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  2020 (1)
Mining Microbial Genomes from Datasets on the Sequence Read Archive. Papudeshi, B.; Leffler, H.; Ganapaneni, S.; Ganote, C.; Sanders, S., A.; and Doak, T., G. Technical Report 1 2020.
Mining Microbial Genomes from Datasets on the Sequence Read Archive [link]Website   bibtex   abstract
  2019 (5)
Abstract 5109: National cyberinfrastructure and bioinformatic analysis support available to the cancer research community. Papudeshi, B.; Ganote, C.; Sanders, S.; and Doak, T., G. In Bioinformatics, Convergence Science, and Systems Biology, pages 5109-5109, 7 2019. American Association for Cancer Research
Abstract 5109: National cyberinfrastructure and bioinformatic analysis support available to the cancer research community [link]Website   bibtex
Developing a workflow for bioacoustic recording devices and frog call analysis within Jetstream. Foran, E.; Anderson, J.; Slayton, T.; Guido, E.; Doak, T.; and Sanders, S. . 4 2019.
Developing a workflow for bioacoustic recording devices and frog call analysis within Jetstream [pdf]Paper   bibtex   abstract
Automatic recognition of frog calls. Foran, Eliza G.; Suggs, Evan D.; Underwood, Tenecious A.; Snapp-Childs, Winona; Sanders, S., A. . 2019.
Automatic recognition of frog calls [pdf]Paper   Automatic recognition of frog calls [link]Website   bibtex   abstract
The Genome of Fish Tapeworm Nippotaenia percotti as a Potential Bookmark for Gene Loci that Facilitates Anthropogenic Infection. Sanders, S.; Papudeshi, B.; Ganote, C.; Doak, T.; Chafin, T.; Reshetnikov, A.; Sokolov, S.; Pummil, J.; Douglas, M.; and Douglas, M. . 1 2019.
The Genome of Fish Tapeworm Nippotaenia percotti as a Potential Bookmark for Gene Loci that Facilitates Anthropogenic Infection. [pdf]Paper   The Genome of Fish Tapeworm Nippotaenia percotti as a Potential Bookmark for Gene Loci that Facilitates Anthropogenic Infection. [link]Website   bibtex   abstract
Population Genetics of Tree Swallows, in Collaboration with NCGAS. Sanders, S.; Papudeshi, B.; Ganote, C.; Doak, T.; Mansfield, C.; Tseng, C., Y.; Custer, T.; Custer, C.; and Matson, C. . 1 2019.
Population Genetics of Tree Swallows, in Collaboration with NCGAS [pdf]Paper   Population Genetics of Tree Swallows, in Collaboration with NCGAS [link]Website   bibtex   abstract
  2018 (3)
Reconstruction of Metagenome-Assembled Microbial Genomes from a Micro-biome (Poster). Papudeshi, B. . 1 2018.
Reconstruction of Metagenome-Assembled Microbial Genomes from a Micro-biome (Poster) [link]Website   bibtex   abstract
Stilbenoid prenylation pathway discovery in peanut using targeted transcriptomics (Poster). Sanders, S.; Podicheti, R.; Yang, T.; Fang, L.; Jayanthi, S.; Rajan, G.; Kumar, T., K., S.; Medina-Bolivar, F.; and Mockaitis, K. . 1 2018.
Stilbenoid prenylation pathway discovery in peanut using targeted transcriptomics (Poster) [pdf]Paper   Stilbenoid prenylation pathway discovery in peanut using targeted transcriptomics (Poster) [link]Website   bibtex   abstract
Solving the challenges of complex genome analysis collaborations on-line using XSEDE resources (Poster). Ganote, C.; Sanders, S.; Wu, L.; Doak, T.; and Mockaitis, K. . 1 2018.
Solving the challenges of complex genome analysis collaborations on-line using XSEDE resources (Poster) [pdf]Paper   Solving the challenges of complex genome analysis collaborations on-line using XSEDE resources (Poster) [link]Website   bibtex   abstract
  2017 (4)
National Center for Genome Analysis Support (NCGAS) as a platform for metagenomic analysis. Bhavya, P.; Sanders, S.; Ganote, C.; Blood, P.; and Doak, T. . 2017.
National Center for Genome Analysis Support (NCGAS) as a platform for metagenomic analysis [link]Website   bibtex   abstract
deNovo assembly and annotation of Ambystoma laterale and Ambystoma jeffersonianum transcriptomes: the first steps toward investigating polyploid salamander expression. Sanders, S.; and Pfrender, M. . 6 2017.
deNovo assembly and annotation of Ambystoma laterale and Ambystoma jeffersonianum transcriptomes: the first steps toward investigating polyploid salamander expression [pdf]Paper   deNovo assembly and annotation of Ambystoma laterale and Ambystoma jeffersonianum transcriptomes: the first steps toward investigating polyploid salamander expression [link]Website   bibtex   abstract
NCGAS: National Resources for Computationally Intensive Bioinformatics. Doak, T.; Ganote, C.; Sanders, S.; and Hallock, B. In Practice & Experience in Advanced Research Computing, 2017. PEARC 2017
NCGAS: National Resources for Computationally Intensive Bioinformatics [pdf]Paper   NCGAS: National Resources for Computationally Intensive Bioinformatics [link]Website   bibtex   abstract
Pushing the limites of job flexibility. Ganote, C.; Sanders, S.; Doak, T.; Brokaw, C.; Bhavya, N., P.; and Haas, B. In Galaxy community confernece, 2017.
Pushing the limites of job flexibility [link]Website   bibtex
  2016 (2)
Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data. Ghaffari, N.; Abante, J.; Singh, R.; Blood, P., D.; and Johnson, C., D. In Proceedings of the XSEDE16 on Diversity, Big Data, and Science at Scale - XSEDE16, pages 1-4, 2016. ACM Press
Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data [pdf]Paper   Computational Considerations in Transcriptome Assemblies and Their Evaluation, using High Quality Human RNA-Seq data [link]Website   bibtex
Indiana University Founds the National Center for Genome Analysis Support: Now Open for Business. Doak, T. In Plant and Animal Genome XX Conference, 2016.
Indiana University Founds the National Center for Genome Analysis Support: Now Open for Business [link]Website   bibtex
  2015 (3)
The National Center for Genomic Analysis Support: creating a national cyberinfrastructure environment for genomics researchers. Barnett, W.; Doak, T.; Wu, L.; and Ganote, C. In European Grid Infrastructure, 2015.
The National Center for Genomic Analysis Support: creating a national cyberinfrastructure environment for genomics researchers. [link]Website   bibtex
A Comparison of Transcript Discovery with Different de novo Assembly Software Tools. Wu, L. In Plant and Animal Genome XXIII Conference, 2015.
A Comparison of Transcript Discovery with Different de novo Assembly Software Tools [link]Website   bibtex
National Resources for Computationally Intensive Genomics. Ganote, C.; and Hallock, B. In Plant and Animal Genome Conference, 2015, 2015.
National Resources for Computationally Intensive Genomics [pdf]Paper   National Resources for Computationally Intensive Genomics [link]Website   bibtex
  2014 (1)
Resolution of Whole-Genome Duplications in Paramecium Species. Doak, T. In Plant and Animal Genome XXII Conference, 2014.
Resolution of Whole-Genome Duplications in Paramecium Species [link]Website   bibtex
  2013 (2)
National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research. LeDuc, R., D., R., R., D.; Wu, L., L.; Ganote, C., L.; Doak, T.; Blood, P., D., P., P., D.; Vaughn, M.; Wu, L., L.; Blood, P., D., P., P., D.; Ganote, C., L.; and Vaughn, M. In Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery, of XSEDE '13, pages 13:1--13:7, 2013. ACM
National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research [pdf]Paper   National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research [link]Website   bibtex   abstract
NCGAS (Poster at AMIA Translational Bioinformatics Summit). Barnett, W.; and LeDuc, R. In AMIA Translational Bioinformatics Summit, 2013.
NCGAS (Poster at AMIA Translational Bioinformatics Summit) [link]Website   bibtex
  2012 (2)
National Center for Genome Analysis Support (Poster). Doak, T., G.; Wu, L.; Stewart, C., A.; Henschel, R.; and Barnett, W., K. In Plant and Animal Genome XXIII Conference, 2012.
National Center for Genome Analysis Support (Poster) [pdf]Paper   National Center for Genome Analysis Support (Poster) [link]Website   bibtex   abstract
National Center for Genome Analysis Support. Doak, T.; Wu, L.; Stewart, C.; Henschel, R.; and Barnett, W. In Pacific Bioscience Computing, 2012.
National Center for Genome Analysis Support [link]Website   bibtex
  undefined (6)
Example to make a scientific poster. Graphicsland; and MakeSignscom Technical Report .
Example to make a scientific poster [pdf]Paper   Example to make a scientific poster [link]Website   bibtex
Navigating the Sequence Read Archive to identify crAssphage, an ubiquitous inhabitant of the human microbiome. Cai, J., X.; Weathers, J., G.; Leffler, H.; Ganapaneni, S.; Papudeshi, B.; Sanders, S., A.; and Doak, T., G. Technical Report .
Navigating the Sequence Read Archive to identify crAssphage, an ubiquitous inhabitant of the human microbiome [pdf]Paper   bibtex
Mining the Sequence Read Archive to identify crAssphage, a ubiquitous inhabitant of the human microbiome, in dog and pig samples. Leffler, H.; Ganapaneni, S.; Papudeshi, B.; Sanders, S., A.; and Doak, T., G. Technical Report .
Mining the Sequence Read Archive to identify crAssphage, a ubiquitous inhabitant of the human microbiome, in dog and pig samples [pdf]Paper   Mining the Sequence Read Archive to identify crAssphage, a ubiquitous inhabitant of the human microbiome, in dog and pig samples [link]Website   bibtex
National Center for Genome Analysis Support (NCGAS): Genomics and other Science in the NSF-Funded Jetstream Cloud. Doak, T.; Sanders, S.; Ganote, C.; Papudeshi, B.; Fischer, J.; and Hancock, D., Y. . .
National Center for Genome Analysis Support (NCGAS): Genomics and other Science in the NSF-Funded Jetstream Cloud [link]Website   bibtex   abstract
Harvesting Field Station Data: Automating Raspberry Pi Sensors to Collaborative Websites, and Update. Sanders, S.; Foran, E.; Guido, E.; Anderson, J.; Slayton, T.; and Doak, T. . .
Harvesting Field Station Data: Automating Raspberry Pi Sensors to Collaborative Websites, and Update [link]Website   bibtex
Coupling metagenomics with high-performance computing to mine the Sequence Read Archive (SRA) to analyze Pseudomonas phage PAK-P1. Ganapaneni, S.; Leffler, H.; Papudeshi, B.; Sanders, S., A.; and Doak, T., A. Technical Report .
Coupling metagenomics with high-performance computing to mine the Sequence Read Archive (SRA) to analyze Pseudomonas phage PAK-P1 [pdf]Paper   Coupling metagenomics with high-performance computing to mine the Sequence Read Archive (SRA) to analyze Pseudomonas phage PAK-P1 [link]Website   bibtex