• He has co-authored over 60 articles in peer-reviewed journals and conferences, and his main areas of research are in parallel algorithms, combinatorial optimization, and computational biology and genomics. (davidbader.net)
  • My research focusses on graph theory and algorithms and more specifically on graph decomposition techniques, combinatorial algorithms and fixed parameterized algorithms. (lirmm.fr)
  • His research has spanned multiple technical foci and includes combinatorial scientific computing, parallel graph algorithms, artificial intelligence and machine learning, and the application of graph theory and game theory to solve problems in application domains, such as scientific computing, power grids, cybersecurity, and life sciences. (pnnl.gov)
  • Questions from molecular biology and genome research have inspired algorithm development in computer science for many years, starting with string algorithms for (small-scale) sequence analysis, and quickly extending to methods from graph and network algorithms, combinatorial optimization, computational statistics and image analysis, to name a few. (mdpi.com)
  • In cases where the sample displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample and compute the averaged refractive index profile to be used as the reference geometry of the unperturbed system. (lbl.gov)
  • Computational genomics with R. With the assistance of Verdan Franke, Bora Uyar and Jonathan Ronen. (zbmath.org)
  • Next-generation sequencing (NGS), also known as high-throughput sequencing, has affected many fields in the study of biology but has dramatically changed the field of genomics by enabling researchers to quickly sequence whole microbial genomes, profile gene expression by sequencing RNA, examine host-pathogen interactions, and study the vast microbial diversity in humans and the environment ( 1 ). (cdc.gov)
  • Particularly heavy attention resulted in health science and transportation, with entries such as 'Algorithms for Genomics,' 'Optimization and Radiotherapy Treatment Design,' and 'Crew Scheduling. (lu.se)
  • Her research includes phase transitions in discrete math and computer science, structural, and dynamical properties of networks, graph theory, graph algorithms, algorithmic game theory, and computational biology. (ias.edu)
  • Generally, this work establishes algorithmic paths to convert classical indexing data structures in graph representations useful for assembly. (cnrs.fr)
  • algorithmic techniques in computational molecular biology. (bio.net)
  • His lab, which is part of the Center for Bioinformatics and Computational Biology , has developed a number of software tools that are now widely used in the field. (umd.edu)
  • Graph methods have an immense potential to transform the information space in bioinformatics and computational biology. (newswise.com)
  • The Master of Science program in Bioinformatics and Computational Biology is an interdisciplinary program offered jointly by the Departments of Mathematical Sciences and Biological Sciences, with the former serving as the administrative unit. (utdallas.edu)
  • I also have interests in computational complexity, combinatorics, computational biology and many others in computer science and discrete mathematics. (lirmm.fr)
  • Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. (biomedcentral.com)
  • Since October 2001, I am a full-time researcher at the CNRS , with the ALgorithms for Graphs and COmbinatorics group ( AlGco ) of the LIRMM . (lirmm.fr)
  • CALDAM 2019 invites papers describing original research in the areas of design, analysis and experimental evaluation of algorithms and in discrete applied mathematics. (iitkgp.ac.in)
  • Jean-Sebastien Sereni, Łukasz Kowalik i Riste Skrekovski, Total colouring of plane graphs with maximum degree nine , Siam Journal On Discrete Mathematics 22 (4) 2008, s. 1462--1479. (edu.pl)
  • By combining coursework from the disciplines of Biology, Computer Science, Mathematics, and Statistics, it caters to the growing demand of a new breed of scientists who have expertise in all these disciplines. (utdallas.edu)
  • A successful applicant to the program is expected to have a Bachelor's degree in Biology, Mathematics, Statistics, or in another science/engineering discipline, and must have completed Differential and Integral Calculus courses. (utdallas.edu)
  • EACM is a comprehensive reference work covering the vast field of applied and computational mathematics. (lu.se)
  • Applied mathematics itself accounts for at least 60 per cent of mathematics, and the emphasis on computation reflects the current and constantly growing importance of computational methods in all areas of applications. (lu.se)
  • EACM emphasizes the strong links of applied mathematics with major areas of science, such as physics, chemistry, biology, and computer science, as well as specific fields like atmospheric ocean science. (lu.se)
  • 3rd ACM Conference on Equity and Access in Algorithms, Mechanisms, and Optimization (EAAMO), 2023. (cornell.edu)
  • We have recently introduced a multistep extension of the greedy algorithm for modularity optimization. (uzh.ch)
  • The building blocks of my research are things like ODE systems, graph algorithms, parameter optimization and more recently also iterative data processing algorithms and machine learning. (lu.se)
  • Les lettres de recommandation peuvent être déposées en ligne jusqu'au 04 décembre 2023 à 23h59 (heure de Paris) . (sciencesmaths-paris.fr)
  • High-Throughput Hyperparameter-Free Sparse Source Location for Massive TDM-MIMO Radar: Algorithm and FPGA Implementation (IEEE Transactions on Geoscience and Remote Sensing, 2023) [ Matlab ]. (lu.se)
  • The International Society for Computational Biology (ISCB) has selected Pop as a Fellow for 2022. (umd.edu)
  • The 2022 Fellows will be recognized at the Intelligent Systems for Molecular Biology conference, held this year from July 10-14 in Madison, Wisconsin. (umd.edu)
  • Workshop on Algorithms in Bioinformatics (WABI 2022) , 242 volume of LIPIcs , pp. 18:1-18:12, 2022. (uniba.sk)
  • 2022 Associate professor, Theoretical Physics specialising in Computational Biology, Lund University. (lu.se)
  • Selected contributions presented at the ninth international workshop of dynamical systems applied to biology and natural sciences, DSABNS, Turin, Italy, February 7-9, 2018. (zbmath.org)
  • The symposium is intended to provide a forum for researchers working in algorithms and theory of computation. (spoonylife.org)
  • Papers presenting original research in the areas of algorithms and theory of computation are sought. (spoonylife.org)
  • The $2.6 million award is supporting Pop's work building software and developing algorithms that can reconstruct nearly-complete microbial genomes from complex mixtures found in the human gut. (umd.edu)
  • The course explores computational methods for biological networks, including network motif discovery, pathway analysis and reconstruction techniques. (helsinki.fi)
  • The methods developed in this project will allow scientists to discover community structures hidden within very large graphs built out of high‐throughput biological data. (newswise.com)
  • In Systems Genetics , Methods in Molecular Biology 1488:75-120 [An updated primer in using GeneNetwork for molecular analysis of mouse and human cohorts. (genenetwork.org)
  • In Systems Genetics , Methods in Molecular Biology 1488:3-29. (genenetwork.org)
  • Methods in Molecular Biology 2243. (zbmath.org)
  • Since the beginning of my research career, I have worked with Boolean gene regulatory network models, the HP model of protein folding, stem cell regulation, circadian clocks in plants, plant-pathogen interactions, evolutionary algorithms, degradation of soil organic matter by fungi and methods for processing spectroscopic imaging data. (lu.se)
  • 2019). Wheeler graphs are a general framework encompassing several indexes based on the Burrows-Wheeler transform (BWT), such as the FM-index. (uniba.sk)
  • Some of the obstacles preventing PHLs from implementing the bioinformatic-dependent analysis are the requirements for large-scale computational capabilities, complex molecular evolutionary analyses, and dedicated bioinformatics staff to perform these analyses. (cdc.gov)
  • In general, the process to build a reconstruction is as follows: Draft a reconstruction Refine the model Convert model into a mathematical/computational representation Evaluate and debug model through experimentation The related method of flux balance analysis seeks to mathematically simulate metabolism in genome-scale reconstructions of metabolic networks. (wikipedia.org)
  • The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. (biomedcentral.com)
  • The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. (biomedcentral.com)
  • These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. (biomedcentral.com)
  • Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. (biomedcentral.com)
  • The foundations laid in the project have allowed us to design scalable (parallel) algorithms for more complex graph problems including parallel influence maximization (with applications to infectious disease modeling), dynamic graph problems, and generating genome assemblies of complex genomes at scale. (newswise.com)
  • In computational biology, for the sake of genome assembly, one wishes to assemble a target sequence from a multitude of input strings, usually called the reads. (cnrs.fr)
  • International workshop on graph decomposition , January 18-24 2015, CIRM Marseille, France - co-chair. (lirmm.fr)
  • 35th International Workshop on Graph Theoretic Concepts in Computer Science (WG 2009), Montpellier (June 24th-26th). (lirmm.fr)
  • Ranjan, D. "ABI Innovation: Advanced Informatics and Eective Algorithms for Improved CryoEM Protein Structure Prediction and Density Analysis" $589,703. (odu.edu)
  • The goal of this research is to develop novel parallel algorithms for graph‐theoretic analysis of biological data on next‐generation supercomputing platforms. (newswise.com)
  • The computational barriers to joint analysis are now minimal. (genenetwork.org)
  • Furthermore, an in-depth analysis of the communities of two real-world networks (the metabolic network of the bacterium E. coli and the graph of coappearing words in the titles of papers coauthored by Martin Karplus) provides evidence that the partition obtained by the multistep greedy algorithm is superior to the one generated by the original greedy algorithm not only with respect to modularity, but also according to objective criteria. (uzh.ch)
  • Heart disease detection based on internet of things data using linear quadratic discriminant analysis and a deep graph convolutional neural network. (cdc.gov)
  • We took a graph-theoretic approach where we first compared sequences with each other. (newswise.com)
  • This problem has nice graph-theoretic formulations situated between Vertex Cover and 3-Hitting Set. (chalmers.se)
  • Mihai Pop , a professor of computer science and the director of the University of Maryland Institute for Advanced Computer Studies (UMIACS), is being recognized for his significant achievements in computational biology and bioinformatics. (umd.edu)
  • Abhinav Sarje is a research scientist in the Performance and Algorithms Research group of the Computer Science department at the Berkeley Lab. (lbl.gov)
  • A dynamic programming algorithm for finding the optimal placement of a secondary structure topology in Cryo-EM data. (odu.edu)
  • ISCB selected Pop for his leadership in the development of algorithms for analyzing metagenomic data, particularly in the context of metagenome assembly and identification of structural variants in assembly graphs, and for his important contributions to large community projects. (umd.edu)
  • Ananth Kalyanaraman is developing scalable algorithms and software for analyzing large-scale biological and network data. (newswise.com)
  • We address the question of algorithms for building the overlap graph and the De Bruijn graph directly from indexing data structures of the read set, and investigate it when the index in an implicit generalised suffix tree. (cnrs.fr)
  • Today, new challenges arise from what is called the ``data deluge'' in biology: In some areas, such as next generation sequencing or bioimaging, the ability to produce data has grown much more rapidly than the ability to analyze and interpret the data sets. (mdpi.com)
  • My research interests include algorithms, data structures, and computational biology. (edu.au)
  • Three data mining techniques, namely, decision tree, logistic regression, and AdaBoost.M1 algorithms were used to predict mortality risk in patients with CHF. (tdl.org)
  • A case study was conducted using data (January 2012 to December 2014) from a community hospital in Upstate New York and a comparison among the three predictive algorithms was performed. (tdl.org)
  • For example, modellers often try pharmacokinetic model, particularly a physiologically several alternative structures as they attempt to reconcile based pharmacokinetic (PBPK) model, to contribute to a the available data and the description of the biology in risk assessment. (cdc.gov)
  • Peng's group will focus on studying molecular dynamics, protein-protein interactions, and cellular heterogeneity involved in neurobiology and cancer biology. (mit.edu)
  • series of the journal, the Computational Molecular Biology Series. (bio.net)
  • Ranjan, D. "Doctoral Student support for computational physics" $65,000. (odu.edu)
  • An Overview of NQR Signal Detection Algorithms , Magnetic Resonance Detection of Explosives and Illicit Materials (NATO Science for Peace and Security Series B: Physics and Biophysics), 2014. (lu.se)
  • Wheeler graphs admit a succinct representation which can be further compacted by employing the idea of tunnelling, which exploits redundancies in the form of parallel, equally-labelled paths called blocks that can be merged into a single path. (uniba.sk)
  • Algorithm Design. (cornell.edu)
  • He co-authored a book on design of parallel graph algorithms on shared-memory architectures and has authored over 90 technical publications for peer-reviewed journals, conferences, and workshops. (pnnl.gov)
  • This situation calls for applying novel ideas from algorithm development to the datasets that each biology lab faces today. (mdpi.com)
  • Therefore, our method enables the use of Wheeler graphs as a pangenomic reference for real-world pangenomic datasets. (uniba.sk)
  • Using those comparisons, we built a network (or graph) and used that network to mine for clusters or groups that represent the key biological building blocks (species groups or functional modules). (newswise.com)
  • My current work is focused on software and algorithms for vibrational spectroscopy imaging in the OCTAVVS project, and as well as biological and medical applications. (lu.se)
  • Compared with constructing a Wheeler graph from the original text without PFP, our method is much faster and uses less memory on collections of pangenomic sequences. (uniba.sk)
  • The efforts led to a series of publications and open source software for performing parallel graph analytics at scale. (newswise.com)
  • His primary research interests are in parallel algorithms, high-performance computing, machine learning, performance engineering, string and graph algorithms, and computational biology. (lbl.gov)
  • My research interests span a wide range of topics around the intersection of biology and computational science. (lu.se)
  • Most of this research has been cross-disciplinary in nature, and I have participated in two interdisciplinary themes: bio-inspired energy conversion and synthetic biology. (lu.se)
  • Anna Gambin , Piotr Krzyżanowski i Piotr Pokarowski , Aggregation Algorithms for Perturbed Markov Chains with Applications to Networks Modeling , Siam Journal On Scientific Computing 31 (1) 2008, s. 45-73. (edu.pl)
  • If we neglect vertex or edge labels, the graphs differ in their information content. (biomedcentral.com)
  • Ranjan, D. "Algorithms and Software Development for QCD computations on Xeon-Phi Architecture. (odu.edu)
  • Dr. Ranjan is primarily interested in the development of efficient algorithms and bioinformatics tools for solving biologically important problems. (odu.edu)
  • Broadly speaking, my research has been a mixture of coarse-grained and detailed modeling, often involving gene regulatory networks, and development of algorithms and open source software. (lu.se)
  • L'appel concerne toutes les disciplines en sciences informatiques théorique et mathématiques. (sciencesmaths-paris.fr)
  • The goal of this Early Career research project was to develop scalable graph algorithms for problems motivated by DOE-relevant life science applications. (newswise.com)