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Sternberg, Paul W. Nature Cell Biology, 1 2. Gonczy, S. In: Advances in ceramic-matrix composites IV. Ceramic Transactions. Samwer, K. Physical Review Letters, 82 3. Wiggins, Stephen Chaos in the dynamics generated by sequences of maps, with applications to chaotic advection in flows with aperiodic time dependence. Wiedenbeck, M. Fine, Philip M. Ledyard, John O. Econometrica, 67 2.

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Biggs, A. In: Cosmological Parameters and the Evolution of the Universe. Kluwer , Dordrecht, p. Physical Review Letters, 83 8. Deser, S. Physical Review Letters, 82 Rosakis, A. Jackson, Matthew O. Ramamoorthi, Ravi and Arvo, James Creating generative models from range images. Schense, Jason C. Bioconjugate Chemistry, 10 1. Sieh, Kerry and Ward, Steven N. Geophysical Research Letters, 26 Hamburger, Zsuzsa A. Clemons, William M. Journal of Molecular Biology, 3.

Bhattacharya, Kaushik Crystallographic attributes of a shape-memory alloy. Journal of Engineering Materials and Technology, 1. Liang, G. International Journal of Modern Physics B, 13 Herman, David M. Vaidyanathan, P. Social Choice and Welfare, 16 4. Physical Review E, 60 2.


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Lewis, Claudia J. Geological Society of America Bulletin, 1. Painter, O. Journal of the Optical Society of America B, 16 2. Hammer, J. Pinatubo, Philippines. Bulletin of Volcanology, 60 5. Peral, Eva and Yariv, Amnon Degradation of modulation and noise characteristics of semiconductor lasers after propagation in optical fiber due to a phase-shift induced by stimulated Brillouin scattering. Kiewiet, D. Engineering and Science, 62 3.

Brongersma, M. Journal of Applied Physics, 86 2. Zinn, Kai and Schmid, Aloisia Derailed axons get on track. Macromolecules, 32 5. Matsuura, Shuji and Blake, Geoffrey A. In: Terahertz and Gigahertz Photonics. Hajimiri, Ali and Lee, Thomas H. Yang, Xing and Grosjean, Charles and Tai, Yu-Chong Design, fabrication, and testing of micromachined silicone rubbermembrane valves. Journal of Microelectromechanical Systems, 8 4. Molecular Biology of the Cell, 10 2. Pahre, Michael A. Anderson, David J. Current Opinion in Neurobiology, 9 1. Marquez, Guillermo and Wang, Lihong V.

Physics in Medicine and Biology, 44 1. Journal of Computational Biology, 6 Experimental Neurology, 2. Weinberger, A. Peters, Jonas C. Journal of Organometallic Chemistry, 59 Holmlin, R. Erik and Yao, Johanna A. Inorganic Chemistry, 38 1. Immunity, 11 1. Miller, R. Journal of Fluid Mechanics, Diau, Eric W.

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Arnold, Frances H. Annals of the New York Academy of Sciences, 1. Zhao, Huimin and Arnold, Frances H. Protein Engineering, 12 1. Current Opinion in Chemical Biology, 3 1. Trends in Biotechnology, 17 4. Burgasser, Adam J. Davy and Brown, Michael E. Macomb, D. Ho, Luis C. Marsden, Jerrold E.

Nonlinearity, 12 6. Jacobsen, Steven E. Development, Chang, Howard Y. Annales Academiae Scientiarum Fennicae. Mathematica, 24 1. Verdi, Joseph M. McBride, Helen J. Effros, Michelle Distortion-rate bounds for fixed- and variable-rate multiresolution source codes. Annals of Mathematics, 3. Aalto, S.

Springer , Dordrecht, pp. Steenberg, C. Wang, Susan L. Cell, 98 4. Desai, Chand J. Development, 7. Bergman, Oren and Gaberdiel, Matthias R. Ceniceros, Hector D. Physics of Fluids, 11 5. Journal of Geophysical Research B, B4. Andrew et al. Perez, Sharon E. Development, 8. Earth and Planetary Science Letters, Journal of Conference Abstracts, 4 1. Simha, N. Materials Science and Engineering A, Piquette, E. Kleeman, Michael J. Environmental Science and Technology, 33 1. Chen, G. Journal of the Mechanics and Physics of Solids, 47 4.

Journal of Differential Equations, 2. Meyer, P. Camerer, Colin F. Journal of Risk and Uncertainty, 19 McKelvey, Richard D. Liao, Hong and Yung, Yuk L. Hunt, M. Physics of Fluids, 11 1. Tandon, S. Cement and Concrete Research, 29 3. Swalley, Susanne E. Grela, M. Journal of Physical Chemistry B, Gibson, Michael A. Buse, Karsten and Adibi, Ali and Psaltis, Demetri Efficient non-volatile holographic recording in doubly doped lithium niobate.

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Journal of Computational Neuroscience, 6 2. Liu, Chong-yang and Bard, Allen J. Electrochemical and Solid-State Letters, 2 Poglitsch, Claudia L. Cell, 98 6. Kelley, Shana O. Marcus, R. Advances in Chemical Physics. Wiley , New York, NY, pp. Winkler, Jay R. Pure and Applied Chemistry, 71 9. McCarthy, Patrick J. Evans, M. Lall, Sanjay and Marsden, Jerrold E. ISBN set. Gabbiani, F. Gabbiani, Fabrizio and Metzner, W. Murray et al. Journal of Neurophysiology, 81 5.

Benjamin and Marshall, Shannon A. Current Opinion in Structural Biology, 9 4. Bhattacharya, Kaushik Energy minimization and nonlinear problems in polycrystalline solids. Flagan, Richard C. Patent number: US 6,, Sturges, Michael R. Nucleic Acids Research, 27 2. Smedley, G. Experiments in Fluids, 26 4. Experiments in Fluids, 26 Hogerheijde, Michiel R. Patty, John W. Sanz-Serna, J. Radovitzky, R. Computer Methods in Applied Mechanics and Engineering, Griffin, Robert J. Anooshehpoor, Abdolrasool and Heaton, Thomas H. Bulletin of the Seismological Society of America, 89 4.

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Journal of Geophysical Research B, B3. Allman, John Morgan Evolving Brains. Scientific American Library. Topoi, 18 2. Charpentier, Michel and Chandy, K. Amorebieta, V. Implications for the Mechanism of Oxygen Activation. Langmuir, 15 8. Econometrica, 67 4.

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Journal of Molecular Evolution, 49 6. Peterson, Kevin J. Developmental Biology, 2. Gowda, Krishne and Clemons, William M. Protein Science, 8 5. Astronomical Society of the Pacific Conference Series. Journal of Applied Physics, 85 8. Choi, S. Journal of Vacuum Science and Technology A, 17 4. Rutledge, David B. Spencer, Robert H. Yu, Hua-Zhong and Baskin, J. Spencer and Steiger, Beat et al. Journal of the American Chemical Society, 2. Fiebig, T. Chachisvilis, Mirianas and Zewail, Ahmed H.

Zhong, Dongping and Bernhardt, Thorsten M. Zhong, Dongping and Zewail, Ahmed H. Chemical Physics Letters, The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant NR and to the Gene Ontology GO protein sequence databases, resulting in 15, matches to 11, proteins in NR and 13, matches to 8, proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions.

Conclusions: The sequences obtained for Hirudo transcripts represent the first major database of genes expressed in this important model system. Phylogenetic comparisons of putative Hirudo innate immune response genes present within the Hirudo transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed. Desulfotomaculum reducens strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available.

The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria.

Based on the genomic information obtained for sulfate reduction in D. In addition, both H 2 -evolving and H 2 -consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H 2 cycling in the bacterium. The mechanism of metal reduction remains unknown. MSI is a molecular imaging technique that allows for the generation of topographic 2D maps for various endogenous and some exogenous molecules without prior specification of the molecule. In this paper, we start with the premise that a region of interest ROI is given to us based on preselected morphological criteria.

Given an ROT, we develop a pipeline, first to determine mass values with distinct expression signatures, localized to the ROI, and second to identify the peptides corresponding to these mass values. To identify spatially differentiated masses, we implement a statistic that allows us to estimate, for each spectral peak, the probability that it is over- or under-expressed within the ROI versus outside.

A novel pipeline based on constructing sequence tags de novo from both original and decharged spectra and a subsequent database search is used to identify peptides. As the MSI signal and the identified peptide are only related by a single mass value, we isolate the corresponding transcript and perform a second validation via in situ hybridization of the transcript. The Hirudo CNS is capable of regenerating itself after injury, thus forming an important model system for neuropeptide identification.

The pipeline helps identify a number of novel peptides. Specifically, we identify a gene that we name HmIF4, which is a member of the intermediate filament family involved in neural development and a second novel, uncharacterized peptide. A third peptide, derived from the histone H2B, is also identified, in agreement with the previously suggested role of histone H2B in axon targeting.

In the present work, spatiotemporal changes in molecular distributions during this phenomenon are explored. Moreover, the hypothesis that neural regeneration involves some molecular factors initially employed during embryonic neural development is tested. RESULTS: Imaging mass spectrometry coupled to peptidomic and lipidomic methodologies allowed the selection of molecules whose spatiotemporal pattern of expression was of potential interest.

Through the parallel use of a classical lipidomic approach and secondary ion mass spectrometry, specific lipids, including cannabinoids, gangliosides and several other types, were detected in adult ganglia following mechanical damage to connected nerves. These observations motivated a search for possible effects of cannabinoids on neurite outgrowth.

Exposing nervous tissues to Transient Receptor Potential Vanilloid TRPV receptor agonists resulted in enhanced neurite outgrowth from a cut nerve, while exposure to antagonists blocked such outgrowth. Our data further suggest that endocannabinoids also play key roles in CNS regeneration, mediated through the activation of leech TRPVs, as a thorough search of leech genome databases failed to reveal any leech orthologs of the mammalian cannabinoid receptors but revealed putative TRPVs. In sum, our observations identify a number of lipids and proteins that may contribute to different aspects of the complex phenomenon of leech nerve regeneration, establishing an important base for future functional assays.

This study presents the first characterization of endogenous small RNAs in a diatom, Thalassiosira pseudonana. Small RNAs act as transcriptional and translational regulators, controlling specific target genes involved in various cellular functions. Diatoms are unicellular photosynthetic organisms that play major roles in environmental processes, such as food webs and global carbon fixation.

From the computational analysis of approximately , sequences in the library and over 17 million sequences in the SOLiD libraries, there exists evidence of a core set of small RNA genes including: novel microRNAs, repeat-associated short interfering RNAs, and endogenous short interfering RNAs. The diatom genome contains elements similar to plant small RNA systems, such as the RNAi machinery, a high percentage of short interfering RNAs originating from protein-coding and repetitive regions of the genome, and putative binding sites of the small RNAs occurring primarily in the coding section of the predicted targets.

The characterization of the small RNA transcriptome of T. Ataxin-7 is a component of two different transcription coactivator complexes, and recent work indicates that disease protein normal function is altered in polyglutamine neurodegeneration. Given this, we studied how ataxin-7 gene expression is regulated.

The ataxin-7 repeat and translation start site are flanked by binding sites for CTCF, a highly conserved multifunctional transcription regulator. Loss of SCAANT1 derepressed ataxin-7 sense transcription in a cis-dependent fashion and was accompanied by chromatin remodeling. Discovery of this pathway underscores the importance of altered epigenetic regulation for disease pathology at repeat loci exhibiting bidirectional transcription. DV was not detected in 19 other African Americans with iron overload who resided in Alabama. DV could explain 'classical' ferroportin hemochromatosis phenotypes in some African Americans.

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Karger AG, Basel. Splicing is a cellular mechanism, which dictates eukaryotic gene expression by removing the noncoding introns and ligating the coding exons in the form of a messenger RNA molecule. Alternative splicing AS adds a major level of complexity to this mechanism and thus to the regulation of gene expression. This widespread cellular phenomenon generates multiple messenger RNA isoforms from a single gene, by utilizing alternative splice sites and promoting different exon-intron inclusions and exclusions.

AS greatly increases the coding potential of eukaryotic genomes and hence contributes to the diversity of eukaryotic proteomes. Mutations that lead to disruptions of either constitutive splicing or AS cause several diseases, among which are myotonic dystrophy and cystic fibrosis. Aberrant splicing is also well established in cancer states.

Identification of rare novel mutations associated with splice-site recognition, and splicing regulation in general, could provide further insight into genetic mechanisms of rare diseases. Here, disease relevance of aberrant splicing is reviewed, and the new methodological approach of starting from disease phenotype, employing exome sequencing and identifying rare mutations affecting splicing regulation is described. Exome sequencing has emerged as a reliable method for finding sequence variations associated with various disease states. To date, genetic studies using exome sequencing to find disease-causing mutations have focused on the discovery of nonsynonymous single nucleotide polymorphisms that alter amino acids or introduce early stop codons, or on the use of exome sequencing as a means to genotype known single nucleotide polymorphisms.

The involvement of splicing mutations in inherited diseases has received little attention and thus likely occurs more frequently than currently estimated. Studies of exome sequencing followed by molecular and bioinformatic analyses have great potential to reveal the high impact of splicing mutations underlying human disease. Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization.

Sequencing reads that pass through the junction of the two joined ends of a kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization.

Alternate year course. As the number of our digital traces continues to grow, so does the opportunity for discovering meaningful patterns in these traces. In this course, students will initially learn how to collect, clean, format, and store data from digital platforms. By adopting a computational approach to statistical analysis, students will then implement in code different statistical metrics and simulation scenarios for hypothesis testing and estimation.

Finally, students will generate meaningful visualizations for data exploration and communicating results. Additionally, we will discuss the ethics of data collection and think critically about current practices of experimenting with online users. Students will work in groups to create their own datasets, ask an interesting question, perform statistical analyses and visualizations, and report the results. Offered: Fall Normally offered alternate years. This course offers an introduction to the theory of computation. Topics include languages, regular expressions, finite automata, grammars, pushdown automata, and Turing machines.

The first part of the course covers the Chomsky hierarchy of languages and their associated computational models. The second part of the course focuses on decidability issues and unsolvable problems. The final part of the course investigates complexity theory. Foundations of Computer Systems with Laboratory.

This course examines how computers run programs, introducing key software and hardware abstractions and implementations between programming languages and transistors. The course traces representation and translation of data and programs through three broad topics in computer systems: computer hardware implementation, including digital logic, computer arithmetic, and machine organization; the hardware-software interface, including instruction set architecture, assembly code, and the C programming language; and abstractions for practical systems, including the physical memory hierarchy, the operating system process model, virtual memory, and memory management.

Students complete extensive hands-on projects in hardware and software systems. Students are required to attend one three-hour laboratory weekly. Prerequisite: , , or permission of instructor. This course satisfies the laboratory requirement. A systems-oriented approach to data networks, including a theoretical discussion of common networking problems and an examination of modern networks and protocols. Topics include point-topoint links, packet switching, internet protocols, end-to-end protocols, congestion control, and security.

Projects may include client-server applications and network measurement tools. This course introduces principles underlying the design, semantics, and implementation of modern programming languages in major paradigms including function-oriented, imperative, and object-oriented. The course examines: language dimensions including syntax, naming, state, data, control, types, abstraction, modularity, and extensibility; issues in the runtime representation and implementation of programming languages; and the expression and management of parallelism and concurrency.

Students explore course topics via programming exercises in several languages, including the development of programming language interpreters. This course covers principle and practice in the design and implementation of modern compilers and programming language runtime systems. Topics include lexical analysis, parsing, symbols tables, semantic analysis, type checking, intermediate representations, program analysis and optimization, code generation, garbage collection, and other runtime support.

As time permits, the course may also survey topics including just-in-time compilation, runtime optimization, concurrent runtime systems, or extended automatic program error detection. Students will construct a full compiler and runtime system for a simple statically-typed programming language over the course of the semester.

CS is recommended, but not required. Offered: Not offered Normally offered in alternate years. A study of the three-layer architecture commonly used for Web-based applications such as e-commerce sites. We will learn to model and design databases uses entity-relationship diagrams, and the Standard Query Language SQL for managing databases.

We will also discuss performance, reliability and security issues. Finally, we will create dynamic Web sites driven by database entries. Machine learning is the science of teaching computers how to learn from observations. It is ubiquitous in our interactions with society, showing up in face recognition, web search, targeted advertising, speech processing, genetic analysis, and even Facebook's selection of posts to display. It is currently at the forefront of research in artificial intelligence, and has been making rapid strides given the vast availability of data today.

This course is a broad introduction to the field, covering the theoretical ideas behind widely used algorithms like support vector machines, neural networks, graphical models, decision trees, and many more. We will also study practical applications of these algorithms to problems in vision, speech, language, biology, and the social sciences. Distribution: Epistemology and Cognition, Mathematical Modeling. A survey of topics in computer graphics with an emphasis on fundamental techniques.

Topics include: graphics hardware, fundamentals of three-dimensional graphics including modeling, projection, coordinate transformation, synthetic camera specification, color, lighting, shading, hidden surface removal, animation, and texture-mapping. We also cover the mathematical representation and programming specification of lines, planes, curves, and surfaces.

Students will build graphics applications using a browser-based platform. When is a cryptographic system secure and how will we ever know? This course introduces the computational models and theory computer scientists use to address these issues. Topics include one-way functions, trapdoor functions, probabilistic complexity classes, pseudorandom generators, interactive proof systems, zero-knowledge proofs, and the application of these theories to modern cryptology.

Prerequisite: or or permission of the instructor. This course will introduce mathematical logic and its applications in Computer Science. Initially, we will cover syntax and semantics of propositional and first-order logics and how those theories are used in Computer Science. From there we will cover undecidability, logic programming, SAT solvers, proving systems and model checking.

The goal is to prepare the students for using logic as a formal tool. Many elegant computational problems arise naturally in the modern study of molecular biology. This course is an introduction to the design, implementation, and analysis of algorithms with applications in genomics. Topics include bioinformatic algorithms for dynamic programming, tree-building, clustering, hidden Markov models, expectation maximization, Gibbs sampling, and stochastic context-free grammars.

Topics will be studied in the context of analyzing DNA sequences and other sources of biological data. Applications include sequence alignment, gene-finding, structure prediction, motif and pattern searches, and phylogenetic inference. Course projects will involve significant computer programming in Java.

No biology background is expected. Offered: Fall.