Travis J. Wheeler - researchr alias

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Viewing Publication 1 - 16 from 16

2023

Reliable Measures of Spread in High Dimensional Latent SpacesAnna C. Marbut, Katy McKinney-Bock, Travis J. Wheeler. icml 2023: 23871-23885 [doi]

2021

An optimized FM-index library for nucleotide and amino acid searchTim Anderson, Travis J. Wheeler. almob, 16(1):25, 2021. [doi]

2019

15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoformsPeter V. Hornbeck, Jon M. Kornhauser, Vaughan Latham, Beth Murray, Vidhisha Nandhikonda, Alex S. Nord, Elzbieta Skrzypek, Travis J. Wheeler, Bin Zhang, Florian Gnad. nar, 47(Database-Issue), 2019. [doi]

2018

Splice-Aware Multiple Sequence Alignment of Protein IsoformsAlex S. Nord, Peter V. Hornbeck, Kaitlin Carey, Travis J. Wheeler. bcb 2018: 200-210 [doi]

ULTRA: A Model Based Tool to Detect Tandem RepeatsDaniel Olson, Travis J. Wheeler. bcb 2018: 37-46 [doi]

2016

The Dfam database of repetitive DNA familiesRobert Hubley, Robert D. Finn, Jody Clements, Sean R. Eddy, Thomas A. Jones, Weidong Bao, Arian F. A. Smit, Travis J. Wheeler. nar, 44(Database-Issue):81-89, 2016. [doi]

2015

HMMER web server: 2015 updateRobert D. Finn, Jody Clements, William Arndt, Benjamin L. Miller, Travis J. Wheeler, Fabian Schreiber, Alex Bateman, Sean R. Eddy. nar, 43(Webserver-Issue), 2015. [doi]

2014

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov modelsTravis J. Wheeler, Jody Clements, Robert D. Finn. bmcbi, 15:7, 2014. [doi]

2013

nhmmer: DNA homology search with profile HMMsTravis J. Wheeler, Sean R. Eddy. bioinformatics, 29(19):2487-2489, 2013. [doi]

Dfam: a database of repetitive DNA based on profile hidden Markov modelsTravis J. Wheeler, Jody Clements, Sean R. Eddy, Robert Hubley, Thomas A. Jones, Jerzy Jurka, Arian F. A. Smit, Robert D. Finn. nar, 41(Database-Issue):70-82, 2013. [doi]

2012

Estimating the Accuracy of Multiple Alignments and its Use in Parameter AdvisingDan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu. recomb 2012: 45-59 [doi]

2010

Aligning Protein Sequences with Predicted Secondary StructureJohn D. Kececioglu, Eagu Kim, Travis J. Wheeler. jcb, 17(3):561-580, 2010. [doi]

2009

Learning Models for Aligning Protein Sequences with Predicted Secondary StructureEagu Kim, Travis J. Wheeler, John D. Kececioglu. recomb 2009: 512-531 [doi]

Large-Scale Neighbor-Joining with NINJATravis J. Wheeler. wabi 2009: 375-389 [doi]

2007

Multiple alignment by aligning alignmentsTravis J. Wheeler, John D. Kececioglu. ismb 2007: 559-568 [doi]

2005

Evaluating and improving cDNA sequence quality with cQCCeline A. Hayden, Travis J. Wheeler, Richard A. Jorgensen. bioinformatics, 21(24):4414-4415, 2005. [doi]

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