevolution.
Meyer X., Dib L., Silvestro D., Salamin N., 2019/03/12. Proceedings of the National Academy of Sciences of the United States of America, 116 (11) pp. 5027-5036. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AA4DD85D4A30]
Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi).
Kapheim K.M., Pan H., Li C., Blatti C., Harpur B.A., Ioannidis P., Jones B.M., Kent C.F., Ruzzante L., Sloofman L. et al., 2019/03/07. G3, 9 (3) pp. 625-634. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_403A684B1A7B]
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