Zobrazeno 1 - 10
of 144
pro vyhledávání: '"Ananth Kalyanaraman"'
Publikováno v:
BMC Bioinformatics, Vol 25, Iss 1, Pp 1-27 (2024)
Abstract Background Genome assembly, which involves reconstructing a target genome, relies on scaffolding methods to organize and link partially assembled fragments. The rapid evolution of long read sequencing technologies toward more accurate long r
Externí odkaz:
https://doaj.org/article/8855adf1018045b6a1925844aeb6bc17
Autor:
Xiaojing An, Priyanka Ghosh, Patrick Keppler, Sureyya Emre Kurt, Sriram Krishnamoorthy, Ponnuswamy Sadayappan, Aravind Sukumaran Rajam, Ümit V. Çatalyürek, Ananth Kalyanaraman
Publikováno v:
iScience, Vol 25, Iss 11, Pp 105273- (2022)
Summary: De novo genome assembly is a fundamental problem in computational molecular biology that aims to reconstruct an unknown genome sequence from a set of short DNA sequences (or reads) obtained from the genome. The relative ordering of the reads
Externí odkaz:
https://doaj.org/article/0651a4b847574ae3a77a993418f600bf
Publikováno v:
BMC Bioinformatics, Vol 19, Iss 1, Pp 1-18 (2018)
Abstract Background Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput sequencing technologies
Externí odkaz:
https://doaj.org/article/aa8bde82f49447489d855b62c8b337bd
Publikováno v:
PLoS ONE, Vol 11, Iss 8, p e0161338 (2016)
BACKGROUND:Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to ann
Externí odkaz:
https://doaj.org/article/f6fab878c4b24b419d68023cec976cce
Autor:
Richard M Sharpe, Tyson Koepke, Artemus Harper, John Grimes, Marco Galli, Mio Satoh-Cruz, Ananth Kalyanaraman, Katherine Evans, David Kramer, Amit Dhingra
Publikováno v:
PLoS ONE, Vol 11, Iss 4, p e0152404 (2016)
High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent c
Externí odkaz:
https://doaj.org/article/2d5b768d14964ab0bd20e78d40b27474
Autor:
Fusheng Wei, Joshua C Stein, Chengzhi Liang, Jianwei Zhang, Robert S Fulton, Regina S Baucom, Emanuele De Paoli, Shiguo Zhou, Lixing Yang, Yujun Han, Shiran Pasternak, Apurva Narechania, Lifang Zhang, Cheng-Ting Yeh, Kai Ying, Dawn H Nagel, Kristi Collura, David Kudrna, Jennifer Currie, Jinke Lin, Hyeran Kim, Angelina Angelova, Gabriel Scara, Marina Wissotski, Wolfgang Golser, Laura Courtney, Scott Kruchowski, Tina A Graves, Susan M Rock, Stephanie Adams, Lucinda A Fulton, Catrina Fronick, William Courtney, Melissa Kramer, Lori Spiegel, Lydia Nascimento, Ananth Kalyanaraman, Cristian Chaparro, Jean-Marc Deragon, Phillip San Miguel, Ning Jiang, Susan R Wessler, Pamela J Green, Yeisoo Yu, David C Schwartz, Blake C Meyers, Jeffrey L Bennetzen, Robert A Martienssen, W Richard McCombie, Srinivas Aluru, Sandra W Clifton, Patrick S Schnable, Doreen Ware, Richard K Wilson, Rod A Wing
Publikováno v:
PLoS Genetics, Vol 5, Iss 11, p e1000728 (2009)
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annot
Externí odkaz:
https://doaj.org/article/f05a3066e1484097b9d8804595e2ea16
Autor:
Dwaipayan Choudhury, Reet Barik, Aravind Sukumaran Rajam, Ananth Kalyanaraman, Partha Pratim Pande
Publikováno v:
ACM Transactions on Design Automation of Electronic Systems. 27:1-22
Manycore GPU architectures have become the mainstay for accelerating graph computations. One of the primary bottlenecks to performance of graph computations on manycore architectures is the data movement. Since most of the accesses in graph processin
Publikováno v:
2022 IEEE 29th International Conference on High Performance Computing, Data, and Analytics (HiPC).
Publikováno v:
Journal of chemical theory and computation. 18(12)
Although community or cluster identification is becoming a standard tool within the simulation community, traditional algorithms are challenging to adapt to time-dependent data. Here, we introduce temporal community identification using the Δ-screen
Autor:
Nitin A. Gawande, Mahantesh Halappanavar, Erik G. Boman, S. M. Ferdous, Marco Minutoli, Karen D. Devine, Ariful Azad, Alex Pothen, Oguz Selvitopi, Arif O. Khan, Antonino Tumeo, Sayan Ghosh, Aydin Buluc, Nathan R. Tallent, Ananth Kalyanaraman, Sivasankaran Rajamanickam, Seher Acer
Publikováno v:
The International Journal of High Performance Computing Applications. 35:553-571
Combinatorial algorithms in general and graph algorithms in particular play a critical enabling role in numerous scientific applications. However, the irregular memory access nature of these algorithms makes them one of the hardest algorithmic kernel