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作者:Sriram P. Chockalingam , Yongchao Liu ...
来源:[J].BMC Bioinformatics(IF 3.024), 2017, Vol.18 (8)Springer
摘要:Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k -mer based methods are predominantly used in real applications, the average ...
作者:Sriram P. Chockalingam , Amanda Sue ...
来源:[J].BMC Genomics(IF 4.397), 2017, Vol.18 (4)Springer
摘要:Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Molecular analysis ha...
作者:Sriram P. Chockalingam , Yongchao Liu ...
来源:[J].2017, Vol.18 (8), pp.238BMC
摘要:Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer based methods are predominantly used in real applications, the average c...
作者:Sriram P. Chockalingam , Amanda Sue ...
来源:[J].2017, Vol.18 (4), pp.372BMC
摘要:Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Molecular analysis ha...
作者:Xiao Yang , Sriram P. Chockalingam , Srinivas Aluru
来源:[J].Briefings in Bioinformatics(IF 5.298), 2013, Vol.14 (1), pp.56-66Oxford U Press
摘要:Error Correction is important for most next-generation sequencing applications because highly accurate sequenced reads will likely lead to higher quality results. Many techniques for error correction of sequencing data from next-gen platforms have been developed in the recent yea...
作者:Sriram P. Chockalingam , Maneesha Aluru ...
来源:[C].Bioinformatics, Computational Biology,and Health Informatics2017ACM
摘要:Motivation: Reverse engineering gene networks from expression data is a widelymstudied problem, for which numerous mathematical models have been developed. Network reconstruction methods can be used to study specific pathways, or can be applied at the whole-genome scale to analyz...
作者:Nagakishore Jammula , Sriram P. Chockalingam , Srinivas Aluru
来源:[C].Bioinformatics, Computational Biology,and Health Informatics2017ACM
摘要:State-of-the-art high-throughput sequencing instruments decipher in excess of a billion short genomic fragments per run. The output sequences are referred to as 'reads'. These read datasets facilitate a wide variety of analyses with applications in areas such as genomics, metagen...
作者:Sriram P. Chockalingam , Sharma V. Thankachan
来源:[C].Bioinformatics, Computational Biology, and Health Informatics2018ACM
摘要:Alignment-free methods for sequence comparisons have become popular in many bioinformatics applications, specifically in the estimation of sequence similarity measures to construct phylogenetic trees. Recently, the average common substring measure, ACS, and its k-mismatch counter...
作者:... Chaitanya Aluru , Sriram P. Chockalingam , Srinivas Aluru
来源:[B].Lecture Notes in Computer Science;;Lecture Notes in Computer Science;;Lecture Notes in Computer Science;;Lecture Notes in Computer Science;;Lecture Notes in Computer Science;;Lecture Notes in Computer Science;;Lecture Notes in Computer Science;;Lecture Notes in Computer Science2018Springer
摘要:Abstract We present a novel algorithmic framework for solving approximate sequence matching problems that permit a bounded total number k of mismatches, insertions, and deletions. The core of the framework relies on transforming an approximate matching problem into a corresp...

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