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The coronavirus disease 19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prompted the development of diagnostic and therapeutic frameworks for timely containment of this pandemic. Here, we utilized our non-conventional computational algorithm, InSiPS, to rapidly design and experimentally validate peptides that bind to SARS-CoV-2 spike (S) surface protein. We previously showed that this method can be used to develop peptides against yeast proteins, however, the applicability of this method to design peptides against other proteins has not been investigated. In the current study, we demonstrate that two sets of peptides developed using InSiPS method can detect purified SARS-CoV-2 S protein via ELISA and Surface Plasmon Resonance (SPR) approaches, suggesting the utility of our strategy in real time COVID-19 diagnostics. Mass spectrometry-based salivary peptidomics shortlist top SARS-CoV-2 peptides detected in COVID-19 patients’ saliva, rendering them attractive SARS-CoV-2 diagnostic targets that, when subjected to our computational platform, can streamline the development of potent peptide diagnostics of SARS-CoV-2 variants of concern. Our approach can be rapidly implicated in diagnosing other communicable diseases of immediate threat.

In this paper, we study the time-dependent shortest paths problem for two types of time-dependent FIFO networks. First, we consider networks where the availability of links, given by a set of disjoint time intervals for each link, changes over time. Here, each interval is assigned a non-negative real value which represents the travel time on the link during the corresponding interval. The resulting shortest path problem is the time-dependent shortest path problem for availability intervals ($\mathcal{TDSP}_{\mathrm{int}}$ ), which asks to compute all shortest paths to any (or all) destination node(s) d for all possible start times at a given source node s. Second, we study time-dependent networks where the cost of using a link is given by a non-decreasing piece-wise linear function of a real-valued argument. Here, each piece-wise linear function represents the travel time on the link based on the time when the link is used. The resulting shortest paths problem is the time-dependent shortest path problem for piece-wise linear functions ($\mathcal{TDSP}_{\mathrm{lin}}$ ) which asks to compute, for a given source node s and destination d, the shortest paths from s to d, for all possible starting times. We present an algorithm for the $\mathcal{TDSP}_{\mathrm{lin}}$ problem that runs in time O((F d +γ)(|E|+|V|log |V|)) where F d is the output size (i.e., number of linear pieces needed to represent the earliest arrival time function to d) and γ is the input size (i.e., number of linear pieces needed to represent the local earliest arrival time functions for all links in the network). We then solve the $\mathcal{TDSP}_{\mathrm{int}}$ problem in O(λ(|E|+|V|log |V|)) time by reducing it to an instance of the $\mathcal{TDSP}_{\mathrm{lin}}$ problem. Here, λ denotes the total number of availability intervals in the entire network. Both methods improve significantly on the previously known algorithms.

Given a set S of s points in the plane, where do we place a new point, p, in order to maximize the area of its region in the Voronoi diagram of S and p? We study the case where the Voronoi neighbors of p are in convex position, and prove that there is at most one local maximum.

Fixed-parameter tractability (FPT) techniques have recently been successful in solving NP-complete problem instances of practical importance which were too large to be solved with previous methods. In this paper, we show how to enhance this approach through the addition of parallelism, thereby allowing even larger problem instances to be solved in practice. More precisely, we demonstrate the potential of parallelism when applied to the bounded-tree search phase of FPT algorithms. We apply our methodology to the k-Vertex Cover problem which has important applications in, for example, the analysis of multiple sequence alignments for computational biochemistry. We have implemented our parallel FPT method for the k-Vertex Cover problem using C and the MPI communication library, and tested it on a 32-node Beowulf cluster. This is the first experimental examination of parallel FPT techniques. As part of our experiments, we solved larger instances of k-Vertex Cover than in any previously reported implementations. For example, our code can solve problem instances with k⩾400 in less than 1.5h.

In this paper we present deterministic parallel algorithms for the coarse-grained multicomputer (CGM) and bulk synchronous parallel (BSP) models for solving the following well-known graph problems: (1) list ranking, (2) Euler tour construction in a tree, (3) computing the connected components and spanning forest, (4) lowest common ancestor preprocessing, (5) tree contraction and expression tree evaluation, (6) computing an ear decomposition or open ear decomposition, and (7) 2-edge connectivity and biconnectivity (testing and component computation). The algorithms require O(log p) communication rounds with linear sequential work per round (p = no. processors, N = total input size). Each processor creates, during the entire algorithm, messages of total size O(log (p) (N/p)) . The algorithms assume that the local memory per processor (i.e., N/p ) is larger than p e , for some fixed e > 0 . Our results imply BSP algorithms with O(log p) supersteps, O(g log (p) (N/p)) communication time, and O(log (p) (N/p)) local computation time. It is important to observe that the number of communication rounds/ supersteps obtained in this paper is independent of the problem size, and grows only logarithmically with respect to p . With growing problem size, only the sizes of the messages grow but the total number of messages remains unchanged. Due to the considerable protocol overhead associated with each message transmission, this is an important property. The result for Problem (1) is a considerable improvement over those previously reported. The algorithms for Problems (2)—(7) are the first practically relevant parallel algorithms for these standard graph problems.

Background Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. Results On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments. Conclusions The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0383-1) contains supplementary material, which is available to authorized users.

We show that the wavefront approach to Voronoi diagrams (a deterministic line-sweep algorithm that does not use geometric transform) can be generalized to distance measures more general than the Euclidean metric. In fact, we provide the first worst-case optimal (O (n logn) time,O(n) space) algorithm that is valid for the full class of what has been callednice metrics in the plane. This also solves the previously open problem of providing anO (nlogn)-time plane-sweep algorithm for arbitraryL k -metrics. Nice metrics include all convex distance functions but also distance measures like the Moscow metric, and composed metrics. The algorithm is conceptually simple, but it copes with all possible deformations of the diagram.

We study scalable parallel computational geometry algorithms for the coarse grained multicomputer model: p processors solving a problem on n data items, were each processor has O(n/p)≫O(1) local memory and all processors are connected via some arbitrary interconnection network (e.g. mesh, hypercube, fat tree). We present O(Tsequential/p+Ts(n, p)) time scalable parallel algorithms for several computational geometry problems. Ts(n, p) refers to the time of a global sort operation. Our results are independent of the multicomputer’s interconnection network. Their time complexities become optimal when Tsequential/p dominates Ts(n, p) or when Ts(n, p) is optimal. This is the case for several standard architectures, including meshes and hypercubes, and a wide range of ratios n/p that include many of the currently available machine configurations. Our methods also have some important practical advantages: For interprocessor communication, they use only a small fixed number of one global routing operation, global sort, and all other programming is in the sequential domain. Furthermore, our algorithms use only a small number of very large messages, which greatly reduces the overhead for the communication protocol between processors. (Note however, that our time complexities account for the lengths of messages.) Experiments show that our methods are easy to implement and give good timing results.

Adigitized plane ź of sizeM is a rectangular źM × źM array of integer lattice points called pixels. A źM × źM mesh-of-processors in which each processorPij represents pixel (i,j) is a natural architecture to store and manipulate images in ź; such a parallel architecture is called asystolic screen. In this paper we consider a variety of computational-geometry problems on images in a digitized plane, and present optimal algorithms for solving these problems on a systolic screen. In particular, we presentO(źM)-time algorithms for determining all contours of an image; constructing all rectilinear convex hulls of an image (peeling); solving the parallel and perspective visibility problem forn disjoint digitized images; and constructing the Voronoi diagram ofn planar objects represented by disjoint images, for a large class of object types (e.g., points, line segments, circles, ellipses, and polygons of constant size) and distance functions (e.g., allLp metrics). These algorithms implyO(źM)-time solutions to a number of other geometric problems: e.g., rectangular visibility, separability, detection of pseudo-star-shapedness, and optical clustering. One of the proposed techniques also leads to a new parallel algorithm for determining all longest common subsequences of two words.

Image processin9 is one of the major fields of application for parallel processing. Some of the first multiprocessors were mainly built for processing images (e.g., the MPP for analyzing LANDSAT satellite data) because for such applications data volumes are often so large that the use of standard sequential machines becomes impracticable. In addition to standard image processing operations such as noise removal, edge detection, filtering, etc., researchers have recently also started to study other "high-level" geometric operations which are well known in computational 9eometry. This special issue of Algorithmica is devoted to parallel algorithms for computational-geometry problems on digitized pictures. The motivation for studying such operations is that in practice geometric data for computationalgeometry applications is often given in the form of an image; hence, parallel algorithms which can be applied directly to the image may be more efficient than applying "standard" parallel computational-geometry methods which require that the image is first converted into, e.g., a set of polygonal chains. For example, consider the standard path-plannin9 problem in robotics: given a set of simple polygons in the plane representing the obstacles and a polygon representing the robot, find the shortest path for the robot to move from point A to point B without colliding with any obstacle. In practice, the robot might be moving in a factory hall; instead of first creating a polygonal description of the obstacles and the robot, it may be more efficient to use as input an image obtained from a camera mounted to the ceiling of the factory. Using an image from a camera might also be more practical for dynamic environments where the locations and shapes of the obstacles are changing. Since the factory, and thus the image of the obstacles, could be very large and the robot's path has to be determined in real-time, a parallel method for solving the path-planning problem directly on the image is desirable. 2 When solving computational-geometry problems for images in parallel, researchers have several different types of parallel machines available. The papers selected for this special issue consider four very commonly used ones: the parallel

External memory (EM) algorithms are designed for large-scale computational problems in which the size of the internal memory of the computer is only a small fraction of the problem size. Typical EM algorithms are specially crafted for the EM situation. In the past, several attempts have been made to relate the large body of work on parallel algorithms to EM, but with limited success. The combination of EM computing, on multiple disks, with multiprocessor parallelism has been posted as a challenge by the ACM Working Group on Storage I/O for Large-Scale Computing. In this paper we provide a simulation technique which produces efficient parallel EM algorithms from efficient BSP-like parallel algorithms. The techniques obtained can accommodate one or multiple processors on the EM target machine, each with one or more disks, and they also adapt to the disk blocking factor of the target machine. When applied to existing BSP-like algorithms, our simulation technique produces improved parallel EM algorithms for a large number of problems.

In this paper, we propose a grid-based On-Line Analytical Processing (OLAP) application which distributes query computation across an enterprise grid. Our application follows a two-tiered process for answering queries based on sharing Cached OLAP data between the users at the local grid site and using grid scheduling approaches to execute the remaining parts of a query amongst a distributed set of OLAP Servers. A new technique for extraction and aggregation of shared Cached OLAP data is proposed, along with an efficient, aggregate-aware Cache controller. An experimental evaluation of the proposed query processing and cooperative Caching methods shows a significant reduction in query times compared to previously proposed methods.

Background Identification of protein interaction networks has received considerable attention in the post-genomic era. The currently available biochemical approaches used to detect protein-protein interactions are all time and labour intensive. Consequently there is a growing need for the development of computational tools that are capable of effectively identifying such interactions. Results Here we explain the development and implementation of a novel Protein-Protein Interaction Prediction Engine termed PIPE. This tool is capable of predicting protein-protein interactions for any target pair of the yeast Saccharomyces cerevisiae proteins from their primary structure and without the need for any additional information or predictions about the proteins. PIPE showed a sensitivity of 61% for detecting any yeast protein interaction with 89% specificity and an overall accuracy of 75%. This rate of success is comparable to those associated with the most commonly used biochemical techniques. Using PIPE, we identified a novel interaction between YGL227W (vid30) and YMR135C (gid8) yeast proteins. This lead us to the identification of a novel yeast complex that here we term vid30 complex (vid30c). The observed interaction was confirmed by tandem affinity purification (TAP tag), verifying the ability of PIPE to predict novel protein-protein interactions. We then used PIPE analysis to investigate the internal architecture of vid30c. It appeared from PIPE analysis that vid30c may consist of a core and a secondary component. Generation of yeast gene deletion strains combined with TAP tagging analysis indicated that the deletion of a member of the core component interfered with the formation of vid30c, however, deletion of a member of the secondary component had little effect (if any) on the formation of vid30c. Also, PIPE can be used to analyse yeast proteins for which TAP tagging fails, thereby allowing us to predict protein interactions that are not included in genome-wide yeast TAP tagging projects. Conclusion PIPE analysis can predict yeast protein-protein interactions. Also, PIPE analysis can be used to study the internal architecture of yeast protein complexes. The data also suggests that a finite set of short polypeptide signals seem to be responsible for the majority of the yeast protein-protein interactions.

Background While there are many methods for predicting protein-protein interaction, very few can determine the specific site of interaction on each protein. Characterization of the specific sequence regions mediating interaction (binding sites) is crucial for an understanding of cellular pathways. Experimental methods often report false binding sites due to experimental limitations, while computational methods tend to require data which is not available at the proteome-scale. Here we present PIPE-Sites, a novel method of protein specific binding site prediction based on pairs of re-occurring polypeptide sequences, which have been previously shown to accurately predict protein-protein interactions. PIPE-Sites operates at high specificity and requires only the sequences of query proteins and a database of known binary interactions with no binding site data, making it applicable to binding site prediction at the proteome-scale. Results PIPE-Sites was evaluated using a dataset of 265 yeast and 423 human interacting proteins pairs with experimentally-determined binding sites. We found that PIPE-Sites predictions were closer to the confirmed binding site than those of two existing binding site prediction methods based on domain-domain interactions, when applied to the same dataset. Finally, we applied PIPE-Sites to two datasets of 2347 yeast and 14,438 human novel interacting protein pairs predicted to interact with high confidence. An analysis of the predicted interaction sites revealed a number of protein subsequences which are highly re-occurring in binding sites and which may represent novel binding motifs. Conclusions PIPE-Sites is an accurate method for predicting protein binding sites and is applicable to the proteome-scale. Thus, PIPE-Sites could be useful for exhaustive analysis of protein binding patterns in whole proteomes as well as discovery of novel binding motifs. PIPE-Sites is available online at http://pipe-sites.cgmlab.org/.

After the number of vertices, Vertex Cover Number is the largest of the classical graph parameters and has more and more frequently been used as a separate parameter in parameterized problems, including problems that are not directly related to the Vertex Cover Number. Here we consider the treewidth and pathwidth problems parameterized by k , the size of a minimum vertex cover of the input graph. We show that the pathwidth and treewidth can be computed in O ∗ ( 3 k ) time. This complements recent polynomial kernel results for treewidth and pathwidth parameterized by the Vertex Cover Number.