Publications by topic

Information about my publications can also be found on Google Scholar and DBLP

Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

Protein Multiple Sequence Alignment

Parameter Advising for Multiple Sequence Alignment Dan DeBlasio and John D. Kececioglu.
Springer International Publishing, ISBN: 978-3-319-64917-7.
Information: SpringerAmazon

Adaptive Local Realignment

  • Boosting alignment accuracy by adaptive local realignment. Dan DeBlasio and John Kececioglu. RECOMB 2017.
    (online) (preprint) (pdf) (slides)
  • Also presented as Late Breaking Research at ISMB 2016.
    (slides) (video)
  • Adaptive local realignment of protein sequences. Dan DeBlasio and John Kececioglu. accepted to Journal of Computational Biology (JCB), special RECOMB 2017 Issue.
    (online) (pdf)

Core Column Prediction

  • Predicting core columns of protein alignments improves parameter advising. Dan DeBlasio and John Kececioglu. WABI 2016.
    (online) (pdf) (slides)
  • Core column prediction for protein multiple sequence alignments. Dan DeBlasio and John Kececioglu. Algorithms for Molecular Biology (AMB), special WABI 2016 Issue, April 2017. 
    (online, open access) (pdf)

Ensemble Multiple Sequence Alignment via Advising. Dan DeBlasio, John Kececioglu. ACM-BCB 2015.
(online, free link) (pdf) (slides)

Advising Sets

  • Learning Parameter Sets for Alignment Advising. Dan DeBlasio, John Kececioglu. ACM-BCB 2014.
    (online, free link) (pdf) (slides)
  • Learning Parameter-Advising Sets for Multiple Sequence Alignment. Dan DeBlasio and John Kececioglu. IEEE Transactions on Computational Biology and Bioinformatics, special ACM-BCB 2014 Issue, September/October 2017. (online May 2015)
    (online) (pdf)

Accuracy Estimation

  • Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. Dan DeBlasio, Travis J. Wheeler, John Kececioglu. RECOMB 2012.
    (online) (pdf) (slides)
  • Accuracy estimation and parameter advising for protein multiple sequence alignment. John Kececioglu and Dan DeBlasio. Journal of Computational Biology (JCB), special RECOMB 2012 Issue, Volume 20, Number 4, April 2013.
    (online) (pdf)

Parameter advising for multiple sequence alignment. Daniel DeBlasio. Doctoral thesis, defended April 2016.
(online) (pdf) (video)

Parameter advising for multiple sequence alignment. Dan DeBlasio and John Kececioglu. Summary of talk at ISCB-SC Symposium, July 2014. BMC Bioinformatics, 2015, 16(Suppl 2):A3.
(online, open access) (slides)

Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

Minimizers

Asymptotically optimal minimizers schemes. Guillaume Marçais, Dan DeBlasio and Carl Kingsford. ISMB 2018.
(online, open access) (preprint) (pdf)

Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

RNA Multiple Sequence Alignment

New Computational Approaches to Multiple RNA Alignment and RNA Search. Daniel DeBlasio. Masters thesis, defended July 2009.
(online) (pdf)

PMFastR

  • PMFastR: A New Approach to Multiple RNA Structure Alignment. Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang. WABI 2009.
    (online) (pdf) (slides)
  • A Memory Efficient Method for Structure-Based RNA Multiple Alignment. Daniel DeBlasio, Jocelyne Bruand, Shaojie Zhang. IEEE Transactions on Computational Biology and Bioinformatics, special WABI 2009 Issue, January/February 2012.
    (online) (pdf)
Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

Transcript Assembly

Automatically eliminating errors induced by suboptimal parameter choices in transcript assembly.  Dan DeBlasio and Carl Kingsford. in preparation
(preprint)
Also presented at ISMB 2018.
(slides) (video)

Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

Phylogenetics

SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees. Dan DeBlasio and Jen Wiscaver. PeerJ, August 2016.
(online, open access) (pdf)

Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

Other

Genome sequence of Ophidiomyces ophiodiicola, an emerging fungal pathogen of snakes. Mana Ohkura, Robert Fitak, Jennifer Wisecaver, Dan DeBlasio, Faheem Niazi, Michael Egholm, Steven Rounsley, Chinnappa Kodira, and Marc Orbach. Genome Announcements, Volume 5, Number 30, July 2017.
(online, open access)

Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

microRNA Expression

Epigenetic Regulation of MicroRNA Genes and the Role of miR-34b in Cell Invasion and Motility in Human Melanoma. Joseph Mazar, Divya Khaitan, Dan DeBlasio, Cuncong Zhong, Subramaniam S. Govindarajan, Sharmila Kopanathi, Shaojie Zhang, Animesh Ray, Ranjan J. Perera PLoS ONE, September 2011.
(online, open access) (pdf)

Epigenetic regulation of microRNA-375 and its role in melanoma development in humans. Joseph Mazar, Dan DeBlasio, Subramaniam S. Govindarajan, Shaojie Zhang and Ranjan J. Perera. FEBS Letters, July 2011.
(online) (pdf)

Jump To: Protein Multiple Sequence Alignment ⋅ Minimizers ⋅ RNA Multiple Sequence Alignment ⋅ Phylogenetics ⋅ Other ⋅ microRNA Expression ⋅ Service Related Publications

Service Related Publications

Highlights of the second ISCB Student Council Symposium in Africa 2017. Candice N. Rafael, Efejiro Ashano, Yumna Moosa, Sayane Shome and Dan DeBlasio.  F1000Research 2017, 6(ISCB Comm J):2183.
(online, open access)

The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide. Jigisha Anupama, Margherita Francescatto, Farzana Rahman, Nazeefa Fatima, Alberto Santos, Pandurang Kolekar, Avinash Kumar Shanmugam, Venkata Satagopam, Dan DeBlasio, Magali Michaut, and Emre Guney. PLOS Computational Biology, 2018. 14(1): e1005802.
(online, open access) (preprint)

Highlights from the 11th ISCB Student Council Symposium 2015. Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman. BMC Bioinformatics, 2016, 17(Suppl 3):A1.
(online, open access)

Highlights from the tenth ISCB Student Council Symposium 2014. Farzana Rahman, Katie Wilkins, Annika Jacobsen, Alexander Junge, Esmeralda Vicedo, Dan DeBlasio, Anupama Jigisha and Tomás Di Domenico. BMC Bioinformatics, 2015, 16(Suppl 2):A1.
(online, open access)

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