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40 results for โgenetic phasingโ
VCF data for genetic polyploid phasing
<p>Used data for evaluation in pending Recomb 2022 submission "Genetic Polyploid Phasing using Marker Signals from Low-Depth Progeny Samples". Data was used in and partly created by the scripts from here: https://github.com/AlBi-HHU/genetic-phasing-scripts</p>
Dataset: A phase field model combined with genetic algorithm for polycrystalline hafnium zirconium oxide ferroelectrics
<p>The folder includes generated data MATLAB scripts to read/plot the polarization-electric field (PE) hysteresis curves. The dataset contains phase field generated polycrystalline grain structure, simulated domain structures during polarization reversal, and symmetric PE curves (measured and simulated).</p> <p><strong>Polycrystalline grain structures</strong>: The output files are in the *.txt format, readable by MTEX to generate orientation maps.<br> Column(1) Column(2) Column(3) Column(4) Column(5)<br> X Y φ(rad) θ(rad) ๐(rad)<br> ... ... ... ... ...<br> ... ... ... ... ...<br> ... ... ... ... ...</p> <p><strong>Domain structures</strong>: The output files are in the *.csv format, which can be visualized by programs like ParaView.<br> Column(1) Column(2) Column(3) Column(4)<br> X Y Z P<br> ... ... ... ...<br> ... ... ... ...<br> ... ... ... ...</p> <p><br> <strong>PE curves</strong>: The output files are in the *.txt format, readable by MATLAB.<br> Column(1) Column(2)<br> E(MV/cm) P(μC/cm²)<br> ... ...<br> ... ...<br> ... ...</p> <p><strong>List of datasets:-</strong><br> Fig. 1: pecurves/calib_func1.txt (Calibrated p(e)), pecurves/measpe_hf50.txt (Measured PE curve), pecurves/simpe_calib.txt (Simulated PE curve).<br> Fig. 2(a): polcr_struc/xy_col.txt (XY top view), polcr_struc/yz_col.txt (YZ side view), polcr_struc/xz_col.txt (ZX side view)<br> Fig. 2(b): pecurves/simpe_gaopt.txt (Simulated PE curve), pecurves/measpe_hf50.txt (Measured PE curve).<br> Fig. 3: pecurves/calib_func.txt (Calibrated p(e)), pecurves/gaopt_func.txt (GA optimized p(e)).<br> Fig. 5: pecurves/simpe_gaopt.txt (Case 1), pecurves/simpe_elast.txt (Case 2).<br> Fig. 4(e): dom_struc/dom_profile1.csv, (f) dom_struc/dom_profile2.csv, (g) dom_struc/dom_profile3.csv, (h) dom_struc/dom_profile4.csv, (m) dom_struc/dom_profile5.csv, (n) dom_struc/dom_profile6.csv, (o) dom_struc/dom_profile7.csv, (p) dom_struc/dom_profile8.csv<br> Fig. 6: pecurves/simpe_gaopt.txt (GA fit coefficients), pecurves/simpe_ldc1.txt (Set 1), pecurves/simpe_ldc2.txt (Set 2).<br> Fig. 7(a): pecurves/simpe_gaopt.txt (๐โ = 1.0), pecurves/simpe_fr80.txt (๐โ = 0.8), pecurves/simpe_fr50.txt (๐โ = 0.5).<br> Fig. 7(b): pecurves/measpe_hf50.txt (Hfโ.โ Zrโ.โ Oโ), pecurves/measpe_hf75.txt (Hfโ.โโ Zrโ.โโ Oโ).<br> Fig. 8: pecurves/simpe_fr38.txt (Simulated PE curve), pecurves/measpe_hf75.txt (Measured PE curve).<br> Fig. 9: pecurves/simpe_gaopt.txt (Random non-textured), pecurves/simpe_tex001.txt ([001] fiber textured), pecurves/simpe_tex111.txt ([111] fiber textured).<br> Fig. 10(a): polcr_struc/xy_equ.txt (XY top view), polcr_struc/yz_equ.txt (YZ side view), polcr_struc/xz_equ.txt (ZX side view)<br> Fig. 10(b): pecurves/simpe_colmor.txt (Columnar grain microstructure), pecurves/simpe_equmor.txt (Equiaxed grain microstructure).</p> <p><strong>List of MATLAB scripts:</strong><br> Fig 1: matlab_scripts/fig1.m<br> Fig 2(b): matlab_scripts/fig2b.m<br> Fig 3: matlab_scripts/fig3.m<br> Fig 5: matlab_scripts/fig5.m<br> Fig 6: matlab_scripts/fig6.m<br> Fig 7(a): matlab_scripts/fig7a.m<br> Fig 7(b): matlab_scripts/fig7b.m<br> Fig 8: matlab_scripts/fig8.m<br> Fig 9: matlab_scripts/fig9.m<br> Fig 10(b): matlab_scripts/fig10b.m<br> </p>
Phase I Study of LDK378 in Pediatric, Malignancies With a Genetic Alteration in Anaplastic Lymphoma Kinase (ALK)
ClinicalTrials.gov study NCT01742286. IPD Sharing: NO. Countries: 10. Publications: 2.
Setmelanotide Phase 2 Treatment Trial in Participants With Rare Genetic Disorders of Obesity
ClinicalTrials.gov study NCT03013543. IPD Sharing: NO. Countries: 9. Publications: 2.
A Phase 1/2A, Randomized Study of a T Follicular Helper (TFH)-Targeting Genetic Vaccine Strategy Designed to Induce Broad, Durable Immune Responses
ClinicalTrials.gov study NCT06810934. IPD Sharing: YES. Countries: 1. Publications: 10.
Phase 2 Study of MGCD265 in Patients With Non-Small Cell Lung Cancer With Activating Genetic Alterations in MET
ClinicalTrials.gov study NCT02544633. IPD Sharing: NO. Countries: 9. Publications: 2.
Phase 1/2 Study of Derazantinib (ARQ 087) in Adult Subjects With Advanced Solid Tumors With FGFR Genetic Alterations
ClinicalTrials.gov study NCT01752920. IPD Sharing: Not stated. Countries: 2. Publications: 3.
Data from: Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex
Closely related species with divergent life-history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and north-eastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale we found a high genetic structure within the brooders (COI: 0.07
Aberrant phase separation and nucleolar dysfunction can underlie rare genetic diseases
<p>This dataset provides companion data to the paper "Aberrant phase separation and nucleolar dysfunction can underlie rare genetic diseases". It includes raw data, images and computational code to generate the figures in the study.</p>
A Phase II Study of Nivolumab in Patients With Genetic Alterations in DNA Damage Repair and Response Who Progressed After Standard Treatment for Metastatic Solid Cancers
ClinicalTrials.gov study NCT04761744. IPD Sharing: NO. Countries: 1. Publications: 33.
A Phase 1/2 Study of High-dose Genetically Targeted Enzyme Replacement Therapy for Advanced Heart Failure
ClinicalTrials.gov study NCT02346422. IPD Sharing: Not stated. Countries: 1. Publications: 3.
A Phase I Study of T-Cells Genetically Modified at the CCR5 Gene by Zinc Finger Nucleases SB-728mR in HIV-Infected Patients
ClinicalTrials.gov study NCT02388594. IPD Sharing: Not stated. Countries: 1. Publications: 1.
An Open Label Phase I Study to Eval the Safety and Tolerability of a Vaccine (GI-6207) Consisting of Whole, Heat-killed Recombinant Saccharomyces Cerevisiae (Yeast) Genetically Modified to Express CEA
ClinicalTrials.gov study NCT00924092. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex
Open the record for dataset details and reuse information.
Data from: Demographic processes shaping genetic variation of the solitarious phase of the desert locust
Open the record for dataset details and reuse information.
Data from: Genetic drift during the spread phase of a biological invasion
Recent theoretical and experimental models have evidenced the role played by evolution during species spread, and particularly question the influence of genetic drift at range edges. By investigating the spread of an aquatic invader in patchy habitats, we quantified genetic drift and explored its consequences on genetic diversity and fitness. We examined the interplay of gene flow and genetic drift in 36 populations of the red swamp crayfish, Procambarus clarkii, in a relatively recently invaded wetland area (30 years, Briรจre, northwestern France). Despite the small spatial scale of our study (15 kmยฒ), populations were highly structured according to the strong barrier of land surfaces and revealed a clear pattern of colonisation through watercourses. Isolated populations exhibited small effective sizes and low dispersal rates that depended on water connectivity, suggesting that genetic drift dominated in the evolution of allele frequencies in these populations. We also observed a significant decrease in the genetic diversity of isolated populations over only a two-year period, but failed to demonstrate an associated fitness cost using fluctuating asymmetry. This study documents the possible strong influence of genetic drift during the spread of a species, and such findings provide critical insights in the current context of profound rearrangements in species distributions due to global change.
Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
<p>Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho G.C., Anglin N.L., Bachem C.W.B., Endelman J.B., Shannon L.M., Strรถmvik M.V., Tai H.H., Usadel B., Buell C.R., and Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.01.003.</p> <p>Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. Theย <em>StCDF1</em>ย locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.</p>
First Year Growth Response Associated Genetic Markers Validation Phase IV Open-label Study in Growth Hormone Deficient and Turner Syndrome Pre-pubertal Children: the PREDICT Pharmacogenetics Validatio
ClinicalTrials.gov study NCT01419249. IPD Sharing: Not stated. Countries: 9. Publications: 0.
Genetically Engineered HSV-1 Phase 1 Study for the Treatment of Recurrent Malignant Glioma
ClinicalTrials.gov study NCT02062827. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Phase II Trial of BIBW 2992 (Afatinib) in Genetically Pre-screened Cancers With EGFR and/or HER2 Gene Amplification.
ClinicalTrials.gov study NCT00748709. IPD Sharing: NO. Countries: 2. Publications: 0.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.