Search Results - "Genomics methods"

Nucleotide dependency analysis of genomic language models detects functional elements

Authors: Tomaz da Silva, Pedro Karollus, Alexander Hingerl, Johannes et al.

Source: Nature Genetics. 57(10):2589-2602

Subject Terms: Genetic, Models, Humans, Nucleic Acid Conformation, Genome/genetics, RNA/genetics, Nucleotides/genetics, Genomics/methods

Access URL: https://research.rug.nl/en/publications/3d5add9d-35f2-4c78-a3dc-7f9d53852abb
https://hdl.handle.net/11370/3d5add9d-35f2-4c78-a3dc-7f9d53852abb

A Case‐Driven Multi‐Omics Analysis for Longitudinal Ibrutinib Response Evaluation of Patients With Chronic Lymphocytic Leukemia

Authors: Sólja Remisdóttir Veyhe Marcus Høy Hansen Oriane Cédile et al.

Source: Eur J Haematol
Veyhe, S R, Hansen, M H, Cédile, O, Møller, M B, Nielsen, M K, Thomassen, M, Juul-Jensen, K, Frederiksen, H, Dybkær, K & Nyvold, C G 2025, 'A Case-Driven Multi-Omics Analysis for Longitudinal Ibrutinib Response Evaluation of Patients With Chronic Lymphocytic Leukemia', European Journal of Haematology, vol. 114, no. 6, pp. 973-981. https://doi.org/10.1111/ejh.14397

Subject Terms: Male, Piperidines/therapeutic use, Protein Kinase Inhibitors/therapeutic use, B-Cell/drug therapy, Pyrazoles/therapeutic use, Piperidines, Humans, Chronic, Protein Kinase Inhibitors, Aged, Leukemia, Adenine, Gene Expression Profiling, Ibrutinib, Pyrimidines/therapeutic use, Genomics, multi-omics, Middle Aged, Multiomics, Leukemia, Lymphocytic, Chronic, B-Cell, Lymphocytic, Genomics/methods, single-cell RNA, Treatment Outcome, Pyrimidines, Pyrazoles, Original Article, Female, Adenine/analogs & derivatives, Transcriptome, clonal stability

Access URL: https://pubmed.ncbi.nlm.nih.gov/39988467
http://www.scopus.com/inward/record.url?scp=85218683625&partnerID=8YFLogxK
https://doi.org/10.1111/ejh.14397
https://vbn.aau.dk/da/publications/2b8ae2cd-cbbe-422b-9be8-bd3f38d9afc2
https://portal.findresearcher.sdu.dk/da/publications/7cdf729a-98ed-4d1b-80f8-df5adf7a8b50
https://doi.org/10.1111/ejh.14397

Population-based, first-tier genomic newborn screening in the maternity ward

Authors: François Boemer Kristine Hovhannesyan Flavia Piazzon et al.

Contributors: François Boemer Kristine Hovhannesyan Flavia Piazzon et al.

Source: Nat Med

Subject Terms: Male, Infant, Newborn, High-Throughput Nucleotide Sequencing, Genetics & genetic processes, Pilot Projects, Genomics, Life sciences, Neonatal Screening/methods, Article, Genomics/methods, Génétique & processus génétiques, Neonatal Screening, Belgium, Sciences du vivant, Humans, Female, Genetic Testing, Prospective Studies, Genetic Testing/methods

Access URL: https://pubmed.ncbi.nlm.nih.gov/39875687
https://hdl.handle.net/2268/329124
https://doi.org/10.1038/s41591-024-03465-x

Comprehensive genomic characterization of early-stage bladder cancer

Authors: Frederik Prip Philippe Lamy Sia Viborg Lindskrog et al.

Source: Nat Genet
Prip, F, Lamy, P, Lindskrog, S V, Strandgaard, T, Nordentoft, I, Birkenkamp-Demtröder, K, Birkbak, N J, Kristjánsdóttir, N, Kjær, A, Andreasen, T G, Ahrenfeldt, J, Pedersen, J S, Rasmussen, A M, Hermann, G G, Mogensen, K, Petersen, A C, Hartmann, A, Grimm, M-O, Horstmann, M, Nawroth, R, Segersten, U, Sikic, D, van Kessel, K E M, Zwarthoff, E C, Maurer, T, Simic, T, Malmström, P-U, Malats, N, Jensen, J B, UROMOL Consortium, Real, F X & Dyrskjøt, L 2025, 'Comprehensive genomic characterization of early-stage bladder cancer', Nature Genetics, vol. 57, no. 1, 2301, pp. 115-125. https://doi.org/10.1038/s41588-024-02030-z
Prip, F, Lamy, P, Lindskrog, S V, Strandgaard, T, Nordentoft, I, Birkenkamp-Demtröder, K, Birkbak, N J, Kristjánsdóttir, N, Kjær, A, Andreasen, T G, Ahrenfeldt, J, Pedersen, J S, Rasmussen, A M, Hermann, G G, Mogensen, K, Petersen, A C, Hartmann, A, Grimm, M O, Horstmann, M, Nawroth, R, Segersten, U, Sikic, D, van Kessel, K E M, Zwarthoff, E C, Maurer, T, Simic, T, Malmström, P U, Malats, N, Jensen, J B, Real, F X, Dyrskjøt, L & UROMOL Consortium 2025, 'Comprehensive genomic characterization of early-stage bladder cancer', Nature Genetics, vol. 57, no. 1, 2301, pp. 115-125. https://doi.org/10.1038/s41588-024-02030-z

Subject Terms: Male, Medizin, Loss of Heterozygosity, Article, Genomic Instability, Tumour biomarkers, SDG 3 - Good Health and Well-being, Exome Sequencing, Humans, Receptor, Fibroblast Growth Factor, Type 3, Aged, Neoplasm Staging, Cancer och onkologi, Whole Genome Sequencing, Bladder cancer, Urinary Bladder Neoplasms/genetics, Genomics, Middle Aged, Genomics/methods, Receptor, Fibroblast Growth Factor, Type 3/genetics, Urinary Bladder Neoplasms, Cancer and Oncology, Mutation, Tumor Suppressor Protein p53/genetics, Female, Tumor Suppressor Protein p53

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39753772
https://vbn.aau.dk/da/publications/de5b839f-abf3-47fe-8ad8-e0784e4b0a92
https://doi.org/10.1038/s41588-024-02030-z
http://www.scopus.com/inward/record.url?scp=85214112361&partnerID=8YFLogxK
https://vbn.aau.dk/ws/files/767142418/Prip_et_al._2025_._Comprehensive_genomic_characterization_of_early-stage_bladder_cancer.pdf
https://pure.eur.nl/en/publications/9b4d926a-442d-4a12-9468-1b6c722e617e
https://doi.org/10.1038/s41588-024-02030-z
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-555253
https://pure.au.dk/portal/en/publications/a1473982-e664-4e40-a883-8d322d8645e2
https://doi.org/10.1038/s41588-024-02030-z
http://www.scopus.com/inward/record.url?scp=85214112361&partnerID=8YFLogxK
https://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&origin=inward&scp=85214112361
https://doi.org/10.1038/s41588-024-02030-z

GenomicLayers: sequence-based simulation of epi-genomes: sequence-based simulation of epi-genomes

Authors: Gerrard, Dave T

Source: Gerrard, D T 2025, 'GenomicLayers : sequence-based simulation of epi-genomes', BMC Bioinformatics, vol. 26, no. 1, 205. https://doi.org/10.1186/s12859-025-06224-y

Subject Terms: Genetic, Computer Simulation, Epigenomics/methods, Software, Epigenesis, Genetic, Saccharomyces cerevisiae/genetics, Epigenesis, Genomics/methods, Telomere/genetics

Access URL: https://research.manchester.ac.uk/en/publications/35b124d1-38a8-4e57-85bf-69e5a05912ea
https://doi.org/10.1186/s12859-025-06224-y

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

Authors: Byerly, Paige A von Thaden, Alina Leushkin, Evgeny et al.

Contributors: Byerly, Paige A von Thaden, Alina Leushkin, Evgeny et al.

Source: Genome Res

Subject Terms: 0301 basic medicine, 0303 health sciences, Genome, Endangered Species, Genetic Variation, Genomics, Life sciences, Resources, Genomics/methods, Europe, Zoologie, 03 medical and health sciences, Genetics, Population, Haplotypes, Genetics, Sciences du vivant, Animals, Zoology, Genetics (clinical)

Access URL: https://pubmed.ncbi.nlm.nih.gov/39542649
https://hdl.handle.net/2268/331026
https://doi.org/10.1101/gr.279066.124

Evaluating the performance of multi-omics integration: a thyroid toxicity case study

Authors: Sebastian Canzler Kristin Schubert Ulrike E. Rolle-Kampczyk et al.

Source: Arch Toxicol

Subject Terms: Proteomics, Male, Thyroid Gland/metabolism [MeSH], Proteomics/methods [MeSH], Thyroid Gland/drug effects [MeSH], Risk Assessment [MeSH], Humans [MeSH], Risk assessment, Rats [MeSH], Thyroid Gland/pathology [MeSH], Transcriptome/drug effects [MeSH], Genomics/methods [MeSH], Data integration, Animals [MeSH], Chemical exposure, Toxicogenomics and Omics Technologies, Multi-omics, Multiomics [MeSH], Toxicology, Male [MeSH], Metabolomics/methods [MeSH], Toxicity Tests/methods [MeSH], Thyroid Gland, Genomics, Multiomics, Risk Assessment, Rats, Toxicity Tests, Animals, Metabolomics, Humans, Transcriptome

Access URL: https://pubmed.ncbi.nlm.nih.gov/39441382
https://repository.publisso.de/resource/frl:6502259

Zoran aSiM v11 — Injector-Engine AllLabs: Towards a unified reproducibility and compliance framework for INSERM, CEA, INRIA, INRAE, IRD

Authors: Tabary, Frédéric

Subject Terms: Polymorphism, Single Nucleotide/immunology, Artificial intelligence, Epidemiology, Polymorphism, Genetic/immunology, Intelligence, Polymorphism, Single-Stranded Conformational/genetics, Confidence interval 95%, Polymorphic engine, Open Science, Clinical trials, CEA, One-Shot Injector, Mimetic AI, Radiation Genomics, Genomics/standards, Imaging Genomics, Canaliculitis/epidemiology, GDPR, Méthodes & techniques, Amplified Fragment Length Polymorphism Analysis, Polymorphism, Genetic/genetics, HPC & quantique, Polymorphism, Single-Stranded Conformational, INRAE, INSERM, Machine learning robustness, Z3 solver, Insurance, Liability/statistics & numerical data, Polymorphism, Restriction Fragment Length/physiology, HPC simulations, Numerical stability, Polymorphism, Restriction Fragment Length/immunology, Reproducibility • Trust Report • Auditability • Compliance • GDPR • AI, Genomics, Biodiversity, intelligence, INRIA, Polymorphism, Single Nucleotide/genetics, Reproducibility, ISO/IEC 42001, Formal verification, Fractals, Zoran aSiM, injecteur, Auditability, Statistical audit, Agro-climate modeling, IRD, KeyGuardian, Polymorphism, Genetic/radiation effects, Ethical AI, Medical imaging, Polymorphism, Genetic/physiology, Fractal, Genomics/history, Polymorphism, Restriction Fragment Length, Polymorphism, Restriction Fragment Length/genetics, Compliance, Sympy, Injecteur polymorphe, Ciliopathies/epidemiology, Trust Report, Mutation testing, ΔM11.3 fractal memory, Polymorphisme, Polymorphism, Single Nucleotide/physiology, Polymorphism, Single Nucleotide, Social Genomics, AI Act, Genomics/ethics, Polymorphism, Single-Stranded Conformational/immunology, Adversarial testing, ZDM, Computational intelligence, Polymorphism, Genetic, Aircraft/ethics, Property-based testing, Intelligence/classification, Polymorphism, Single-Stranded Conformational/physiology, Chaos testing, Scientific governance, Quantum computing, iA Mimetique, AI Mimetic, Genomics/methods, Polymorphism, Genetic/drug effects, Error propagation, EthicChain, Polymorphism, Single Nucleotide/radiation effects, Conformité & gouvernance

A deep learning approach to prediction of blood group antigens from genomic data

Authors: Camous Moslemi Susanne Sækmose Rune Larsen et al.

Source: Moslemi, C, Sækmose, S, Larsen, R, Brodersen, T, Bay, J T, Didriksen, M, Nielsen, K R, Bruun, M T, Dowsett, J, Dinh, K M, Mikkelsen, C, Hyvärinen, K, Ritari, J, Partanen, J, Ullum, H, Erikstrup, C, Ostrowski, S R, Olsson, M L & Pedersen, O B 2024, 'A deep learning approach to prediction of blood group antigens from genomic data', Transfusion, vol. 64, no. 11, pp. 2179-2195. https://doi.org/10.1111/trf.18013
Moslemi, C, Sækmose, S, Larsen, R, Brodersen, T, Bay, J T, Didriksen, M, Nielsen, K R, Bruun, M T, Dowsett, J, Dinh, K M, Mikkelsen, C, Hyvärinen, K, Ritari, J, Partanen, J, Ullum, H, Erikstrup, C, Ostrowski, S R, Olsson, M L & Pedersen, O B 2024, ' A deep learning approach to prediction of blood group antigens from genomic data ', Transfusion, vol. 64, no. 11, pp. 2179-2195 . https://doi.org/10.1111/trf.18013

Subject Terms: Male, Neural Networks, Genotype, Denmark, convolutional neural network, deep learning, Blood Donors, Genomics, Blood Group Antigens/genetics, Genomics/methods, Computer, genetic prediction, Deep Learning, AI, denoising autoencoder, Blood Group Antigens, blood types, Humans, Female, Neural Networks, Computer, Illumina GSA, Finland, blood antigen

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39268576
https://vbn.aau.dk/da/publications/4f9f608b-0303-44a0-81ff-d5b29ee88a03
http://www.scopus.com/inward/record.url?scp=85203695657&partnerID=8YFLogxK
https://doi.org/10.1111/trf.18013
https://vbn.aau.dk/ws/files/754336085/Moslemi_et_al._2024_._A_deep_learning_approach_to_prediction_of_blood_group_antigens_from_genomic_data.pdf
https://curis.ku.dk/ws/files/413547537/Transfusion_2024_Moslemi_A_deep_learning_approach_to_prediction_of_blood_group_antigens_from_genomic_data.pdf
https://portal.findresearcher.sdu.dk/da/publications/dfe236f4-64ee-47aa-9884-5bb074600aec
https://doi.org/10.1111/trf.18013
https://pure.au.dk/portal/en/publications/50522a1c-a772-43cf-ba37-273fe15e2bf0
http://www.scopus.com/inward/record.url?scp=85203695657&partnerID=8YFLogxK
https://doi.org/10.1111/trf.18013

A decision-making framework to maximise the evolutionary potential of populations - Genetic and genomic insights from the common midwife toad (Alytes obstetricans) at its range limits

Authors: Christopher D. Barratt Kathleen Preißler Pauline R. Jennert et al.

Source: Heredity (Edinb)
Heredity vol. 2024

Subject Terms: Conservation of Natural Resources, Conservation biology, Population genetics, Climate Change, Decision Making, Genetic Variation, Genomics, Bufonidae/genetics [MeSH], 631/208/457, Europe [MeSH], Climate Change [MeSH], Polymorphism, Single Nucleotide [MeSH], Adaptation, Physiological/genetics [MeSH], Genetics, Population [MeSH], Genomics/methods [MeSH], Animals [MeSH], Biological Evolution [MeSH], Article, 631/158/2452, 45/77, 45/23, Microsatellite Repeats/genetics [MeSH], Conservation of Natural Resources [MeSH], Anura/genetics [MeSH], 704/158/672, Bufonidae/classification [MeSH], Genetic Variation [MeSH], Decision Making [MeSH], article, Polymorphism, Single Nucleotide, Biological Evolution, Adaptation, Physiological, Bufonidae, Europe, Genetics, Population, Life Science, Animals, Molecular ecology, Anura, Microsatellite Repeats

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Access URL: https://pubmed.ncbi.nlm.nih.gov/39223228
https://repository.publisso.de/resource/frl:6491744
https://research.wur.nl/en/publications/a-decision-making-framework-to-maximise-the-evolutionary-potentia
https://doi.org/10.1038/s41437-024-00710-4
https://repository.naturalis.nl/pub/800756

Genomic analysis of intracranial and subcortical brain volumes yields polygenic scores accounting for variation across ancestries

Authors: Luis M. García-Marín Adrian I. Campos Santiago Diaz-Torres et al.

Contributors: Luis M. García-Marín Adrian I. Campos Santiago Diaz-Torres et al.

Source: medRxiv
Digital.CSIC. Repositorio Institucional del CSIC
Consejo Superior de Investigaciones Científicas (CSIC)
Nature genetics 56(11), 2333-2344 (2024). doi:10.1038/s41588-024-01951-z
Nature Genetics, 56, 11, pp. 2333-2344
Nature Genetics, vol 56, iss 11

Subject Terms: Male, Organ Size/genetics, Multifactorial Inheritance, Biological Psychology, 270 Language and Computation in Neural Systems, Human Genetics - Radboud University Medical Center - DCMN, genetics [Attention Deficit Disorder with Hyperactivity], Medical and Health Sciences, Psychiatry - Radboud University Medical Center - DCMN, pathology [Brain], genetics [Parkinson Disease], Psychology, 2.1 Biological and endogenous factors, Parkinson Disease/genetics, genetics [Multifactorial Inheritance], methods [Genomics], 220 Statistical Imaging Neuroscience, Cognitive Neuroscience - Radboud University Medical Center - DCMN, Brain, Parkinson Disease, Pharmacology and Pharmaceutical Sciences, Single Nucleotide, Organ Size, Genomics, Biological Sciences, Middle Aged, Mental Illness, Bioinformatics and computational biology, Mental Health, Neurological, Mental health, Female, [SHS] Humanities and Social Sciences, Attention Deficit Disorder with Hyperactivity/genetics, White People/genetics, Biotechnology, Adult, Agricultural biotechnology, genetics [White People], Polymorphism, Single Nucleotide, 150 000 MR Techniques in Brain Function, Article, White People, ddc:570, Journal Article, Genetics, Humans, Brain/pathology, Genetic Predisposition to Disease, Polymorphism, Multifactorial Inheritance/genetics, Biomedical and Clinical Sciences, genetics [Organ Size], Human Genome, Neurosciences, pathology [Attention Deficit Disorder with Hyperactivity], Genomics/methods, Brain Disorders, pathology [Parkinson Disease], Good Health and Well Being, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Attention Deficit Disorder with Hyperactivity, name=Bristol Population Health Science Institute, Developmental Biology, Genome-Wide Association Study

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Access URL: https://pubmed.ncbi.nlm.nih.gov/39433889
https://pubmed.ncbi.nlm.nih.gov/39371125
http://hdl.handle.net/10261/382948
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https://research.vu.nl/en/publications/58f7979b-939d-43c2-803d-c9907b080eb4
https://doi.org/10.1038/s41588-024-01951-z
https://hdl.handle.net/1871.1/58f7979b-939d-43c2-803d-c9907b080eb4
https://cris.maastrichtuniversity.nl/en/publications/7059d74f-7105-4417-827c-58fdf7a066b9
https://doi.org/10.1038/s41588-024-01951-z
https://cris.maastrichtuniversity.nl/en/publications/df387d7a-d54e-41be-97eb-9535da578ecd
https://doi.org/10.1101/2024.08.13.24311922
https://dspace.library.uu.nl/handle/1874/459118
https://dspace.library.uu.nl/handle/1874/461144
https://pure.amsterdamumc.nl/en/publications/c860cd0e-54aa-4ba2-975d-b1ba9e2199c1
https://doi.org/10.1038/s41588-024-01951-z
https://repository.ubn.ru.nl//bitstream/handle/2066/313586/313586.pdf
https://hdl.handle.net/2066/313586
https://juser.fz-juelich.de/record/1032350
https://hdl.handle.net/11391/1589699
https://doi.org/10.1038/s41588-024-01951-z
https://hal.science/hal-04797532v1
https://doi.org/10.1038/s41588-024-01951-z
https://escholarship.org/uc/item/4g85k360
https://escholarship.org/content/qt4g85k360/qt4g85k360.pdf
https://escholarship.org/content/qt9bp1077g/qt9bp1077g.pdf
https://escholarship.org/uc/item/9bp1077g

PneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae

Authors: Axel B. Janssen Paddy S. Gibson Afonso M. Bravo et al.

Source: Nucleic Acids Res
Nucleic acids research, vol. 53, no. D1, pp. D839-D851

Subject Terms: Streptococcus pneumoniae, Databases, Genetic, Database Issue, Humans, Streptococcus pneumoniae/genetics, Molecular Sequence Annotation, Genome, Bacterial, Genomics/methods, Software, Multiomics, Genomics, 3. Good health

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39436044
https://serval.unil.ch/notice/serval:BIB_8FB8F0A27BF6
https://serval.unil.ch/resource/serval:BIB_8FB8F0A27BF6.P001/REF.pdf
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_8FB8F0A27BF64

Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases

Authors: Maja Thiele Ida Falk Villesen Lili Niu et al.

Source: Thiele, M, Villesen, I F, Niu, L, Johansen, S, Sulek, K, Nishijima, S, Espen, L V, Keller, M, Israelsen, M, Suvitaival, T, Zawadzki, A D, Juel, H B, Brol, M J, Stinson, S E, Huang, Y, Silva, M C A, Kuhn, M, Anastasiadou, E, Leeming, D J, Karsdal, M, Matthijnssens, J, Arumugam, M, Dalgaard, L T, Legido-Quigley, C, Mann, M, Trebicka, J, Bork, P, Jensen, L J, Hansen, T, Krag, A, MicrobLiver Consortium & GALAXY Consortium 2024, ' Opportunities and barriers in omics-based biomarker discovery for steatotic liver diseases ', Journal of Hepatology, vol. 81, no. 2, pp. 345-359 . https://doi.org/10.1016/j.jhep.2024.03.035
Journal of Hepatology

Subject Terms: Proteomics, viromics, microbiome, ALCOHOL, Biomarkers/analysis, GUT MICROBIOME, VALIDATION, 1117 Public Health and Health Services, VIROME, proteomics, Genetics, Metabolomics/methods, FIBROSIS, Humans, Metabolomics, genetics, GENOME-WIDE ASSOCIATION, GALAXY consortium, Fatty Liver/diagnosis, metagenomics, Science & Technology, metatranscriptomics, Gastroenterology & Hepatology, Non-invasive test, NONALCOHOLIC STEATOHEPATITIS, 3202 Clinical sciences, INCREASED INTESTINAL PERMEABILITY, 1103 Clinical Sciences, Genomics, metabolomics, Genomics/methods, 3. Good health, Fatty Liver, SYSTEMS BIOLOGY, lipidomics, MicrobLiver consortium, Viromics, MULTI-OMICS, Metagenomics, Microbiome, Proteomics/methods, Life Sciences & Biomedicine, Biomarkers

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38552880
https://lirias.kuleuven.be/handle/20.500.12942/740356
https://doi.org/10.1016/j.jhep.2024.03.035
https://curis.ku.dk/ws/files/400206035/1_s2.0_S0168827824002198_main.pdf
https://portal.findresearcher.sdu.dk/da/publications/14c4e941-2b9a-403a-9206-c88f75ebec1f
https://doi.org/10.1016/j.jhep.2024.03.035

Genomic events stratifying prognosis of early gastric cancer

Authors: Molinari C. Solaini L. Rebuzzi F. et al.

Source: Gastric Cancer

Subject Terms: Male, Adult, 0301 basic medicine, LRP1B, 03 medical and health sciences, Stomach Neoplasms, ARID1A, EGC, Pen, Prognosis, Biomarkers, Tumor, Humans, Aged, Aged, 80 and over, 0303 health sciences, Genomics, Middle Aged, DNA-Binding Proteins, Receptors, LDL, Aged, 80 and over [MeSH], Aged [MeSH], Transcription Factors/genetics [MeSH], Stomach Neoplasms/pathology [MeSH], Stomach Neoplasms/surgery [MeSH], Neoplasm Recurrence, Local/pathology [MeSH], Stomach Neoplasms/mortality [MeSH], DNA-Binding Proteins/genetics [MeSH], Original Article, Male [MeSH], Neoplasm Recurrence, Local/genetics [MeSH], Stomach Neoplasms/genetics [MeSH], Female [MeSH], Follow-Up Studies [MeSH], Mutation [MeSH], Adult [MeSH], Humans [MeSH], Genomics/methods [MeSH], Middle Aged [MeSH], Microsatellite Instability [MeSH], Receptors, LDL [MeSH], Biomarkers, Tumor/genetics [MeSH], Prognosis [MeSH], Mutation, Female, Microsatellite Instability, Neoplasm Recurrence, Local, Transcription Factors, Follow-Up Studies

File Description: application/pdf; application/vnd.openxmlformats-officedocument.wordprocessingml.document

Access URL: https://pubmed.ncbi.nlm.nih.gov/39028418
https://repository.publisso.de/resource/frl:6492499
https://link.springer.com/article/10.1007/s10120-024-01536-z
https://doi.org/10.1007/s10120-024-01536-z
https://hdl.handle.net/11585/1001645

Annotation matters: the effect of structural gene annotation on orthology inference

Authors: Silvia Prieto-Baños Yannis Nevers Adrian Altenhoff et al.

Source: Bioinformatics
Bioinformatics, vol. 41, no. 7
Bioinformatics, 41 (7)

Subject Terms: Original Paper, Molecular Sequence Annotation/methods, Genomics/methods, Databases, Genetic, Genome, Computational Biology/methods

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Access URL: http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_1F0C64C7E8640
https://serval.unil.ch/resource/serval:BIB_1F0C64C7E864.P001/REF.pdf
https://serval.unil.ch/notice/serval:BIB_1F0C64C7E864
http://hdl.handle.net/20.500.11850/746800

Combining cross-sectional and longitudinal genomic approaches to identify determinants of cognitive and physical decline

Authors: Tabea Schoeler Jean-Baptiste Pingault Zoltán Kutalik

Source: Nat Commun
Nature Communications, Vol 16, Iss 1, Pp 1-12 (2025)
Nature communications, vol. 16, no. 1, pp. 4524

Subject Terms: Male, Aged, 80 and over, Aging, Science, Genomics, Humans, Cross-Sectional Studies, Genome-Wide Association Study, Longitudinal Studies, Female, Mendelian Randomization Analysis, Aging/genetics, Cognitive Dysfunction/genetics, Aged, Cognition/physiology, Genomics/methods, Middle Aged, Bone Density/genetics, Alzheimer Disease/genetics, Phenotype, Article, Cognition, Bone Density, Alzheimer Disease, Cognitive Dysfunction

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Access URL: https://pubmed.ncbi.nlm.nih.gov/40374629
https://doaj.org/article/1d5722d901134b34ac3082cb3f4ea048
https://serval.unil.ch/resource/serval:BIB_92EB414A7847.P001/REF.pdf
https://serval.unil.ch/notice/serval:BIB_92EB414A7847
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_92EB414A78470

The Estonian Biobank’s journey from biobanking to personalized medicine

Authors: Lili Milani Maris Alver Sven Laur et al.

Source: Nat Commun
Nature Communications, Vol 16, Iss 1, Pp 1-13 (2025)
Nature communications, vol. 16, no. 1, pp. 3270
Nature Communications

Subject Terms: Estonia, Science, Humans, Review Article, Genomics, Precision Medicine, Precision Medicine/methods, Biological Specimen Banks/trends, Biological Specimen Banks/organization & administration, Genomics/methods, Biological Specimen Banks

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40188112
https://doaj.org/article/0e497bbfd7f146d584f1ac321ebeea5f
http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_D419B2E5E20B1
https://serval.unil.ch/notice/serval:BIB_D419B2E5E20B
https://serval.unil.ch/resource/serval:BIB_D419B2E5E20B.P001/REF.pdf

IMBB-FORTH bioinformatics/computational resources & tools

Authors: FORTH Institute of Molecular Biology and Biotechnology Pittis, Alexandros

Subject Terms: transcriptomics, FOS: Clinical medicine, Neurosciences, DNA, Ancient, ancient DNA, Genomics/methods

Implementation of Oxygen Enhanced Magnetic Resonance Imaging (OE-MRI) and a Pilot Genomic Study of Hypoxia in Bladder Cancer Xenografts

Authors: Shabbir, Rekaya Telfer, Brian A Dickie, Ben et al.

Source: Shabbir, R, Telfer, B A, Dickie, B, Reardon, M, Babur, M, Williams, K, West, C M L, Choudhury, A & Smith, T A D 2024, 'Implementation of Oxygen Enhanced Magnetic Resonance Imaging (OE-MRI) and a Pilot Genomic Study of Hypoxia in Bladder Cancer Xenografts', Cancer genomics & proteomics, vol. 21, no. 4, pp. 380-387. https://doi.org/10.21873/cgp.20455

Subject Terms: Tumor, Nude, Urinary Bladder Neoplasms/genetics, Mice, Nude, Hypoxia/diagnostic imaging, Pilot Projects, Genomics, Oxygen/metabolism, Tumor Hypoxia/genetics, Magnetic Resonance Imaging, Xenograft Model Antitumor Assays, Magnetic Resonance Imaging/methods, Genomics/methods, Cell Line, Oxygen, Mice, Urinary Bladder Neoplasms, Cell Line, Tumor, Animals, Humans, Tumor Hypoxia, Heterografts, Female, Hypoxia

Access URL: https://pubmed.ncbi.nlm.nih.gov/38944425

Analysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology

Authors: Kinnersley, B Sud, A Everall, A et al.

Contributors: Kinnersley, B Sud, A Everall, A et al.

Source: Nat Genet
Kinnersley, B, Sud, A, Everall, A, Cornish, A J, Chubb, D, Culliford, R, Gruber, A J, Lärkeryd, A, Mitsopoulos, C, Wedge, D & Houlston, R 2024, 'Analysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology', Nature Genetics, vol. 56, no. 9, pp. 1868-1877. https://doi.org/10.1038/s41588-024-01785-9

Subject Terms: 0301 basic medicine, 0303 health sciences, Genome, Whole Genome Sequencing, Medical Oncology/methods, Genome, Human, Precision Medicine/methods, Genomics, Medical Oncology, Neoplasms/genetics, Article, Genomics/methods, 3. Good health, 03 medical and health sciences, Neoplasms, Mutation, Humans, Precision Medicine, Human

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Access URL: https://pubmed.ncbi.nlm.nih.gov/38890488
https://research.manchester.ac.uk/en/publications/e981cddb-fb21-422c-b305-393cac8407fa
https://doi.org/10.1038/s41588-024-01785-9
https://research.manchester.ac.uk/en/publications/e981cddb-fb21-422c-b305-393cac8407fa
https://doi.org/10.1038/s41588-024-01785-9
http://www.scopus.com/inward/record.url?scp=85196181626&partnerID=8YFLogxK