... a useful method for determining promoter |
complexity
Genomic analysis of gene regulation complexity Genomic analysis of gene regulation complexity Barker, Brandon; Lund, Jim |
. ... |
... Background High |
complexity
The complexity of gene expression dynamics revealed by permutation entropy The complexity of gene expression dynamics revealed by permutation entropy Sun, Xiaoliang; Zou, Yong; Nikiforova, Victoria; Kurths, Jürgen; Walther, Dirk |
is considered a hallmark of living ... |
... to quantify the relationship between |
complexity
How genome complexity can explain the difficulty of aligning reads to genomes How genome complexity can explain the difficulty of aligning reads to genomes Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S |
of genomes and difficulty of short-read ... |
... a new measure, Ndim, estimating the |
complexity
A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain A new method to measure complexity in binary or weighted networks and applications to functional connectivity in the human brain Hahn, Klaus; Massopust, Peter R.; Prigarin, Sergei |
of arbitrary networks. ... |
... a new measure for quantifying the |
complexity
Quantitative measures for the management and comparison of annotated genomes Quantitative measures for the management and comparison of annotated genomes Eilbeck, Karen; Moore, Barry; Holt, Carson; Yandell, Mark |
of alternative splicing, which we call ... |
... resulting in a high computational |
complexity
ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database Yu, Fengchao; Li, Ning; Yu, Weichuan |
. ... |
... the same analysis by identifying low- |
complexity
Identification of putative domain linkers by a neural network – application to a large sequence database Identification of putative domain linkers by a neural network – application to a large sequence database Miyazaki, Satoshi; Kuroda, Yutaka; Yokoyama, Shigeyuki |
regions (LCR), which are known to encode ... |
... algorithm that has an O(n3) expected time |
complexity
Efficient alignment of RNA secondary structures using sparse dynamic programming Efficient alignment of RNA secondary structures using sparse dynamic programming Zhong, Cuncong; Zhang, Shaojie |
, where n is the average number of base ... |
... ambiguously mapped to repetitive and low |
complexity
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data Dozmorov, Mikhail G; Adrianto, Indra; Giles, Cory B; Glass, Edmund; Glenn, Stuart B; Montgomery, Courtney; Sivils, Kathy L; Olson, Lorin E; Iwayama, Tomoaki; Freeman, Willard M; Lessard, Christopher J; Wren, Jonathan D |
regions can also be problematic for ... |
... a novel way to measure the informational |
complexity
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure Liu, Qi; Yang, Yu; Chen, Chun; Bu, Jiajun; Zhang, Yin; Ye, Xiuzi |
of RNA structural data, raising the ... |
... for analyzing the impact of repeats on the |
complexity
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies Wetzel, Joshua; Kingsford, Carl; Pop, Mihai |
of genome assembly [3]. ... |
... on research focus. Results We define the |
complexity
Assessing the impact of human genome annotation choice on RNA-seq expression estimates Assessing the impact of human genome annotation choice on RNA-seq expression estimates Wu, Po-Yen; Phan, John H; Wang, May D |
of human genome annotations in terms of ... |
... cubic or similar) polynomial computational |
complexity
Algorithms for reconstruction of chromosomal structures Algorithms for reconstruction of chromosomal structures Lyubetsky, Vassily; Gershgorin, Roman; Seliverstov, Alexander; Gorbunov, Konstantin |
among them to our knowledge. ... |
... the most efficient among them, has space |
complexity
On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types Zhang, Yun; Phillips, Charles A; Rogers, Gary L; Baker, Erich J; Chesler, Elissa J; Langston, Michael A |
O ( B ) and time ... |
... decrease, depending on the similarity and |
complexity
Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation Mozhayskiy, Vadim; Tagkopoulos, Ilias |
of the intermediate and final ... |
... the proposed algorithm has polynomial-time |
complexity
Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization Cheng, Kin-On; Law, Ngai-Fong; Siu, Wan-Chi; Liew, Alan Wee-Chung |
in the worst case instead of ... |
... considered in the past, the computational |
complexity
Metabolic network alignment in large scale by network compression Metabolic network alignment in large scale by network compression Ay, Ferhat; Dang, Michael; Kahveci, Tamer |
of the existing solutions has so far ... |
... classifier with an appropriate level of |
complexity
The identification of informative genes from multiple datasets with increasing complexity The identification of informative genes from multiple datasets with increasing complexity Anvar, S Yahya; 't Hoen, Peter AC; Tucker, Allan |
by evaluation of predictive performance on ... |
... biological accuracy and / or computational |
complexity
MUSCLE: a multiple sequence alignment method with reduced time and space complexity MUSCLE: a multiple sequence alignment method with reduced time and space complexity Edgar, Robert C |
. ... |
... chance of finding a palindrome in low |
complexity
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins Sheari, Armita; Kargar, Mehdi; Katanforoush, Ali; Arab, Shahriar; Sadeghi, Mehdi; Pezeshk, Hamid; Eslahchi, Changiz; Marashi, Sayed-Amir |
sequences (i.e. sequences with extreme ... |
... the different measures of genome |
complexity
A linear model for predicting performance of short-read aligners using genome complexity A linear model for predicting performance of short-read aligners using genome complexity Tran, Quang; Gao, Shanshan; Vo, Nam S; Phan, Vinhthuy |
[1] that correlated best to the ... |
... signal genomic regions of high structural |
complexity
Modelling and visualizing fine-scale linkage disequilibrium structure Modelling and visualizing fine-scale linkage disequilibrium structure Edwards, David |
. ... |
... is computationally expensive whose |
complexity
Efficient experimental design for uncertainty reduction in gene regulatory networks Efficient experimental design for uncertainty reduction in gene regulatory networks Dehghannasiri, Roozbeh; Yoon, Byung-Jun; Dougherty, Edward R |
grows exponentially with the number of ... |
... Our algorithm reduces computational |
complexity
Efficient motif finding algorithms for large-alphabet inputs Efficient motif finding algorithms for large-alphabet inputs Kuksa, Pavel P; Pavlovic, Vladimir |
of the current motif finding algorithms ... |
... own constraints (e.g., high time or space |
complexity
A fast weak motif-finding algorithm based on community detection in graphs A fast weak motif-finding algorithm based on community detection in graphs Jia, Caiyan; Carson, Matthew B; Yu, Jian |
for finding long motifs, low precision in ... |