Expression.- Spectral Clustering Gene Ontology Terms to Group Genes by Function.- Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.- Clustering Gene Expression Series with Prior Knowledge.- A Linear Time Biclustering Algorithm for Time Series Gene Expression Data.- Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds.- Phylogeny.- A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem.- Computing the Quartet Distance Between Trees of Arbitrary Degree.- Using Semi-definite Programming to Enhance Supertree Resolvability.- An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree.- Pattern Identification in Biogeography.- On the Complexity of Several Haplotyping Problems.- A Hidden Markov Technique for Haplotype Reconstruction.- Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event.- Networks.- A Faster Algorithm for Detecting Network Motifs.- Reaction Motifs in Metabolic Networks.- Reconstructing Metabolic Networks Using Interval Analysis.- Genome Rearrangements.- A 1.375-Approximation Algorithm for Sorting by Transpositions.- A New Tight Upper Bound on the Transposition Distance.- Perfect Sorting by Reversals Is Not Always Difficult.- Minimum Recombination Histories by Branch and Bound.- Sequences.- A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds.- Generalized Planted (l,d)-Motif Problem with Negative Set.- Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).- The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity.- Multiple Structural RNA Alignment with Lagrangian Relaxation.- Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons.- Ortholog Clustering on a Multipartite Graph.- Linear Time Algorithm for Parsing RNA Secondary Structure.- A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance.- Structure.- Optimal Protein Threading by Cost-Splitting.- Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment.- Rotamer-Pair Energy Calculations Using a Trie Data Structure.- Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity.- The Main Structural Regularities of the Sandwich Proteins.- Discovery of Protein Substructures in EM Maps.

Algorithms in Bioinformatics: 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings (Lecture Notes in Computer Science / Lecture Notes in Bioinformatics)

Two-dimensional layered MoS2 shows great potential for nanoelectronic and optoelectronic devices due to its high photosensitivity, which is the result of its indirect to direct band gap transition when the bulk dimension is reduced to a single monolayer. Here, we present an exhaustive study of the band alignment and relativistic properties of a van der Waals heterostructure formed between single layers of MoS2 and graphene. A sharp, high-quality MoS2-graphene interface was obtained and characterized by micro-Raman spectroscopy, high-resolution X-ray photoemission spectroscopy (HRXPS), and scanning high-resolution transmission electron microscopy (STEM/HRTEM). Moreover, direct band structure determination of the MoS2/graphene van der Waals heterostructure monolayer was carried out using angle-resolved photoemission spectroscopy (ARPES), shedding light on essential features such as doping, Fermi velocity, hybridization, and band-offset of the low energy electronic dynamics found at the interface. We show th...

Band Alignment and Minigaps in Monolayer MoS2-Graphene van der Waals Heterostructures

DESIRS is a new undulator-based VUV beamline on the 2.75 GeV storage ring SOLEIL (France) optimized for gas-phase studies of molecular and electronic structures, reactivity and polarization-dependent photodynamics on model or actual systems encountered in the universe, atmosphere and biosphere. It is equipped with two dedicated endstations: a VUV Fourier-transform spectrometer (FTS) for ultra-high-resolution absorption spectroscopy (resolving power up to 106) and an electron/ion imaging coincidence spectrometer. The photon characteristics necessary to fulfill its scientific mission are: high flux in the 5–40 eV range, high spectral purity, high resolution, and variable and well calibrated polarizations. The photon source is a 10 m-long pure electromagnetic variable-polarization undulator producing light from the very near UV up to 40 eV on the fundamental emission with tailored elliptical polarization allowing fully calibrated quasi-perfect horizontal, vertical and circular polarizations, as measured with an in situ VUV polarimeter with absolute polarization rates close to unity, to be obtained at the sample location. The optical design includes a beam waist allowing the implementation of a gas filter to suppress the undulator high harmonics. This harmonic-free radiation can be steered toward the FTS for absorption experiments, or go through a highly efficient pre-focusing optical system, based on a toroidal mirror and a reflective corrector plate similar to a Schmidt plate. The synchrotron radiation then enters a 6.65 m Eagle off-plane normal-incidence monochromator equipped with four gratings with different groove densities, from 200 to 4300 lines mm−1, allowing the flux-to-resolution trade-off to be smoothly adjusted. The measured ultimate instrumental resolving powers are 124000 (174 µeV) around 21 eV and 250000 (54 µeV) around 13 eV, while the typical measured flux is in the 1010–1011 photons s−1 range in a 1/50000 bandwidth, and 1012–1013 photons s−1 in a 1/1000 bandwidth, which is very satisfactory although slightly below optical simulations. All of these features make DESIRS a state-of-the-art VUV beamline for spectroscopy and dichroism open to a broad scientific community.

DESIRS: a state‐of‐the‐art VUV beamline featuring high resolution and variable polarization for spectroscopy and dichroism at SOLEIL

We present a set of novel algorithms which we call sequenceMiner that detect and characterize anomalies in large sets of high-dimensional symbol sequences that arise from recordings of switch sensors in the cockpits of commercial airliners. While the algorithms that we present are general and domain-independent, we focus on a specific problem that is critical to determining the system-wide health of a fleet of aircraft. The approach taken uses unsupervised clustering of sequences using the normalized length of the longest common subsequence as a similarity measure, followed by detailed outlier analysis to detect anomalies. In this method, an outlier sequence is defined as a sequence that is far away from the cluster center. We present new algorithms for outlier analysis that provide comprehensible indicators as to why a particular sequence is deemed to be an outlier. The algorithms provide a coherent description to an analyst of the anomalies in the sequence when compared to more normal sequences. In the final section of the paper, we demonstrate the effectiveness of sequenceMiner for anomaly detection on a real set of discrete-sequence data from a fleet of commercial airliners. We show that sequenceMiner discovers actionable and operationally significant safety events. We also compare our innovations with standard hidden Markov models, and show that our methods are superior.

Anomaly Detection and Diagnosis Algorithms for Discrete Symbol Sequences with Applications to Airline Safety

Motivation: Phylogenetic trees are omnipresent in evolutionary biology and the comparison of trees plays a central role there. Tree congruence statistics are based on the null hypothesis that two given trees are not more congruent (topologically similar) than expected by chance. Usually, one searches for the most parsimonious evolutionary scenario relating two trees and then one tests the null hypothesis by generating a high number of random trees and comparing these to the one between the observed trees. However, this approach requires a lot of computational work (human and machine) and the results depend on the evolutionary assumptions made.

Results: We propose an index, Icong, for testing the topological congruence between trees with any number of leaves, based on maximum agreement subtrees (MAST). This index is straightforward, simple to use, does not rely on parametrizing the likelihood of evolutionary events, and provides an associated confidence level.

Availability: A web site has been created that allows rapid and easy online computation of this index and of the associated P-value at http://www.ese.u-psud.fr/bases/upresa/pages/devienne/index.html

Contact: damien.de-vienne@u-psud.fr

http://max2.ese.u-psud.fr/publications/DeVienneBioinfoProofs.pdf

A congruence index for testing topological similarity between trees

Hardness Results for the Center and Median String Problems under the Weighted and Unweighted Edit Distances

We delimit a regime, valid for most ground-based lidar probings of cirrus clouds, in which the field-of-view dependence of multiple scattering reaches a plateau. In this regime and assuming the phase function to be constant around pi, we formally demonstrate Platt's modification of the single-scattering lidar equation, with a parameter eta(P) accounting for the reduction of the effective scattering coefficient defined so that (1 - eta(P)) is the amount of energy scattered in the forward peak. Then, to cope with nonconstant backscattering functions, we discuss the introduction of an effective backscattering coefficient that is an average of the scattering probabilities around pi.

Lidar effective multiple-scattering coefficients in cirrus clouds.

https://hal-lirmm.ccsd.cnrs.fr/lirmm-00194239/document

Maximum agreement and compatible supertrees

Given a finite set of strings, the MEDIAN STRING problem consists in finding a string that minimizes the sum of the distances to the strings in the set. Approximations of the median string are used in a very broad range of applications where one needs a representative string that summarizes common information to the strings of the set. It is the case in Classification, in Speech and Pattern Recognition, and in Computational Biology. In the latter, MEDIAN STRING is related to the key problem of Multiple Alignment. In the recent literature, one finds a theorem stating the NP-completeness of the MEDIAN STRING for unbounded alphabets. However, in the above mentioned areas, the alphabet is often finite. Thus, it remains a crucial question whether the MEDIAN STRING problem is NP-complete for finite and even binary alphabets. In this work, we provide an answer to this question and also give the complexity of the related CENTRE STRING problem. Moreover, we study the parametrized complexity of both problems with respect to the number of input strings.

/pdf/complexities-of-the-centre-and-median-string-problems-50cuz47su1.pdf

Complexities of the centre and median string problems

Given a set of leaf-labelled trees with identical leaf sets, the MAST problem, respectively MCT problem, consists of finding a largest subset of leaves such that all input trees restricted to these leaves are isomorphic, respectively compatible. In this paper, we propose extensions of these problems to the context of supertree inference, where input trees have non-identical leaf sets. This situation is of particular interest in phylogenetics. The resulting problems are called SMAST and SMCT.

A sufficient condition is given that identifies cases where these problems can be solved by resorting to MAST and MCT as subproblems. This condition is met, for instance, when only two input trees are considered. Then we give algorithms for SMAST and SMCT that benefit from the link with the subtree problems. These algorithms run in time linear to the time needed to solve MAST, respectively MCT, on an instance of the same or smaller size.

It is shown that arbitrary instances of SMAST and SMCT can be turned in polynomial time into instances composed of trees with a bounded number of leaves.

SMAST is shown to be W[2]-hard when the considered parameter is the number of input leaves that have to be removed to obtain the agreement of the input trees. A similar result holds for SMCT. Moreover, the corresponding optimization problems, that is the complements of SMAST and SMCT, cannot be approximated in polynomial time within any constant factor, unless . These results also hold when the input trees have a bounded number of leaves.

The presented results apply to both collections of rooted and unrooted trees.

/pdf/maximum-agreement-and-compatible-supertrees-2qvliyl6t1.pdf

François Nicolas

Papers

Hardness Results for the Center and Median String Problems under the Weighted and Unweighted Edit Distances

Lidar effective multiple-scattering coefficients in cirrus clouds.

Maximum agreement and compatible supertrees

Complexities of the centre and median string problems

Maximum Agreement and Compatible Supertrees