ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

Unknown

Public data and open source tools for multi-assay genomic investigation of disease (2016)

Kannan, L., Ramos, M., Re, A., El-Hachem, N., Safikhani, Z., Gendoo, D. M. A., Davis, S., Gomez-Cabrero, D., Castelo, R., Hansen, K. D., Carey, V. J., Morgan, M., Culhane, A. C., Haibe-Kains, B., Waldron, L.

Oxford University Press

In: Briefings in Bioinformatics

add to mindlist on the mindlist

Details

Publication Date: 2016-07-16

Description: Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.

Print ISSN: 1467-5463

Electronic ISSN: 1477-4054

Topics: Biology , Computer Science

Published by Oxford University Press

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

2

Unknown

Anisotropy from SKS splitting across the Pacific-North America plate boundary offshore southern California (2016)

Ramsay, J., Kohler, M. D., Davis, P. M., Wang, X., Holt, W., Weeraratne, D. S.

Oxford University Press

In: Geophysical Journal International

add to mindlist on the mindlist

Details

Publication Date: 2016-08-25

Description: SKS arrivals from ocean bottom seismometer (OBS) data from an offshore southern California deployment are analysed for shear wave splitting. The project involved 34 OBSs deployed for 12 months in a region extending up to 500 km west of the coastline into the oceanic Pacific plate. The measurement process consisted of removing the effects of anisotropy using a range of values for splitting fast directions and delay times to minimize energy along the transverse seismometer axis. Computed splitting parameters are unexpectedly similar to onland parameters, exhibiting WSW–ENE fast polarization directions and delays between 0.8 and 1.8 s, even for oceanic plate sites. This is the first SKS splitting study to extend across the entire boundary between the North America and Pacific plates, into the oceanic part of the Pacific plate. The splitting results show that the fast direction of anisotropy on the Pacific plate does not align with absolute plate motion (APM), and they extend the trend of anisotropy in southern California an additional 500 km west, well onto the oceanic Pacific plate. We model the finite strain and anisotropy within the asthenosphere associated with density–buoyancy driven mantle flow and the effects of APM. In the absence of plate motion effects, such buoyancy driven mantle flow would be NE-directed beneath the Pacific plate observations. The best-fit patterns of mantle flow are inferred from the tomography-based models that show primary influences from foundering higher-density zones associated with the history of subduction beneath North America. The new offshore SKS measurements, when combined with measurements onshore within the plate boundary zone, indicate that dramatic lateral variations in density-driven upper-mantle flow are required from offshore California into the plate boundary zone in California and western Basin and Range.

Keywords: Seismology

Print ISSN: 0956-540X

Electronic ISSN: 1365-246X

Topics: Geosciences

Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

3

Unknown

The action dimension of right-angled Artin groups (2016)

Avramidi, G., Davis, M. W., Okun, B., Schreve, K.

Oxford University Press

In: Bulletin of the London Mathematical Society

add to mindlist on the mindlist

Details

Publication Date: 2016-01-23

Description: The action dimension of a discrete group $\Gamma $ is the smallest dimension of a contractible manifold that admits a proper action of $\Gamma $ . Associated to any flag complex $L$ there is a right-angled Artin group, $A_L$ . We compute the action dimension of $A_L$ for many $L$ . Our calculations come close to confirming the conjecture that if an $\ell ^2$ -Betti number of $A_L$ in degree $l$ is nonzero, then the action dimension of $A_L$ is $\geqslant 2l$ .

Print ISSN: 0024-6093

Electronic ISSN: 1469-2120

Topics: Mathematics

Published by Oxford University Press

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

4

Unknown

Function spectra and continuous G-spectra (2011)

Davis, D. G.

Oxford University Press

In: Bulletin of the London Mathematical Society

add to mindlist on the mindlist

Details

Publication Date: 2011-11-24

Description: Let G be a profinite group, { X α } α be a cofiltered diagram of discrete G -spectra, and Z be a spectrum with trivial G -action. We show how to define the homotopy fixed point spectrum F ( Z , holim α X α ) hG and that when G has finite virtual cohomological dimension (vcd), it is equivalent to F ( Z , holim α ( X α ) hG ). With these tools, we show that the K ( n )-local Spanier–Whitehead dual is always a homotopy fixed point spectrum, a well-known Adams-type spectral sequence is actually a descent spectral sequence, and, for a sufficiently nice k -local profinite G -Galois extension E , with K G and closed, the equivalence (due to Behrens and the author), where denotes k -local homotopy fixed points, can be upgraded to an equivalence that just uses ordinary ( non-local ) homotopy fixed points, when G / K has finite vcd.

Print ISSN: 0024-6093

Electronic ISSN: 1469-2120

Topics: Mathematics

Published by Oxford University Press

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

5

Unknown

Observations of discards in the Scottish mixed demersal trawl fishery (2011)

Fernandes, P. G., Coull, K., Davis, C., Clark, P., Catarino, R., Bailey, N., Fryer, R., Pout, A.

Oxford University Press

In: ICES Journal of Marine Science

add to mindlist on the mindlist

Details

Publication Date: 2011-11-24

Description: Fernandes, P. G., Coull, K., Davis, C., Clark, P., Catarino, R., Bailey, N., Fryer, R., and Pout, A. 2011. Observations of discards in the Scottish mixed demersal trawl fishery. – ICES Journal of Marine Science, 68: 1734–1742. The Marine Laboratory in Aberdeen (now part of Marine Scotland Science) has operated a scientific observer programme in the Scottish mixed demersal trawl fishery for more than 20 years. Discards of the main demersal species (cod, haddock, whiting, and saithe) have been sampled according to a stratified design based on gear, area, and month, with quota sampling used to select vessels. The aim of the programme is to estimate the quantity (at age) of the discarded component of the catch, to contribute to estimates of total catch for these species so that assessments of each stock can be made. Trends of discards from this observer programme from 1987 to 2009 are reported. Notable features include the sudden practice of discarding marketable cod in 2007. This was due to a number of factors including, paradoxically, improvements in compliance measures which meant that fish could no longer be landed illegally. Methods for raising the sampled discards to the level of the fleet are also explored and discussed in relation to changes in discarding patterns. These are particularly relevant at a time when, in northern Europe at least, there is a move towards standardizing methods for estimating total quantities of discards.

Print ISSN: 1054-3139

Electronic ISSN: 1095-9289

Topics: Biology , Geosciences , Physics

Published by Oxford University Press

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

6

Unknown

Fast solution of geophysical inversion using adaptive mesh, space-filling curves and wavelet compression (2011)

Kristofer Davis; Yaoguo Li

Oxford University Press

In: Geophysical Journal International

add to mindlist on the mindlist

Details

Publication Date: 2011-02-04

Description: SUMMARY Many geophysical inverse problems involve large and dense coefficient matrices that often exceed the limitations of physical memory in commonly available computers. The repeated multiplications of such matrices to vectors during processing or inversion require an immense amount of computing power. These two factors pose a significant challenge to solving large-scale inverse problems in practice and can render many realistic problems intractable. To overcome these limitations, we develop a new computational approach for this class of problems by combining an adaptive quadtree or octree model discretization and wavelet transforms on reordered parameter sets. The adaptive mesh discretizes the model region according to the required resolutions based on localized anomalies. Hilbert space-filling curves and similar ordering of the reduced parameter set then enable a higher compression of the coefficient matrix by forming its sparse representation in the 1-D wavelet domain. This combination can reduce the storage requirement by 100 to 1000 times and, therefore, also speeds up the computation during the processing stage by the same factor. As a result, problems can now be solved that were computationally prohibitive. We present the algorithm and illustrate its effectiveness with an example from equivalent source construction in potential-field processing.

Print ISSN: 0956-540X

Electronic ISSN: 1365-246X

Topics: Geosciences

Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

7

Unknown

Towards using direct methods in seismic tomography: computation of the full resolution matrix using high-performance computing and sparse QR factorization (2016)

Bogiatzis, P., Ishii, M., Davis, T. A.

Oxford University Press

In: Geophysical Journal International

add to mindlist on the mindlist

Details

Publication Date: 2016-03-14

Description: For more than two decades, the number of data and model parameters in seismic tomography problems has exceeded the available computational resources required for application of direct computational methods, leaving iterative solvers the only option. One disadvantage of the iterative techniques is that the inverse of the matrix that defines the system is not explicitly formed, and as a consequence, the model resolution and covariance matrices cannot be computed. Despite the significant effort in finding computationally affordable approximations of these matrices, challenges remain, and methods such as the checkerboard resolution tests continue to be used. Based upon recent developments in sparse algorithms and high-performance computing resources, we show that direct methods are becoming feasible for large seismic tomography problems. We demonstrate the application of QR factorization in solving the regional P -wave structure and computing the full resolution matrix with 267 520 model parameters.

Keywords: Seismology

Print ISSN: 0956-540X

Electronic ISSN: 1365-246X

Topics: Geosciences

Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).

Permalink

	Location	Call Number	Expected	Availability

Others were also interested in ...

PAPER CURRENT

S·F·X

Fulltext

8

Unknown

STAMS: STRING-assisted module search for genome wide association studies and application to autism (2016)

Hillenmeyer, S., Davis, L. K., Gamazon, E. R., Cook, E. H., Cox, N. J., Altman, R. B.

Oxford University Press

In: Bioinformatics

add to mindlist on the mindlist

Details

Publication Date: 2016-12-20

Description: Motivation: Analyzing genome wide association data in the context of biological pathways helps us understand how genetic variation influences phenotype and increases power to find associations. However, the utility of pathway-based analysis tools is hampered by undercuration and reliance on a distribution of signal across all of the genes in a pathway. Methods that combine genome wide association results with genetic networks to infer the key phenotype-modulating subnetworks combat these issues, but have primarily been limited to network definitions with yes/no labels for gene-gene interactions. A recent method (EW_dmGWAS) incorporates a biological network with weighted edge probability by requiring a secondary phenotype-specific expression dataset. In this article, we combine an algorithm for weighted-edge module searching and a probabilistic interaction network in order to develop a method, STAMS, for recovering modules of genes with strong associations to the phenotype and probable biologic coherence. Our method builds on EW_dmGWAS but does not require a secondary expression dataset and performs better in six test cases. Results: We show that our algorithm improves over EW_dmGWAS and standard gene-based analysis by measuring precision and recall of each method on separately identified associations. In the Wellcome Trust Rheumatoid Arthritis study, STAMS-identified modules were more enriched for separately identified associations than EW_dmGWAS (STAMS P -value 3.0 x 10 –4 ; EW_dmGWAS- P -value = 0.8). We demonstrate that the area under the Precision-Recall curve is 5.9 times higher with STAMS than EW_dmGWAS run on the Wellcome Trust Type 1 Diabetes data. Availability and Implementation: STAMS is implemented as an R package and is freely available at https://simtk.org/projects/stams . Contact: rbaltman@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Print ISSN: 1367-4803

Electronic ISSN: 1460-2059

Topics: Biology , Computer Science , Medicine

Published by Oxford University Press

Permalink