UNLABELLED: Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows. AVAILABILITY AND IMPLEMENTATION: The R package SomaticSignatures is available as part of the Bioconductor project. Its documentation provides additional details on the methods and demonstrates applications to biological datasets. CONTACT: [email protected], [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: As applications of genome sequencing, including exomes and whole genomes, are expanding, there is a need for analysis tools that are scalable to large sets of samples and/or ultra-deep coverage. Many current tool chains are based on the widely used file formats BAM and VCF or VCF-derivatives. However, for some desirable analyses, data management with these formats creates substantial implementation overhead, and much time is spent parsing files and collating data. We observe that a tally data structure, i.e. the table of counts of nucleotides × samples × strands × genomic positions, provides a reasonable intermediate level of abstraction for many genomics analyses, including single nucleotide variant (SNV) and InDel calling, copy-number estimation and mutation spectrum analysis. Here we present h5vc, a data structure and associated software for managing tallies. The software contains functionality for creating tallies from BAM files, flexible and scalable data visualization, data quality assessment, computing statistics relevant to variant calling and other applications. Through the simplicity of its API, we envision making low-level analysis of large sets of genome sequencing data accessible to a wider range of researchers. AVAILABILITY AND IMPLEMENTATION: The package H5VC for the statistical environment R is available through the Bioconductor project. The HDF5 system is used as the core of our implementation. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

UNLABELLED: High-throughput microscopy data require a diversity of analytical approaches. However, the construction of workflows that use algorithms from different software packages is difficult owing to a lack of interoperability. To overcome this limitation, we present CellH5, an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs. CellH5Browser, an interactive gallery image browser, demonstrates the versatility and performance of the file format on live imaging data of dividing human cells. CellH5 provides new opportunities for integrated data analysis by multiple software platforms. AVAILABILITY: Source code is freely available at www.github.com/cellh5 under the GPL license and at www.bioconductor.org/packages/release/bioc/html/rhdf5.html under the Artistic-2.0 license. Demo datasets and the CellH5Browser are available at www.cellh5.org. A Fiji importer for cellh5 will be released soon.

BACKGROUND: Systematic measurement of genetic interactions by combinatorial RNAi (co-RNAi) is a powerful tool for mapping functional modules and discovering components. It also provides insights into the role of epistasis on the way from genotype to phenotype. The interpretation of co-RNAi data requires computational and statistical analysis in order to detect interactions reliably and sensitively. RESULTS: We present a comprehensive approach to the analysis of univariate phenotype measurements, such as cell growth. The method is based on a quantitative model and is demonstrated on two example Drosophila cell culture data sets. We discuss adjustments for technical variability, data quality assessment, model parameter fitting and fit diagnostics, choice of scale, and assessment of statistical significance. CONCLUSIONS: As a result, we obtain quantitative genetic interactions and interaction networks reflecting known biological relationships between target genes. The reliable extraction of presence, absence, and strength of interactions provides insights into molecular mechanisms.

Automatic, defect tolerant registration of transmission electron microscopy (TEM) images poses an important and challenging problem for biomedical image analysis, e.g. in computational neuroanatomy. In this paper we demonstrate a fully automatic stitching and distortion correction method for TEM images and propose a probabilistic approach for image registration. The technique identifies image defects due to sample preparation and image acquisition by outlier detection. A polynomial kernel expansion is used to estimate a non-linear image transformation based on intensities and spatial features. Corresponding points in the images are not determined beforehand, but they are estimated via an EM-algorithm during the registration process which is preferable in the case of (noisy) TEM images. Our registration model is successfully applied to two large image stacks of serial section TEM images acquired from brain tissue samples in a computational neuroanatomy project and shows significant improvement over existing image registration methods on these large datasets.

The Group-Lasso method for finding important explanatory factors suffers from the potential non-uniqueness of solutions and also from high computational costs. We formulate conditions for the uniqueness of Group-Lasso solutions which lead to an easily implementable test procedure that allows us to identify all potentially active groups. These results are used to derive an efficient algorithm that can deal with input dimensions in the millions and can approximate the solution path efficiently. The derived methods are applied to large-scale learning problems where they exhibit excellent performance and where the testing procedure helps to avoid misinterpretations of the solutions.

Abstract Motivation: Tandem mass spectrometry allows for high-throughput identification of complex protein samples. Searching tandem mass spectra against sequence databases is the main analysis method nowadays. Since many peptide variations are possible, including them in the search space seems only logical. However, the search space usually grows exponentially with the number of independent variations and may therefore overwhelm computational resources. Results: We provide fast, cache-efficient search algorithms to screen large peptide search spaces including non-tryptic peptides, whole genomes, dozens of posttranslational modifications, unannotated point mutations and even unannotated splice sites. All these search spaces can be screened simultaneously. By optimizing the cache usage, we achieve a calculation speed that closely approaches the limits of the hardware. At the same time, we control the size of the overall search space by limiting the combinations of variations that can co-occur on the same peptide. Using a hypergeometric scoring scheme, we applied these algorithms to a dataset of 1 420 632 spectra. We were able to identify a considerable number of peptide variations within a modest amount of computing time on standard desktop computers. Availability: PepSplice is available as a C++ application for Linux, Windows and OSX at www.ti.inf.ethz.ch/pw/software/pepsplice/. It is open source under the revised BSD license. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

BACKGROUND: Quantitative analysis of differential protein expressions requires to align temporal elution measurements from liquid chromatography coupled to mass spectrometry (LC/MS). We propose multiple Canonical Correlation Analysis (mCCA) as a method to align the non-linearly distorted time scales of repeated LC/MS experiments in a robust way. RESULTS: Multiple canonical correlation analysis is able to map several time series to a consensus time scale. The alignment function is learned in a supervised fashion. We compare our approach with previously published methods for aligning mass spectrometry data on a large proteomics dataset. The proposed method significantly increases the number of proteins that are identified as being differentially expressed in different biological samples. CONCLUSION: Jointly aligning multiple liquid chromatography/mass spectrometry samples by mCCA substantially increases the detection rate of potential bio-markers which significantly improves the interpretability of LC/MS data.

BACKGROUND: We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. RESULTS: Explicit modeling of multilabels significantly improves the capability of learning protein function from multiple kernels. The performance and the interpretability of the inference model are further improved by simultaneously predicting the subcellular localization of proteins and by combining pairwise classifiers to consistent class membership estimates. CONCLUSION: For the purpose of functional prediction of proteins, multilabels provide valuable information that should be included adequately in the training process of classifiers. Learning of functional categories gains from co-prediction of subcellular localization. Pairwise separation rules allow very detailed insights into the relevance of different measurements like sequence, structure, interaction data, or expression data. A preliminary version of the software can be downloaded from http://www.inf.ethz.ch/personal/vroth/KernelHMM/.

De novo Sequencing of peptides is a challenging task in proteome re- search. While there exist reliable DNA-sequencing methods, the high- throughput de novo sequencing of proteins by mass spectrometry is still an open problem. Current approaches suffer from a lack in precision to detect mass peaks in the spectrograms. In this paper we present a novel method for de novo peptide sequencing based on a hidden Markov model. Experiments effectively demonstrate that this new method signif- icantly outperforms standard approaches in matching quality.

Clustering aims at extracting hidden structure in dataset. While the prob- lem of finding compact clusters has been widely studied in the litera- ture, extracting arbitrarily formed elongated structures is considered a much harder problem. In this paper we present a novel clustering algo- rithm which tackles the problem by a two step procedure: first the data are transformed in such a way that elongated structures become compact ones. In a second step, these new objects are clustered by optimizing a compactness-based criterion. The advantages of the method over related approaches are threefold: (i) robustness properties of compactness-based criteria naturally transfer to the problem of extracting elongated struc- tures, leading to a model which is highly robust against outlier objects; (ii) the transformed distances induce a Mercer kernel which allows us to formulate a polynomial approximation scheme to the generally NP- hard clustering problem; (iii) the new method does not contain free kernel parameters in contrast to methods like spectral clustering or mean-shift clustering.

Perceptual grouping organizes image parts in clusters based on psychophysically plausible similarity measures. We propose a novel grouping method in this paper, which stresses connectedness of image elements via mediating elements rather than favoring high mutual similarity. This grouping principle yields superior clustering results when objects are distributed on low-dimensional extended manifolds in a feature space, and not as local point clouds. In addition to extracting connected structures, objects are singled out as outliers when they are too far away from any cluster structure. The objective function for this perceptual organization principle is optimized by a fast agglomerative algorithm. We report on perceptual organization experiments where small edge elements are grouped to smooth curves. The generality of the method is emphasized by results from grouping textured images with texture gradients in an unsupervised fashion.

A resampling scheme for clustering with similarity to bootstrap aggregation (bagging) is presented. Bagging is used to improve the quality of path-based clustering, a data clustering method that can extract elongated structures from data in a noise robust way. The results of an agglomerative optimization method are influenced by small fluctuations of the input data. To increase the reliability of clustering solutions, a stochastic resampling method is developed to infer consensus clusters. A related reliability measure allows us to estimate the number of clusters, based on the stability of an optimized cluster solution under resampling. The quality of path-based clustering with resampling is evaluated on a large image data set of human segmentations.