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-BakerDevelopmental 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. ArmbrustSci Rep 8:1, 2018.

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. GorodkinGenome Res, 2017.

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 BiologyHumana 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. StamatoyannopoulosMetagenomics 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. TapscottSkeletal Muscle 3:1, 2013.

Accelerating ncRNA homology search with FPGAs

N. McVicar, W.L. Ruzzo, S. Hauckthe ACM/SIGDA international symposiumProceedings of the ACM/SIGDA international symposium on Field programmable gate arrays - FPGA '13ACM 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. TapscottDevelopmental Cell 22:4, 2012.

Hardware Acceleration of Short Read Mapping

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

Direct maximization of protein identifications from tandem mass spectra.

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

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. TapscottDevelopmental Cell 22:1, 2012.

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. TewariNucleic acids research 40:2, 2012.

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. BaileyBioinformatics (Oxford, England) 28:1, 2012.

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. NobleNucleic Acids Research In Press, 2012.

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. TapscottDevelopmental cell 18:4, 2010.

De novo prediction of structured RNAs from genomic sequences.

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

Finding non-coding RNAs through genome-scale clustering.

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

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. TewariStem cells (Dayton, Ohio) 26:10, 2008.

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. BreakerRNA (New York, N.Y.) 14:5, 2008.

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. BreakerMolecular microbiology 68:4, 2008.

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. GorodkinGenome research 18:2, 2008.

Finding non-coding RNAs through genome-scale clustering

Tseng,  Weinberg,  Gore,  Breaker,  RuzzoSixth 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. RuzzoPLoS computational biology 3:7, 2007.

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. BreakerNucleic acids research 35:14, 2007.

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. MulvihillBMC genomics 8, 2007.

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. OriasPLoS biology 4:9, 2006.

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

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

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. ClowesJournal of vascular surgery : official publication, the Society for Vascular Surgery [and] International Society for Cardiovascular Surgery, North American Chapter 43:1, 2006.

6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.

J.E. Barrick, N. Sudarsan, Z. Weinberg, W.L. Ruzzo, R.R. BreakerRNA (New York, N.Y.) 11:5, 2005.

A glycine-dependent riboswitch that uses cooperative binding to control gene expression.

M. Mandal, M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo, R.R. BreakerScience (New York, N.Y.) 306:5694, 2004.

Atherosclerotic plaque smooth muscle cells have a distinct phenotype.

E.R. Mulvihill, J. Jaeger, R. Sengupta, W.L. Ruzzo, C. Reimer, S. Lukito, S.M. SchwartzArteriosclerosis, thrombosis, and vascular biology 24:7, 2004.

Faster Genome Annotation of Non-coding RNA Families Without Loss of Accuracy

Weinberg,  RuzzoEighth Annual International Conference on Research in Computational Molecular Biology, 2004.

Improved gene selection for classification of microarrays.

J. Jaeger, R. Sengupta, W.L. RuzzoPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2003.

Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae.

M.T. Barrett, K.Y. Yeung, W.L. Ruzzo, L. Hsu, P.L. Blount, R. Sullivan, H. Zarbl, J. Delrow, P.S. Rabinovitch, B.J. ReidNeoplasia (New York, N.Y.) 4:2, 2002.

Pre-mRNA secondary structure prediction aids splice site prediction.

D.J. Patterson, K. Yasuhara, W.L. RuzzoPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2002.

Model-based clustering and data transformations for gene expression data.

K.Y. Yeung, C. Fraley, A. Murua, A.E. Raftery, W.L. RuzzoBioinformatics (Oxford, England) 17:10, 2001.

Validating clustering for gene expression data.

K.Y. Yeung, D.R. Haynor, W.L. RuzzoBioinformatics (Oxford, England) 17:4, 2001.

Algorithms for a Simple Point Placement Problem

Redstone,  RuzzoAlgorithms and Complexity, 4th Italian Conference, 2000.

A Linear Time Algorithm for Finding All Maximal Scoring Subsequences

W.L. Ruzzo, M. TompaSeventh International Conference on Intelligent Systems for Molecular Biology, 1999.

A linear time algorithm for finding all maximal scoring subsequences.

W.L. Ruzzo, M. TompaProceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1999.