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On error-tolerant DNA screening

Weili Wu, Yaochun Huang, Xiao Huang, Yingshu Li
2006 Discrete Applied Mathematics  
Given n clones with some positive ones, the problem of DNA screening is to identify all positive clones with a set of tests each on a subset of clones, called a pool and the outcome is either the pool  ...  In this paper, we show that for a class of designs, if we apply those for samples with d positive clones to samples with at most d − 1 positive clones, the error-tolerant property will have an interesting  ...  In this paper, we will generalize Macula's construction [6] with simplicial complexity and moreover, show that if we apply those designs for samples with d positive clones to samples with at most d −  ... 
doi:10.1016/j.dam.2006.02.006 fatcat:ijn6his3sfbtplic7wy7btapyi

Construction of d(H)-disjunct matrix for group testing in hypergraphs

Hong Gao, F. K. Hwang, My T. Thai, Weili Wu, Taieb Znati
2006 Journal of combinatorial optimization  
of eukaryotic DNA transcription and RNA translation.  ...  Given a hypergraph with at most d positive edges, identify all positive edges with the minimum number of tests each of which tests on a subset of nodes, called a pool, and the outcome is positive if and  ...  Main results Marathe MV, Percus AG, Torney DC (2000) Combinatorial optimization in biology, manuscript Park H, Wu W, Wu X, Zhao HG (2003) DNA screening, nonadaptive group testing, and simplicial complex  ... 
doi:10.1007/s10878-006-9634-z fatcat:qbeumpavcrfsfcyiw5eidbxcny

A Construction of Pooling Designs with Some Happy Surprises

A. D'Yachkov, Frank Hwang, Antony Macula, Pavel Vilenkin, Chih-Wen Weng
2005 Journal of Computational Biology  
A collection of tested pools is called a pooling design. Pooling designs are standard experimental tools in many biotechnical applications.  ...  The screening of data sets for "positive data objects" is essential to modern technology.  ...  Ngo and Du [16] further extended the construction to some geometric structures like simplicial complexes, and some graph properties like matchings.  ... 
doi:10.1089/cmb.2005.12.1129 pmid:16241902 fatcat:hxul2xkegrb4njmcmj37q3fwa4

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

Zixuan Cang, Lin Mu, Guo-Wei Wei, Jian Peng
2018 PLoS Computational Biology  
scoring power and the virtual screening power of the proposed topological approaches.  ...  , and description of small molecules and biomolecular complexes.  ...  A filtration of a simplicial complex K is a nested sequence of sub- complexes of K such that ⌀ = K 0 & K 1 & . . . & K m = K. Each K i is itself a simplicial complex.  ... 
doi:10.1371/journal.pcbi.1005929 pmid:29309403 pmcid:PMC5774846 fatcat:ezbtv4gmazep3emu74smdho7zq

Molecular Biology and Pooling Design [chapter]

Weili Wu, Yingshu Li, Chih-hao Huang, Ding-Zhu Du
Data Mining in Biomedicine  
Therefore, the efficiency of testing and screening becomes very important. Pooling design is a very helpful tool, which has developed a lot of applications in molecular biology.  ...  The study of gene functions requires high quality of a DNA library. A large amount of testing and screening needs to be performed to obtain a highquality DNA library.  ...  Theorems 3 and 4 established connections between error-tolerant designs and simplicial complexes.  ... 
doi:10.1007/978-0-387-69319-4_8 fatcat:ugo5ybasibgi7igf337cuq4kmm

A construction of dz-disjunct matrices in a dual space of symplectic space

Geng-sheng Zhang, Bo-li Li, Xiao-lei Sun, Feng-xia Li
2008 Discrete Applied Mathematics  
As the smaller the ratio efficiency is, the better the pooling design is. We discuss the ratio efficiency of this construction and compare it with others, such as in [Anthony J.  ...  In this paper, we construct a d z -disjunct matrix with subspaces in a dual space of symplectic space F (2ν) q , then give its several properties and a new definition, ratio efficiency t/n.  ...  Acknowledgment The authors express their gratitude to the referee for his helpful suggestions and comments.  ... 
doi:10.1016/j.dam.2007.11.003 fatcat:pst6g3d3evaxdct3pwauj2m5vi

Error-correcting pooling designs associated with some distance-regular graphs

Yujuan Bai, Tayuan Huang, Kaishun Wang
2009 Discrete Applied Mathematics  
Their performances as pooling designs are better than those given by Ngo and Du. Moreover, pooling designs associated with other special distance-regular graphs are also considered.  ...  Motivated by the pooling designs over the incidence matrices of matchings with various sizes of the complete graph K 2n considered by Ngo and Du [Ngo and Du, Discrete Math. 243 (2003) 167-170], two families  ...  Acknowledgment The third author is partially supported by NCET-08-0052 and NSF of China (10871027).  ... 
doi:10.1016/j.dam.2009.04.024 fatcat:w7ec3hre5zhipkw4j5bwpwbwze

Two constructions of new error-correcting pooling designs from orthogonal spaces over a finite field of characteristic 2

Zengti Li, Suogang Gao, Hongjie Du, Feng Zou, Weili Wu
2009 Journal of combinatorial optimization  
In this paper, we construct two classes of t × n, s e -disjunct matrix with subspaces in orthogonal space F (2ν+1) q of characteristic 2 and exhibit their disjunct properties.  ...  Acknowledgement The authors are grateful to the referees for their valuable suggestions and comments.  ...  A non-adaptive testing algorithm is useful in many areas such as DNA library screening (Du and Hwang 2006; Ngo and Zu 2000) .  ... 
doi:10.1007/s10878-009-9210-4 fatcat:rgc4lfsiz5bqvdeadsfikrmcia

Group testing with geometry of classical groups over finite fields

Suogang Gao, Zengti Li, Weili Wu, Panos M. Pardalos, Dingzhu Du
2018 Journal of Algebraic Combinatorics  
In this paper, we give an overview of combinatorial group testing and algebra.  ...  [28] employed simplicial complex to perform the idea of containment design.  ...  Introduction The basic problem of DNA library screening is to determine which clone (a DNA segment) from the library contains which probe from a given collection of probes in an efficient fashion.  ... 
doi:10.1007/s10801-018-0828-0 fatcat:2xpjz27mdfgdjb277xy3ywufhu

Two error-correcting pooling designs from symplectic spaces over a finite field

Zengti Li, Tayuan Huang, Suogang Gao
2010 Linear Algebra and its Applications  
In this paper, we construct two classes of t × n, s e -disjunct matrix with subspaces in a symplectic space F (2ν) q and prove that the ratio efficiency t/n of two constructions are smaller than that of  ...  Acknowledgements The authors are grateful to the referees for their valuable suggestions and comments.  ...  A2008000128) and Natural Science Foundation of Langfang Normal University, China (LSZZ200901).  ... 
doi:10.1016/j.laa.2010.04.040 fatcat:rj7dgrzofvfj7a6hizidintzca

The 2019 Mathematical Oncology Roadmap

Russell C. Rockne, Andrea Hawkins-Daarud, Kristin R. Swanson, James P Sluka, James A. Glazier, Paul Macklin, David Hormuth, Angela M Jarrett, Ernesto Augutso Bueno da Fonseca Lima, J Oden, George Biros, Thomas E Yankeelov (+23 others)
2019 Physical Biology  
This is achieved through the use of patient-specific clinical data to: develop individualized screening strategies to detect cancer earlier; make predictions of response to therapy; design adaptive, patient-specific  ...  As a result, Mathematical Oncology has a broad scope, ranging from theoretical studies to clinical trials designed with mathematical models.  ...  Anderson* and Robert A.  ... 
doi:10.1088/1478-3975/ab1a09 pmid:30991381 pmcid:PMC6655440 fatcat:sb4ms7zygngd3pp5xuxundp3gy

COVID-19 and SARS-CoV-2. Modeling the present, looking at the future

Ernesto Estrada
2020 Physics reports  
Here, we review these three main areas of modeling research against SARS CoV-2 and COVID-19: (1) epidemiology; (2) drug repurposing; and (3) vaccine design.  ...  vaccine design, to mention just a few.  ...  The 0, 1, 2, 3-simplex corresponds to single vertex, edge, triangle, and tetrahedron, respectively. Simplicial complex, K .  ... 
doi:10.1016/j.physrep.2020.07.005 pmid:32834430 pmcid:PMC7386394 fatcat:ytcgwdnjvjffhpe2qpxivpv5ge

Prediction of Carbon Nanostructure Mechanical Properties and Role of Defects Using Machine Learning [article]

Qi Zhao, Jordan J. Winetrout, Yanxun Xu, Yusu Wang, Hendrik Heinz
2021 arXiv   pre-print
screening of 3D structures for enhanced mechanical properties.  ...  Carbon fiber and graphene-based nanostructures such as carbon nanotubes (CNTs) and defective structures have extraordinary potential as strong and lightweight materials.  ...  Work by Wang and Zhao are partially supported by NSF under grants OAC-2039794 and CCF-2051197.  ... 
arXiv:2110.00517v2 fatcat:fgiwxi46encq5lvwrqd3kgbaby

Geometric cooperativity and anticooperativity of three-body interactions in native proteins

Xiang Li, Jie Liang
2005 Proteins: Structure, Function, and Bioinformatics  
Salt-bridge and regular hydrogen-bonding interactions such as those involving ionizable residues and polar residues are cooperative.  ...  When located on protein surface, these salt-bridge and regular hydrogen bonding interactions are anti-cooperative, and hydrophobic interactions involving alkyl residues become cooperative.  ...  This work is supported by grants from National Science Foundation (CAREER DBI0133856 and DBI0078270), National Institute of Health (GM68958), and Office of Naval Research (N000140310329).  ... 
doi:10.1002/prot.20438 pmid:15849756 fatcat:k6h5ky2tajgexn74c6rn3kzhrm

Page 2739 of Mathematical Reviews Vol. , Issue Index [page]

Mathematical Reviews  
DNA screening, pooling design and simplicial complex. (English summary) J. Comb.  ...  (Summary) 2004h:90061 90C27 (68W25, 90C60) — (with Li, Chungui; Wu, Xiaoyu; Huang, Xiao) Decoding in pooling designs. (English summary) J. Comb.  ... 
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