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15th Annual international conference on Computational Science (ICCS)

作者： LeBlanc, Mark D. Drout, Michael D. C. Wheaton Coll Comp Sci Norton MA 02766 USA Wheaton Coll English Norton MA 02766 USA

the ability to write software (to script, to program, to code) is a vital skill for students and their future data-centric, multidisciplinary careers. We present a ten-year effort to teach introductory programming skills in domain-focused courses to students across divisions in our liberal arts college. By creatively working with colleagues in Biology, Statistics, and now English, we have designed, modified, and offered six iterations of two courses: "dna" and "computing for Poets". Larger percentages of women have consistently enrolled in these two courses vs. the traditional first course in the major. We share our open source course materials and present here our use of a blended learning classroom that leverages the increasing quality of online video lectures and programming practice sites in an attempt to maximize faculty-student interactions in class.

关键词： programming interdisciplinary multidisciplinary genomics bioinformatics digital humanities blended learning

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Understanding B-dna to A-dna transition in the right-handed dna helix: Perspective from a local to global transition

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PROGRESS IN BIOPHYSICS & molecular BIOLOGY 2017年 128卷 63-73页

作者： Kulkarni, Mandar Mukherjee, Arnab Indian Inst Sci Educ & Res Dept Chem Pune 411008 Maharashtra India

the right-handed dna helix exhibits two major conformations, A-dna and B-dna, depending on the environmental conditions. the B-dna to A-dna (B -> A) transition is sequence specific, cooperative, and reversible. the reduced water activity due to the addition of solvents like ethanol or the presence of protein or drug molecules causes B -> A transition. In several biological cases, B -> A transition occurs at a local level where small fragments of a long dna sequence undergoes B -> A transition. In this review, we have discussed various aspects of B -> A transition such as the role of water, sequence specificity, mechanism of B -> A transition, etc. the review primarily focuses on the B -> A mechanism involved at a local level, and finally its connection to the global transition in theoretical and experimental studies. (C) 2017 Published by Elsevier Ltd.

关键词： A-dna B-dna Cooperative transition Free energy dna polymorphism Sequence specificity

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Algorithms for the typing of related dna sequences

Algorithms for the typing of related DNA sequences

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15th international conference on Electronics, Communications and Computers (CONIELECOMP 2005)

作者： Rodríguez, RS Roldán, CYC Eisele, JG Gill, PG Galindo, MJO Univ Americas Puebla Dept Comp Sci Cholula Mexico

ISBN: (纸本)0769522831

this article presents an approach to solve the typing problem using algorithms for set covering. Two algorithms to solve this problem were designed and compared. the typing problem consists of distinguishing all sequences using the least possible reagents. For each reagent, their capacity to distinguish between pairs of sequences is represented in a matrix and then mapped to the set-covering problem. In [1], a proof of the equivalence of this problem with the set covering problem is presented;here, the results of an exact algorithm to solve the set-covering problem are presented. this algorithm uses a branch and bound method based on some intuitive properties of the solution, applying recursion as the final resource. Two approximation algorithms were also implemented and tested. One is an improved greedy algorithm and the other is based on dynamic programming. Real as well as randomly created instances were used to test the algorithms.

关键词： dna

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the Osmium Tetroxide Bipyridine-labeled dna Probe: Hairpin Conformations and Characterization of Redox-label Behavior

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ELECTROANALYSIS 2017年第1期29卷 51-59页

作者： Joda, Hamdi Sedova, Ada Awan, Waqas Flechsig, Gerd-Uwe SUNY Albany 1400 Washington Ave Albany NY 12222 USA Univ Miami Miller Sch Med Dept Biochem & Mol Biol 1011 NW 15th St Miami FL 33136 USA Oak Ridge Natl Lab Sci Comp Grp Natl Ctr Computat Sci 1 Bethel Valley Rd Oak Ridge TN 37831 USA

Osmium tetroxide bipyridine ([OsO4(bpy)]) is a versatile label for dna electrochemistry. Here we report our efforts to create an osmium tetroxide-labeled immobilized dna probe for use in biosensing experiments. Our label is applied in-house, as opposed to many other covalent redox labels used with dna. We developed an on-electrode labeling method that was able to avoid attack of our disulfide-based linker by the [OsO4(bpy)]. Our results include two different hairpin-based signal-off hybridization detection assays, each with robust, reproducible signal decrease on binding to complementary target. We also found that 6-mercapto-1-hexa-nol was able to interact with [OsO4(bpy)] in a stable manner when assembled at the surface, but was able to remove excess [OsO4(bpy)], which was found to adsorb strongly to the gold surface, and avoid MCH transformation, when applied after the labeling process. Furthermore, we found an increased adsorption affinity of [OsO4(bpy)]-labeled dna onto gold, characterized the redox behavior of adsorbed [OsO4(bpy)], and determined voltammetric signals on the HMDE of our intact disulfide linker while verifying that this linker is attacked by [OsO4(bpy)] when in solution.

关键词： Voltammetry Gold electrode Osmium tetroxide bipyridine dna Hybridization molecular beacon

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Epigenetic analysis of a single dna molecule by microfluidic device with quantum dot

Epigenetic analysis of a single DNA molecule by microfluidic...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Sano, Tatsuki Okamoto, Yukihiro Kaji, Noritada Tokeshi, Manabu Baba, Yoshinobu Department of Applied Chemistry Graduated School of Engineering Nagoya University Japan FIRST Research Center for Innovative Nanobiodevices Nagoya University Japan Graduate School of Science ERATO Higashiyama Live-Holonics Project Nagoya University Japan Japan

ISBN: (纸本)9781618395955

We report a rapid and simple epigenetic analysis based on microfluidic single dna molecular methylation detection. We developed a microfluidic device to stretch a single dna molecule and subsequent detection of a methylated dna base by quantum dot (QD)-immobilized methyl binding domain (MBD) protein. A QD-MBD complex specifically bound to a methylated base of stretched dna and was detected by a total internal reflection fluorescence microscope (TIRFM). Our method enables us to detect a number of methylation sites and identify the positions methylated simultaneously in the simple and rapid manner compared with the conventional methods. Copyright © (2011) by the Chemical and Biological Microsystems Society.

关键词： dna

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Spiking dna neural trees with applications to conceptual design

Spiking DNA neural trees with applications to conceptual des...

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international conference on Computer Supported Cooperative Work in Design

作者： Liu, Xiyu Zhang, Hongyan School of Management and Economics Shandong Normal University Jinan 250014 China

ISBN: (纸本)9781457703874

this paper presents a design evaluation technique by dna neural trees. We propose a new dna tree computing model to represent a neural tree. the optimization of the neural tree is performed by the dna operations. this is a new technique different with other evolutionary optimization methods and scale well for large optimizations. Finally, we present an application framework in conceptual architectural design. © 2011 IEEE.

关键词： dna

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FLR: A Revolutionary Alignment-Free Similarity Analysis Methodology for dna-Sequences

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1924-1936页

作者： Medhat, Belal Shawish, Ahmed British Univ Egypt Dept Comp Sci Fac Informat & Comp Sci Cairo 11837 Egypt German Univ Cairo Dept Comp Sci Fac Media Engn & Technol Cairo 11837 Egypt Arab Open Univ Fac Comp Studies Headquarters Kuwait Kuwait Ain Shams Univ Fac Comp & Informat Sci Cairo 11566 Egypt

this paper introduces a novel alignment-free sequence analysis methodology. Its main idea is based on introducing a new representation of the dna-Sequence. this representation breaks the dependency between the dna bases that exist in the traditional string presentation. We called it the Four-Lists-Representation (FLR). Based on the FLR, a series of revolutionary algorithms for searching, map-discovery, similarity-score analysis, and similarity-visualization have been developed. they are combined in what we call the FLR Methodology. the paper also studies most of the available similarity analysis techniques in a comprehensive state-of-art review. the conducted extensive simulation and theoretical studies confirm the outperformance of the whole set of FLR-based algorithms in terms of speed and memory consumption in comparison to a long list of available similarity analysis algorithms. the ability to provide a similarity-map, similarity-score, and similarity-graph as a set of evidence-based rationales makes the quality of results provided by the proposed methodology presents a new edge in this field and promises a new area of genome-based research.

关键词： dna Sequences Genomics Bioinformatics Acceleration Organisms Diseases Sequence analysis similarity-score similarity analysis similarity measurements FLR alignment-free sequence analysis

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On-chip synthesis of mutant gfp library using ultra-large self-aligned dna-bound beads microarray

On-chip synthesis of mutant gfp library using ultra-large se...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Sato, Shusuke Biyani, Manish Akagi, Takanori Ichiki, Takanori School of Engineering University of Tokyo Japan Center for Medical System Innovation Japan Core Research of Evolutional Science and Technology JST Japan not available 2-11-16 Yayoi Bunkyo-ku Tokyo 113-8656 Japan

An ultralarge-scale (1.4415;108) microreactor array chip was developed as a platform for the one-step synthesis of a wide variety of mutant proteins from a dna library. On-chip mutant protein synthesis and evaluati... 详细信息

ISBN: (纸本)9781618395955

An ultralarge-scale (1.44×108) microreactor array chip was developed as a platform for the one-step synthesis of a wide variety of mutant proteins from a dna library. On-chip mutant protein synthesis and evaluation were successfully demonstrated using a model library of GFP (Green fluorescence protein)-encoding dna including random sequences in the chromophore region. the developed technology provides an innovative tool for the high-throughput screening for protein functions that are required in directed molecular evolution. Copyright © (2011) by the Chemical and Biological Microsystems Society.

关键词： dna

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Exploring dna translocation through a nanopore via a multiscale Lattice-Boltzmann molecular-Dynamics methodology

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international JOURNAL OF MODERN PHYSICS C 2007年第4期18卷 685-692页

作者： Melchionna, Simone Fyta, Marla G. Kaxiras, Efthimios Succi, Sauro Univ Roma La Sapienza Dept Phys I-00185 Rome Italy Harvard Univ Dept Phys Cambridge MA 02138 USA Harvard Univ Dept Phys Div Engn & Appl Sci Cambridge MA 02138 USA CNR Ist Applicaz Calcolo I-00161 Rome Italy

A multiscale approach is used to simulate the translocation of dna through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of various initial configurations and lengths we map the probability distibutions of the passage times of the dna through the nanopore. A scaling law behavior for the most probable of these times with respect to length is derived, and shown to exhibit an exponent that is in a good agreement with the experimental findings. the essential features of the dna dynamics as it passes through the pore are explored.

关键词： multiscale modeling translocation hydrodynamics dna

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Compiling dna strand displacement reactions using a functional programming language

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15th international conference on Verification, Model Checking, and Abstract Interpretation, VMCAI 2014

作者： Lakin, Matthew R. Phillips, Andrew Biological Computation Group Microsoft Research Cambridge CB1 2FB United Kingdom Department of Computer Science University of New Mexico NM 87131 United States

ISBN: (纸本)9783319041315

dna nanotechnology is a rapidly-growing field, with many potential applications in nanoscale manufacturing and autonomous in vivo diagnostic and therapeutic devices. As experimental techniques improve it will become increasingly important to develop software tools and programming abstractions, to enable rapid and correct design of increasingly sophisticated computational circuits. this is analogous to the need for hardware description languages for VLSI. In this paper we discuss our experience implementing a domain-specific language for dna nanotechnology using a functional programming language. the ability to use abstract data types to describe molecular structures and to recurse over these types to derive the various interactions between structures was a major reason for the use of a functional language in this project. © 2014 Springer international Publishing.

关键词： Calculations

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