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Pennsylvania State University

EducationState College, Pennsylvania, United States
About: Pennsylvania State University is a(n) education organization based out in State College, Pennsylvania, United States. It is known for research contribution in the topic(s): Population & Poison control. The organization has 79763 authors who have published 196876 publication(s) receiving 8318601 citation(s). The organization is also known as: Penn State & PSU. more

Topics: Population, Poison control, Dielectric more

Showing all 79763 results

Robert Langer2812324326306
Zhong Lin Wang2452529259003
Donald P. Schneider2421622263641
David J. Hunter2131836207050
Robert M. Califf1961561167961
Martin White1962038232387
Eric J. Topol1931373151025
Charles A. Dinarello1901058139668
Jing Wang1844046202769
Dennis S. Charney179802122408
David Haussler172488224960
Chad A. Mirkin1641078134254
Ian A. Wilson15897198221
David Cella1561258106402
Jay Hauser1552145132683

Journal ArticleDOI: 10.1016/S0022-2836(05)80360-2
Stephen F. Altschul1, Warren Gish1, Webb Miller2, Eugene W. Myers3  +1 moreInstitutions (3)
Abstract: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straight-forward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity. more

Topics: Substitution matrix (59%), Sim4 (58%), Alignment-free sequence analysis (57%) more

81,150 Citations

Open accessJournal ArticleDOI: 10.1093/NAR/25.17.3389
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily. more

Topics: Substitution matrix (57%), Sequence database (54%), Sequence profiling tool (53%) more

66,744 Citations

Open accessJournal ArticleDOI: 10.1093/MOLBEV/MSR121
Abstract: Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from more

Topics: Computational phylogenetics (63%), Tree rearrangement (60%), Phylogenetic tree (55%) more

37,583 Citations

Open accessJournal ArticleDOI: 10.1093/MOLBEV/MSM092
Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at ( more

Topics: Mega- (52%), Software versioning (51%)

28,578 Citations

Open accessJournal ArticleDOI: 10.1021/JA00124A002
Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone. more

Topics: Molecular dynamics (60%), van der Waals force (58%), Force field (chemistry) (55%) more

12,107 Citations

No. of papers from the Institution in previous years

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Institution's top 5 most impactful journals

Social Science Research Network

2.9K papers, 70.8K citations

The Astrophysical Journal

2.4K papers, 232.5K citations

Journal of the American Ceramic Society

1.1K papers, 56.2K citations


1.1K papers, 3.6K citations

Physical Review B

926 papers, 38.5K citations

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