Summary: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

Top Publications

  1. Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol. 2013;31:1143-7 pubmed publisher
    ..Our approach can theoretically bridge any gap size and should be applicable to any species for which global chromatin interaction data can be generated. ..
  2. Burton J, Adey A, Patwardhan R, Qiu R, Kitzman J, Shendure J. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol. 2013;31:1119-25 pubmed publisher
    ..Hi-C data can also be used to validate chromosomal translocations in cancer genomes. ..
  3. Marino S, Baxter N, Huffnagle G, Petrosino J, Schloss P. Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A. 2014;111:439-44 pubmed publisher
    ..These results suggest future animal and in silico experiments. Our modeling approach can be applied to other systems to provide a greater understanding of the dynamics of communities associated with health and disease. ..
  4. Small A, Stahlheber S. Fluorophore localization algorithms for super-resolution microscopy. Nat Methods. 2014;11:267-79 pubmed publisher
    ..switchable fluorophores (which blink on and off and can be sequentially imaged) and powerful localization algorithms (which estimate the positions of the fluorophores in the images)...
  5. Cuevas Tello J, Hernández Ramírez D, Garcia Sepulveda C. Support vector machine algorithms in the search of KIR gene associations with disease. Comput Biol Med. 2013;43:2053-62 pubmed publisher
    ..Here we describe our results at applying artificial intelligence algorithms (support vector machines) to identify associations between KIR genes and disease...
  6. Russo V, Rago A, Papa A, Politano L, Golino P, Russo M, et al. Does a high percentage of right ventricular pacing influence the incidence of paroxysmal atrial fibrillation in myotonic dystrophy type 1 patients?. Kardiol Pol. 2013;71:1147-53 pubmed publisher
    ..The effect of right ventricular pacing on AF incidence is still controversial...
  7. Bendall S, Davis K, Amir E, Tadmor M, Simonds E, Chen T, et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 2014;157:714-25 pubmed publisher
    ..This study provides a comprehensive analysis of human B lymphopoiesis, laying a foundation to apply this approach to other tissues and "corrupted" developmental processes including cancer. ..
  8. Aryee M, Jaffe A, Corrada Bravo H, Ladd Acosta C, Feinberg A, Hansen K, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30:1363-9 pubmed publisher
    ..; Supplementary data are available at Bioinformatics online. ..
  9. Chenouard N, Bloch I, Olivo Marin J. Multiple hypothesis tracking for cluttered biological image sequences. IEEE Trans Pattern Anal Mach Intell. 2013;35:2736-3750 pubmed publisher
    ..We thus demonstrate the benefits of advanced Bayesian tracking techniques for the accurate computational modeling of dynamical biological processes, which is promising for further developments in this domain. ..

More Information


  1. Deckard A, Anafi R, Hogenesch J, Haase S, Harer J. Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data. Bioinformatics. 2013;29:3174-80 pubmed publisher
    ..Additionally, these results can also be used to inform the design of large-scale biological rhythm experiments so that the resulting data can be used with these algorithms to detect periodic signals more effectively.
  2. Wu S, Shen Y, Zhou Z, Lin L, Zeng Y, Gao X. Research of fetal ECG extraction using wavelet analysis and adaptive filtering. Comput Biol Med. 2013;43:1622-7 pubmed publisher
    ..The results indicated that the proposed algorithm can be used for extracting fetal ECG from abdominal signals. ..
  3. Hu J, Kehr B, Reinert K. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics. 2014;30:540-8 pubmed publisher
    ..Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful ..
  4. Antunes O, Filippi J, Hebuterne X, Peyrin Biroulet L. Treatment algorithms in Crohn's - up, down or something else?. Best Pract Res Clin Gastroenterol. 2014;28:473-83 pubmed publisher
    ..In the remaining patients, a rapid step-up approach based on a tight monitoring is recommended. ..
  5. Köpcke F, Lubgan D, Fietkau R, Scholler A, Nau C, Sturzl M, et al. Evaluating predictive modeling algorithms to assess patient eligibility for clinical trials from routine data. BMC Med Inform Decis Mak. 2013;13:134 pubmed publisher
    ..operating characteristic curves and comparing the area under the curve (ROC-AUC) for different prediction algorithms, different sizes of the learning set and different numbers and aggregation levels of the patient attributes...
  6. Janda J, Meier A, Merkl R. CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data. Bioinformatics. 2013;29:3029-35 pubmed publisher
    ..In contrast, five additionally tested 3D features did not increase the classification performance achieved with evolutionary signals deduced from the multiple sequence alignment. ..
  7. Shin H, Chung Y, Lee Y, Choi J, Park M, Kim M, et al. Radiation dose reduction via sinogram affirmed iterative reconstruction and automatic tube voltage modulation (CARE kV) in abdominal CT. Korean J Radiol. 2013;14:886-93 pubmed publisher
    ..Combining CARE kV, reduction of mAs from 240 to 170 mAs and noise reduction by applying SAFIRE strength 3 or 4 reduced the radiation dose by 41.3% without increasing image noise compared with the standard-dose FBP images. ..
  8. Jiao W, Vembu S, Deshwar A, Stein L, Morris Q. Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinformatics. 2014;15:35 pubmed publisher
    ..But automated methods to do this reconstruction are not available and the conditions under which reconstruction is possible have not been described...
  9. Maska M, Ulman V, Svoboda D, Matula P, Matula P, Ederra C, et al. A benchmark for comparison of cell tracking algorithms. Bioinformatics. 2014;30:1609-17 pubmed publisher
    ..A novel framework for objective evaluation of cell tracking algorithms has been established under the auspices of the IEEE International Symposium on Biomedical Imaging 2013 Cell ..
  10. Zhou X, Stephens M. Efficient multivariate linear mixed model algorithms for genome-wide association studies. Nat Methods. 2014;11:407-9 pubmed publisher
    ..We present efficient algorithms in the genome-wide efficient mixed model association (GEMMA) software for fitting mvLMMs and computing ..
  11. Tate A, Beloff N, Al Radwan B, Wickson J, Puri S, Williams T, et al. Exploiting the potential of large databases of electronic health records for research using rapid search algorithms and an intuitive query interface. J Am Med Inform Assoc. 2014;21:292-8 pubmed publisher
    ..Our fast search algorithms and simple query algorithms represent a significant advance for users of clinical research databases.
  12. Liao Y, Smyth G, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923-30 pubmed publisher
    ..featureCounts is available under GNU General Public License as part of the Subread ( or Rsubread ( software packages. ..
  13. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30:2725-9 pubmed publisher
    ..This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management ..
  14. Yu X, Sun S. Comparing a few SNP calling algorithms using low-coverage sequencing data. BMC Bioinformatics. 2013;14:274 pubmed publisher
    ..Under different coverage cutoff values, we compare four algorithms and calculate the empirical positive calling rate and sensitivity...
  15. David C, Jacobs D. Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol Biol. 2014;1084:193-226 pubmed publisher
    ..Therefore, considerable time is spent on describing how to judge the significance of results, highlighting pitfalls. The topic of PCA is reviewed from the perspective of many practical considerations, and useful recipes are provided. ..
  16. Elgendi M. Fast QRS detection with an optimized knowledge-based method: evaluation on 11 standard ECG databases. PLoS ONE. 2013;8:e73557 pubmed publisher
    ..There is a need to develop numerically efficient algorithms to accommodate the new trend towards battery-driven ECG devices and to analyze long-term recorded signals in a ..
  17. Kastorini C, Papadakis G, Milionis H, Kalantzi K, Puddu P, Nikolaou V, et al. Comparative analysis of a-priori and a-posteriori dietary patterns using state-of-the-art classification algorithms: a case/case-control study. Artif Intell Med. 2013;59:175-83 pubmed publisher
    ..Both approaches were modeled using six classification algorithms: multiple logistic regression (MLR), naïve Bayes, decision trees, repeated incremental pruning to produce error ..
  18. Leutheuser H, Schuldhaus D, Eskofier B. Hierarchical, multi-sensor based classification of daily life activities: comparison with state-of-the-art algorithms using a benchmark dataset. PLoS ONE. 2013;8:e75196 pubmed publisher
    ..Hence, it is difficult to compare newly proposed classification algorithms to existing approaches in literature and no commonly used dataset exists...
  19. Sunagawa S, Mende D, Zeller G, Izquierdo Carrasco F, Berger S, Kultima J, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods. 2013;10:1196-9 pubmed publisher
    ..An implementation of the method is available at ..
  20. Elgendi M, Norton I, Brearley M, Abbott D, Schuurmans D. Systolic peak detection in acceleration photoplethysmograms measured from emergency responders in tropical conditions. PLoS ONE. 2013;8:e76585 pubmed publisher
    ..Accurate systolic-peak detection is an important first step for the analysis of heart rate variability. Algorithms based on local maxima-minima, first-derivative, and slope sum are evaluated, and a new algorithm is introduced ..
  21. Bansal M, Eulenstein O. Algorithms for genome-scale phylogenetics using gene tree parsimony. IEEE/ACM Trans Comput Biol Bioinform. 2013;10:939-56 pubmed publisher
    ..However, a lack of efficient algorithms has limited the use of this approach...
  22. Singal A, Mukherjee A, Elmunzer B, Higgins P, Lok A, Zhu J, et al. Machine learning algorithms outperform conventional regression models in predicting development of hepatocellular carcinoma. Am J Gastroenterol. 2013;108:1723-30 pubmed publisher
    ..Machine-learning algorithms offer a novel methodology, which may improve HCC risk prognostication among patients with cirrhosis...
  23. Goodswen S, Kennedy P, Ellis J. A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms. BMC Bioinformatics. 2013;14:315 pubmed publisher
    ..This study focuses on how to reduce the number of false candidates using machine learning algorithms rather than relying on expensive laboratory validation. Proteins from Toxoplasma gondii, Plasmodium sp...
  24. Culpin R, Sieniawski M, Angus B, Menon G, Proctor S, Milne P, et al. Prognostic significance of immunohistochemistry-based markers and algorithms in immunochemotherapy-treated diffuse large B cell lymphoma patients. Histopathology. 2013;63:788-801 pubmed publisher
    To reassess the prognostic validity of immunohistochemical markers and algorithms identified in the CHOP era in immunochemotherapy-treated diffuse large B cell lymphoma patients...
  25. Appleton E, Tao J, Haddock T, Densmore D. Interactive assembly algorithms for molecular cloning. Nat Methods. 2014;11:657-62 pubmed publisher
    ..We demonstrate that Raven's solutions are significantly better than unoptimized solutions at small and large scales and that Raven's assembly instructions are experimentally valid. ..
  26. Zhou J, Lamichhane S, Sterne G, Ye B, Peng H. BIOCAT: a pattern recognition platform for customizable biological image classification and annotation. BMC Bioinformatics. 2013;14:291 pubmed publisher
    Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes...
  27. Steijger T, Abril J, Engström P, Kokocinski F, Hubbard T, Guigo R, et al. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013;10:1177-84 pubmed publisher
    ..Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete ..
  28. Jungreuthmayer C, Nair G, Klamt S, Zanghellini J. Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinformatics. 2013;14:318 pubmed publisher
    ..However, in their original formulation both algorithms are not fully comparable...
  29. Chen W, Hung C, Tsai S, Lin Y. Novel and efficient tag SNPs selection algorithms. Biomed Mater Eng. 2014;24:1383-9 pubmed publisher
    ..In fact, the existing tag SNP selection algorithms are notoriously time-consuming...
  30. Rodriguez A, Laio A. Machine learning. Clustering by fast search and find of density peaks. Science. 2014;344:1492-6 pubmed publisher
    ..We demonstrate the power of the algorithm on several test cases. ..
  31. Chapal Ilani N, Maruvka Y, Spiro A, Reizel Y, Adar R, Shlush L, et al. Comparing algorithms that reconstruct cell lineage trees utilizing information on microsatellite mutations. PLoS Comput Biol. 2013;9:e1003297 pubmed publisher
    ..cells in human and mice in order to validate and quantify the utility of known lineage tree reconstruction algorithms in this context...
  32. Karim R, Housden R, Balasubramaniam M, Chen Z, Perry D, Uddin A, et al. Evaluation of current algorithms for segmentation of scar tissue from late gadolinium enhancement cardiovascular magnetic resonance of the left atrium: an open-access grand challenge. J Cardiovasc Magn Reson. 2013;15:105 pubmed publisher
    ..In this paper we present a standardised evaluation benchmarking framework for algorithms segmenting fibrosis and scar from LGE CMR images...
  33. Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, et al. PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014;11:396-8 pubmed publisher
    ..Single-cell sequencing validation demonstrates PyClone's accuracy. ..
  34. Kursa M. Robustness of Random Forest-based gene selection methods. BMC Bioinformatics. 2014;15:8 pubmed publisher
    ..method, the Boruta algorithm's computational demands could be reduced to levels comparable to those of other algorithms by replacing the Random Forest importance with a comparable measure from Random Ferns (a similar but simplified ..
  35. Kunde Ramamoorthy G, Coarfa C, Laritsky E, Kessler N, Harris R, Xu M, et al. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Res. 2014;42:e43 pubmed publisher
    ..tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker...
  36. Alkan F, Erten C. BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. Bioinformatics. 2014;30:531-9 pubmed publisher
    ..of the BEAMS algorithm in terms of execution speed and memory requirements is more reasonable than the competing algorithms. Supplementary material including code implementations in LEDA C++, experimental data and the results are ..
  37. Hu J, Tse P. A relevance vector machine-based approach with application to oil sand pump prognostics. Sensors (Basel). 2013;13:12663-86 pubmed publisher
    ..Compared with standalone exponential fitting, the proposed RVM-based model was much better able to predict the remaining useful life of pump impellers. ..
  38. Nicolae M, Rajasekaran S. Efficient sequential and parallel algorithms for planted motif search. BMC Bioinformatics. 2014;15:34 pubmed publisher
    ..The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging...
  39. Isnard R, Hammoudi N, Legrand L, Pousset F. [Main novelties of the last set of European guidelines for the management of heart failure]. Presse Med. 2017;46:758-765 pubmed publisher
    ..fraction (LVEF) with a new class, called heart failure with mid-range ejection fraction (LVEF 40-50 %), new algorithms for diagnosis and treatment, including the diagnosis of heart failure with preserved ejection fraction, a ..
  40. Mossi G, Scardicchio A. Ergodic and localized regions in quantum spin glasses on the Bethe lattice. Philos Trans A Math Phys Eng Sci. 2017;375: pubmed publisher
    ..This has implications for the analysis of the performance of quantum adiabatic algorithms.This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic ..
  41. Keitel K, Kagoro F, Samaka J, Masimba J, Said Z, Temba H, et al. A novel electronic algorithm using host biomarker point-of-care tests for the management of febrile illnesses in Tanzanian children (e-POCT): A randomized, controlled non-inferiority trial. PLoS Med. 2017;14:e1002411 pubmed publisher
  42. Skeem J, Manchak S, Montoya L. Comparing Public Safety Outcomes for Traditional Probation vs Specialty Mental Health Probation. JAMA Psychiatry. 2017;74:942-948 pubmed publisher
    ..Probation is a cornerstone of efforts to reduce mass incarceration. Although it is understudied, specialty probation could improve outcomes for the overrepresented group of people with mental illness...
  43. Merigo L, Beschi M, Padula F, Latronico N, Paltenghi M, Visioli A. Event-Based control of depth of hypnosis in anesthesia. Comput Methods Programs Biomed. 2017;147:63-83 pubmed publisher
    ..The tuning of the parameters is performed off-line by using genetic algorithms by considering a given data set of patients...
  44. Chakravarty A, Sivaswamy J. Joint optic disc and cup boundary extraction from monocular fundus images. Comput Methods Programs Biomed. 2017;147:51-61 pubmed publisher
    ..Since our method requires a single fundus image per eye during testing it can be employed in the large-scale screening of glaucoma where expensive 3D imaging is unavailable. ..
  45. Erard N, Knott S, Hannon G. A CRISPR Resource for Individual, Combinatorial, or Multiplexed Gene Knockout. Mol Cell. 2017;67:348-354.e4 pubmed publisher
    ..By conducting parallel loss-of-function screens, we compare our approach to existing sgRNA design and expression strategies. ..
  46. Johnston K, Allen L, Melanson T, Pitts S. A "Patch" to the NYU Emergency Department Visit Algorithm. Health Serv Res. 2017;52:1264-1276 pubmed publisher
    ..Our update improves the classification rate by 43 percent in 2012 (p < .01). Our patch significantly improves the precision and usefulness of the most commonly used ED visit classification system in health services research. ..
  47. Pardakhti M, Moharreri E, Wanik D, Suib S, Srivastava R. Machine Learning Using Combined Structural and Chemical Descriptors for Prediction of Methane Adsorption Performance of Metal Organic Frameworks (MOFs). ACS Comb Sci. 2017;19:640-645 pubmed publisher
    ..Machine learning (ML) algorithms trained on fundamental material properties can potentially provide quick and accurate methods for screening ..
  48. Best M, Sol N, In t Veld S, Vancura A, Muller M, Niemeijer A, et al. Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets. Cancer Cell. 2017;32:238-252.e9 pubmed publisher
    ..Here we demonstrate that particle-swarm optimization (PSO)-enhanced algorithms enable efficient selection of RNA biomarker panels from platelet RNA-sequencing libraries (n = 779)...
  49. Sauwen N, Acou M, Bharath H, Sima D, Veraart J, Maes F, et al. The successive projection algorithm as an initialization method for brain tumor segmentation using non-negative matrix factorization. PLoS ONE. 2017;12:e0180268 pubmed publisher multi-parametric magnetic resonance imaging (MRI) datasets for brain tumor segmentation using different NMF algorithms. Comparison with common initialization methods shows that SPA achieves similar segmentation quality and it is ..
  50. Fai T, Leo Macias A, Stokes D, Peskin C. Image-based model of the spectrin cytoskeleton for red blood cell simulation. PLoS Comput Biol. 2017;13:e1005790 pubmed publisher
    ..The methods presented here could form the basis of disease- and patient-specific computational studies of hereditary diseases affecting the red cell cytoskeleton...
  51. Dimri M, Bilogan C, Pierce L, Naegele G, Vasanji A, Gibson I, et al. Three-dimensional structural analysis reveals a Cdk5-mediated kinase cascade regulating hepatic biliary network branching in zebrafish. Development. 2017;144:2595-2605 pubmed publisher
    ..A small-molecule compound that interferes with the downstream kinase cascade rescued the mutant phenotype. These results provide new insights into branching morphogenesis of the intrahepatic biliary network. ..
  52. Cho Y, Julier S, Marquardt N, Bianchi Berthouze N. Robust tracking of respiratory rate in high-dynamic range scenes using mobile thermal imaging. Biomed Opt Express. 2017;8:4480-4503 pubmed publisher
    ..We also demonstrate how our algorithm outperformed standard algorithms in settings with different amounts of environmental thermal changes and human motion...
  53. Alfaro J, Ignatchenko A, Ignatchenko V, Sinha A, Boutros P, Kislinger T. Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines. Genome Med. 2017;9:62 pubmed publisher
    ..We developed a set of recommendations for the detection of variants using three search algorithms, a split target-decoy approach for FDR estimation, and multiple post-search filters. We examined 7...
  54. Huang Y, Huang Y. An efficient error correction algorithm using FM-index. BMC Bioinformatics. 2017;18:524 pubmed publisher
    ..The assembly results indicated different algorithms has its own strength and weakness, whereas FMOE is good for long or good-quality reads...
  55. Zheng Y, Joyce B, Liu L, Zhang Z, Kibbe W, Zhang W, et al. Prediction of genome-wide DNA methylation in repetitive elements. Nucleic Acids Res. 2017;45:8697-8711 pubmed publisher
    ..Our work has the potential to improve our understanding of the role of global methylation in human diseases, especially cancer. ..
  56. Jin F, Yao E, Zhang Y, Liu S. Metro passengers' route choice model and its application considering perceived transfer threshold. PLoS ONE. 2017;12:e0185349 pubmed publisher
    ..In addition, personalized route planning based on route choice preferences can meet passengers' diversified travel demands. ..