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| 2. |
- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Adcox, K, et al.
(författare)
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PHENIX detector overview
- 2003
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 499:2-3, s. 469-479
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Tidskriftsartikel (refereegranskat)abstract
- The PHENIX detector is designed to perform a broad study of A-A, p-A, and p-p collisions to investigate nuclear matter under extreme conditions. A wide variety of probes, sensitive to all timescales, are used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon. Designing for the needs of the heavy-ion and polarized-proton programs has produced a detector with unparalleled capabilities. PHENIX measures electron and muon pairs, photons, and hadrons with excellent energy and momentum resolution. The detector consists of a large number of subsystems that are discussed in other papers in this volume. The overall design parameters of the detector are presented. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 4. |
- Noguchi, S, et al.
(författare)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Tidskriftsartikel (refereegranskat)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 5. |
- Ramilowski, JA, et al.
(författare)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 6. |
- Shrestha, R, et al.
(författare)
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Molecular pathogenesis of progression to myeloid leukemia from TET-insufficient status
- 2020
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Ingår i: Blood advances. - : American Society of Hematology. - 2473-9537 .- 2473-9529. ; 4:5, s. 845-854
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Tidskriftsartikel (refereegranskat)abstract
- Loss-of-function mutations in ten-eleven translocation-2 (TET2) are recurrent events in acute myeloid leukemia (AML) as well as in preleukemic hematopoietic stem cells (HSCs) of age-related clonal hematopoiesis. TET3 mutations are infrequent in AML, but the level of TET3 expression in HSCs has been found to decline with age. We examined the impact of gradual decrease of TET function in AML development by generating mice with Tet deficiency at various degrees. Tet2f/f and Tet3f/f mice were crossed with mice expressing Mx1-Cre to generate Tet2f/wtTet3f/fMx-Cre+ (T2ΔT3), Tet2f/fTet3f/wtMx-Cre+ (ΔT2T3), and Tet2f/fTet3f/fMx-Cre+ (ΔT2ΔT3) mice. All ΔT2ΔT3 mice died of aggressive AML at a median survival of 10.7 weeks. By comparison, T2ΔT3 and ΔT2T3 mice developed AML at longer latencies, with a median survival of ∼27 weeks. Remarkably, all 9 T2ΔT3 and 8 ΔT2T3 mice with AML showed inactivation of the remaining nontargeted Tet2 or Tet3 allele, respectively, owing to exonic loss in either gene or stop-gain mutations in Tet3. Recurrent mutations other than Tet3 were not noted in any mice by whole-exome sequencing. Spontaneous inactivation of residual Tet2 or Tet3 alleles is a recurrent genetic event during the development of AML with Tet insufficiency.
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| 7. |
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| 8. |
- Teslovich, Tanya M., et al.
(författare)
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Biological, clinical and population relevance of 95 loci for blood lipids
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 466:7307, s. 707-713
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Tidskriftsartikel (refereegranskat)abstract
- Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P<5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
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| 9. |
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| 11. |
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| 12. |
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| 13. |
- Gerostathopoulos, Ilias, et al.
(författare)
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Continuous Data-driven Software Engineering : Towards a Research Agenda
- 2019
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Ingår i: Software Engineering Notes. - : Association for Computing Machinery (ACM). - 0163-5948 .- 1943-5843. ; 44:3, s. 60-64
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Tidskriftsartikel (refereegranskat)abstract
- The rapid pace with which software needs to be built, together with the increasing need to evaluate changes for end users both quantitatively and qualitatively calls for novel software engineering approaches that focus on short release cycles, continuous deployment and delivery, experiment-driven feature development, feedback from users, and rapid tool-assisted feedback to developers. To realize these approaches there is a need for research and innovation with respect to automation and tooling, and furthermore for research into the organizational changes that support flexible data-driven decision-making in the development lifecycle. Most importantly, deep synergies are needed between software engineers, managers, and data scientists. This paper reports on the results of the joint 5th International Workshop on Rapid Continuous Software Engineering (RCoSE 2019) and the 1st International Workshop on Data-Driven Decisions, Experimentation and Evolution (DDrEE 2019), which focuses on the challenges and potential solutions in the area of continuous data-driven software engineering.
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| 14. |
- Winkler, C., et al.
(författare)
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Effect of surfactant redistribution on weld pool shape during gas tungsten arc welding
- 2000
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Ingår i: Science and technology of welding and joining. - : Informa UK Limited. - 1362-1718 .- 1743-2936. ; 5:1, s. 8-20
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Tidskriftsartikel (refereegranskat)abstract
- In previous evaluations, of GTA welding stainless steel plates the surfactant content in the workplace has been assumed to be in a state of equilibrium. However surfactant concentration usually had to be adjusted in order to achieve agreement between the weld pool shapes in experiments and those in simulations. In this study a physiochemical approach to the redistribution of surfactant at the surface and in the bulk is presented for the first time. Sulphur was considered as a represenative surfactant. The model allows surfactant molecular transport via convection, diffusion, and sorption. It is shown that sulphur atoms accumulate at the surface at stagnation points, affecting the coefficient of surface tension and thus the final weld pool shape. Thus, the sulphur content in the simulation approaches the nominal sulphur content in the steel plate. The theory is strenghtened by both electron probe microanalysis and Auger electron spectroscopy. At the time the work was carried out, Mr Winkler, Dr Inoue and Mr Fuji were at the Welding and Joining Reserach Center, Steel Reserach Laboratories, Technical Development Bureau, Nippon Steel Corp., 20-1 Shintomi, Futtsu, Chiba 293, Japan, Dr Amberg was in the Department of Mechanics, Royal Institute of Technology, Osquars Backe 18, 100-44 Stockholm, Sweden, and Dr Koseki was at the Oita R&D Laboratories, Nippon Steel Corp., 1 Nishinosu, Oita 870, Japan. Mr Winkler is now in the Department of Mechanics, Royal Institute of Technology, Manuscript received 4 March 1999; accepted 8 April 1999.
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