Publications by Research Area | Paul G. Allen School of Computer Science & Engineering

Metabolic Control over mTOR-Dependent Diapause-like State

A.M. Hussein, Y. Wang, J. Mathieu, L. Margaretha, C. Song, D.C. Jones, C. Cavanaugh, J.W. Miklas, E. Mahen, M.R. Showalter, W.L. Ruzzo, O. Fiehn, C.B. Ware, A. Blau, H. Ruohola-Baker, Developmental Cell 52:2, 2020.

Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana.

J.A. Koester, C.T. Berthiaume, N. Hiranuma, M.S. Parker, V. Iverson, R. Morales, W.L. Ruzzo, V. Armbrust, Sci Rep 8:1, 2018.

http://www.ncbi.nlm.nih.gov/pubmed/30002405?dopt=Abstract

Associating transcription factors and conserved RNA structures with gene regulation in the human brain.

N. Hecker, S.E. Seemann, A. Silahtaroglu, W.L. Ruzzo, J. Gorodkin, Sci Rep 7:1, 2017. Stable URL http://rdcu.be/uknk.

http://www.ncbi.nlm.nih.gov/pubmed/28720872?dopt=Abstract

The identification and functional annotation of RNA structures conserved in vertebrates.

S.E. Seemann, A.H. Mirza, C. Hansen, C.H. Bang-Berthelsen, C. Garde, M. Christensen-Dalsgaard, E. Torarinsson, Z. Yao, C.T. Workman, F. Pociot, H. Nielsen, N. Tommerup, W.L. Ruzzo, J. Gorodkin, Genome Res, 2017.

http://www.ncbi.nlm.nih.gov/pubmed/28487280?dopt=Abstract

Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments

D.C. Jones, K.T. Kuppusamy, N.J. Palpant, X. Peng, C.E. Murry, H. Ruohola-Baker, W.L. Ruzzo, 2016. bioRxiv

RNA Sequence, Structure and Function: Computational and Bioinformatic Methods

J. Gorodkin (Editor), W.L. Ruzzo (Editor), Methods in Molecular Biology, Humana Press:1097, 2014.

(Springer Protocols)

A Microbial Profiling Method for the Human Microbiota Using High-Throughput Sequencing

H.H.E. Tseng, M.A.J. Hullar, F. Li, J.W. Lampe, R. Sandstrom, A.K. Johnson, L.L. Strate, W.L. Ruzzo, J. Stamatoyannopoulos, Metagenomics 2, 2013.

Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.

Z. Yao, A.P. Fong, Y. Cao, W.L. Ruzzo, R.C. Gentleman, S.J. Tapscott, Skeletal Muscle 3:1, 2013.

http://www.ncbi.nlm.nih.gov/pubmed/23566431?dopt=Abstract

Accelerating ncRNA homology search with FPGAs

N. McVicar, W.L. Ruzzo, S. Hauck, the ACM/SIGDA international symposiumProceedings of the ACM/SIGDA international symposium on Field programmable gate arrays - FPGA '13, ACM Press, 2013.

Genetic and epigenetic determinants of neurogenesis and myogenesis.

A.P. Fong, Z. Yao, J.W. Zhong, Y. Cao, W.L. Ruzzo, R.C. Gentleman, S.J. Tapscott, Developmental Cell 22:4, 2012.

http://www.ncbi.nlm.nih.gov/pubmed/22445365?dopt=Abstract

Hardware Acceleration of Short Read Mapping

C.B. Olson, M. Kim, C. Clauson, B. Kogon, C. Ebeling, S. Hauck, W.L. Ruzzo, FCCM 2012: The 20th Annual IEEE International Symposium on Field-Programmable Custom Computing Machines, 2012. (Best Paper Award)

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

M.M. Hoffman, O.J. Buske, J. Wang, Z. Weng, J.A. Bilmes, W.S. Noble, Nature Methods 9:5, 2012.

http://www.nature.com/nmeth/journal/v9/n5/pdf/nmeth.1937.pdf PDF http://www.nature.com/nmeth/journal/v9/n5/full/nmeth.1937.html HTML http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3340533/pdf/nihms360739.pdf Author Manuscript PDF http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3340533/ Author Manuscript HTML http://www.ncbi.nlm.nih.gov/pubmed/22426492 PubMed

Direct maximization of protein identifications from tandem mass spectra.

M. Spivak, J. Weston, D. Tomazela, M.J. MacCoss, W.S. Noble, Molecular & cellular proteomics : MCP 11:2, 2012.

http://www.ncbi.nlm.nih.gov/pubmed/22052992?dopt=Abstract

Faster Mass Spectrometry-based Protein Inference: Junction Trees are More Efficient than Sampling and Marginalization by Enumeration.

O. Serang, W.S. Noble, IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 2012.

http://www.ncbi.nlm.nih.gov/pubmed/22331862?dopt=Abstract

DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.

L.N. Geng, Z. Yao, L. Snider, A.P. Fong, J.N. Cech, J.M. Young, S.M. Maarel, W.L. Ruzzo, R.C. Gentleman, R. Tawil, S.J. Tapscott, Developmental Cell 22:1, 2012.

http://www.ncbi.nlm.nih.gov/pubmed/22209328?dopt=Abstract

An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.

E.C. Knouf, K. Garg, J.D. Arroyo, Y. Correa, D. Sarkar, R.K. Parkin, K. Wurz, K.C. O'Briant, A.K. Godwin, N.D. Urban, W.L. Ruzzo, R. Gentleman, C.W. Drescher, E.M. Swisher, M. Tewari, Nucleic acids research 40:2, 2012.

http://www.ncbi.nlm.nih.gov/pubmed/21917857?dopt=Abstract

Epigenetic priors for identifying active transcription factor binding sites.

G. Cuellar-Partida, F.A. Buske, R.C. McLeay, T. Whitington, W.S. Noble, T.L. Bailey, Bioinformatics (Oxford, England) 28:1, 2012.

http://www.ncbi.nlm.nih.gov/pubmed/22072382?dopt=Abstract

Integrative annotation of chromatin elements from ENCODE data

M.M. Hoffman, J. Ernst, S.P. Wilder, A. Kundaje, R.S. Harris, M. Libbrecht, B. Giardine, P.M. Ellenbogen, J.A. Bilmes, E. Birney, R.C. Hardison, I. Dunham, M. Kellis, W.S. Noble, Nucleic Acids Research In Press, 2012.

A unified multitask architecture for predicting local protein properties.

Y. Qi, M. Oja, J. Weston, W.S. Noble, PloS one 7:3, 2012.

http://www.ncbi.nlm.nih.gov/pubmed/22461885?dopt=Abstract

Faster SEQUEST searching for peptide identification from tandem mass spectra.

B.J. Diament, W.S. Noble, Journal of proteome research 10:9, 2011.

http://www.ncbi.nlm.nih.gov/pubmed/21761931?dopt=Abstract

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

Y. Cao, Z. Yao, D. Sarkar, M. Lawrence, G.J. Sanchez, M.H. Parker, K.L. MacQuarrie, J. Davison, M.T. Morgan, W.L. Ruzzo, R.C. Gentleman, S.J. Tapscott, Developmental cell 18:4, 2010.

http://www.ncbi.nlm.nih.gov/pubmed/20412780?dopt=Abstract Abstract

De novo prediction of structured RNAs from genomic sequences.

J. Gorodkin, I.L. Hofacker, E. Torarinsson, Z. Yao, J.H. Havgaard, W.L. Ruzzo, Trends in biotechnology 28:1, 2010.

http://www.ncbi.nlm.nih.gov/pubmed/19942311?dopt=Abstract Abstract

Finding non-coding RNAs through genome-scale clustering.

H.H. Tseng, Z. Weinberg, J. Gore, R.R. Breaker, W.L. Ruzzo, Journal of bioinformatics and computational biology 7:2, 2009.

http://www.ncbi.nlm.nih.gov/pubmed/19340921?dopt=Abstract Abstract

MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.

M. Bar, S.K. Wyman, B.R. Fritz, J. Qi, K.S. Garg, R.K. Parkin, E.M. Kroh, A. Bendoraite, P.S. Mitchell, A.M. Nelson, W.L. Ruzzo, C. Ware, J.P. Radich, R. Gentleman, H. Ruohola-Baker, M. Tewari, Stem cells (Dayton, Ohio) 26:10, 2008.

http://www.ncbi.nlm.nih.gov/pubmed/18583537?dopt=Abstract Abstract

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.

Z. Weinberg, E.E. Regulski, M.C. Hammond, J.E. Barrick, Z. Yao, W.L. Ruzzo, R.R. Breaker, RNA (New York, N.Y.) 14:5, 2008.

http://www.ncbi.nlm.nih.gov/pubmed/18369181?dopt=Abstract Abstract

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.

E.E. Regulski, R.H. Moy, Z. Weinberg, J.E. Barrick, Z. Yao, W.L. Ruzzo, R.R. Breaker, Molecular microbiology 68:4, 2008.

http://www.ncbi.nlm.nih.gov/pubmed/18363797?dopt=Abstract Abstract

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

E. Torarinsson, Z. Yao, E.D. Wiklund, J.B. Bramsen, C. Hansen, J. Kjems, N. Tommerup, W.L. Ruzzo, J. Gorodkin, Genome research 18:2, 2008.

http://www.ncbi.nlm.nih.gov/pubmed/18096747?dopt=Abstract Abstract

Finding non-coding RNAs through genome-scale clustering

Tseng, Weinberg, Gore, Breaker, Ruzzo, Sixth Asia-Pacific Bioinformatics Conference, 2008.

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.

Z. Yao, J. Barrick, Z. Weinberg, S. Neph, R. Breaker, M. Tompa, W.L. Ruzzo, PLoS computational biology 3:7, 2007.

http://www.ncbi.nlm.nih.gov/pubmed/17616982?dopt=Abstract Abstract

How accurately is ncRNA aligned within whole-genome multiple alignments?

A.X. Wang, W.L. Ruzzo, M. Tompa, BMC bioinformatics 8, 2007.

http://www.ncbi.nlm.nih.gov/pubmed/17963514?dopt=Abstract Abstract

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.

Z. Weinberg, J.E. Barrick, Z. Yao, A. Roth, J.N. Kim, J. Gore, J.X. Wang, E.R. Lee, K.F. Block, N. Sudarsan, S. Neph, M. Tompa, W.L. Ruzzo, R.R. Breaker, Nucleic acids research 35:14, 2007.

http://www.ncbi.nlm.nih.gov/pubmed/17621584?dopt=Abstract

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts.

Z. Yao, J.C. Jaeger, W.L. Ruzzo, C.Z. Morale, M. Emond, U. Francke, D.M. Milewicz, S.M. Schwartz, E.R. Mulvihill, BMC genomics 8, 2007.

http://www.ncbi.nlm.nih.gov/pubmed/17850668?dopt=Abstract Abstract

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

J.A. Eisen, R.S. Coyne, M. Wu, D. Wu, M. Thiagarajan, J.R. Wortman, J.H. Badger, Q. Ren, P. Amedeo, K.M. Jones, L.J. Tallon, A.L. Delcher, S.L. Salzberg, J.C. Silva, B.J. Haas, W.H. Majoros, M. Farzad, J.M. Carlton, R.K. Smith, J. Garg, R.E. Pearlman, K.M. Karrer, L. Sun, G. Manning, N.C. Elde, A.P. Turkewitz, D.J. Asai, D.E. Wilkes, Y. Wang, H. Cai, K. Collins, A.B. Stewart, S.R. Lee, K. Wilamowska, Z. Weinberg, W.L. Ruzzo, D. Wloga, J. Gaertig, J. Frankel, C.C. Tsao, M.A. Gorovsky, P.J. Keeling, R.F. Waller, N.J. Patron, M.J. Cherry, N.A. Stover, C.J. Krieger, C. Toro, H.F. Ryder, S.C. Williamson, R.A. Barbeau, E.P. Hamilton, E. Orias, PLoS biology 4:9, 2006.

http://www.ncbi.nlm.nih.gov/pubmed/16933976?dopt=Abstract Abstract

CMfinder--a covariance model based RNA motif finding algorithm.

Z. Yao, Z. Weinberg, W.L. Ruzzo, Bioinformatics (Oxford, England) 22:4, 2006.

http://www.ncbi.nlm.nih.gov/pubmed/16357030?dopt=Abstract

Sequence-based heuristics for faster annotation of non-coding RNA families.

Z. Weinberg, W.L. Ruzzo, Bioinformatics (Oxford, England) 22:1, 2006.

http://www.ncbi.nlm.nih.gov/pubmed/16267089?dopt=Abstract

Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.

P.C.H. Hsieh, R.D. Kenagy, E.R. Mulvihill, J.P. Jeanette, X. Wang, C.M.C. Chang, Z. Yao, W.L. Ruzzo, S. Justice, K.L. Hudkins, C.E. Alpers, S. Berceli, A.W. Clowes, Journal of vascular surgery : official publication, the Society for Vascular Surgery [and] International Society for Cardiovascular Surgery, North American Chapter 43:1, 2006.

http://www.ncbi.nlm.nih.gov/pubmed/16414402?dopt=Abstract