Recent Submissions

  • Systematic Reverse Engineering of Network Topologies: A Case Study of Resettable Bistable Cellular Responses 

    Mondal, Debasish; Dougherty, Edward T.; Mukhopadhyay, Abhishek; Carbo, Adria; Yao, Guang; Xing, Jianhua (Public Library of Science, 2014-08-29)
    A focused theme in systems biology is to uncover design principles of biological networks, that is, how specific network structures yield specific systems properties. For this purpose, we have previously developed a reverse ...
  • Results of a digital library curriculum field test 

    Oh, Sanghee; Yang, Seungwon; Pomerantz, Jeffrey P.; Wildemuth, Barbara M.; Fox, Edward A. (Springer, 2015-05-20)
    The DL Curriculum Development project was launched in 2006, responding to an urgent need for consensus on DL curriculum across the fields of computer science and information and library science. Over the course of several ...
  • Summarizing cellular responses as biological process networks 

    Lasher, Christopher D; Rajagopalan, Padmavathy; Murali, T M (2013-07-29)
    Abstract Background Microarray experiments can simultaneously identify thousands of genes that show significant perturbation in expression between two experimental conditions. ...
  • Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii 

    Moreira, Leandro M; Almeida, Nalvo F; Potnis, Neha; Digiampietri, Luciano A; Adi, Said S; Bortolossi, Julio C; da Silva, Ana C; da Silva, Aline M; de Moraes, Fabrício E; de Oliveira, Julio C; de Souza, Robson F; Facincani, Agda P; Ferraz, André L; Ferro, Maria I; Furlan, Luiz R; Gimenez, Daniele F; Jones, Jeffrey B; Kitajima, Elliot W; Laia, Marcelo L; Leite, Rui P; Nishiyama, Milton Y; Rodrigues Neto, Julio; Nociti, Letícia A; Norman, David J; Ostroski, Eric H; Pereira, Haroldo A; Staskawicz, Brian J; Tezza, Renata I; Ferro, Jesus A; Vinatzer, Boris A; Setubal, João C (2010-04-13)
    Abstract Background Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three ...
  • JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations 

    Palmisano, Alida; Hoops, Stefan; Watson, Layne T; Jones, Thomas C; Tyson, John J; Shaffer, Clifford A (2015-12-24)
    Abstract Background Most biomolecular reaction modeling tools allow users to build models with a single list of parameter values. However, a common scenario involves different ...
  • Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos 

    Aghamirzaie, Delasa; Batra, Dhruv; Heath, Lenwood S; Schneider, Andrew; Grene, Ruth; Collakova, Eva (2015-11-14)
    Abstract Background Transcriptomics reveals the existence of transcripts of different coding potential and strand orientation. Alternative splicing (AS) can yield proteins ...
  • CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements 

    Badr, Eman; Heath, Lenwood S. (2015-09-04)
    Abstract Background Alternative splicing (AS) is a post-transcriptional regulatory mechanism for gene expression regulation. Splicing decisions are affected by the combinatorial behavior of different splicing factors that ...
  • Performance evaluation of indel calling tools using real short-read data 

    Hasan, Mohammad S; Wu, Xiaowei; Zhang, Liqing (2015-08-19)
    Abstract Background Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. With the advance of next-generation sequencing technology, ...
  • Predicting the combined effect of multiple genetic variants 

    Liu, Mingming; Watson, Layne T; Zhang, Liqing (2015-07-30)
    Abstract Background Many genetic variants have been identified in the human genome. The functional effects of a single variant have been intensively studied. However, the joint effects of multiple variants in the same genes ...
  • Privacy-Preserving Scanning of Big Content for Sensitive Data Exposure with MapReduce 

    Liu, Fang; Shu, Xiaokui; Yao, Danfeng (Daphne); Butt, Ali R. (2015-02-06)
    The exposure of sensitive data in storage and transmission poses a serious threat to organizational and personal security. Data leak detection aims at scanning content (in storage or transmission) for exposed sensitive ...
  • Vindel: a simple pipeline for checking indel redundancy 

    Li, Zhiyi; Wu, Xiaowei; He, Bin; Zhang, Liqing (2014-11-19)
    Abstract Background With the advance of next generation sequencing (NGS) technologies, a large number of insertion and deletion (indel) variants have been identified in human populations. Despite much research into variant ...
  • Steady state analysis of Boolean molecular network models via model reduction and computational algebra 

    Veliz-Cuba, Alan; Aguilar, Boris; Hinkelmann, Franziska; Laubenbacher, Reinhard (2014-06-26)
    Abstract Background A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, an increasingly ...
  • Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study 

    Song, Zhuo; Cao, Yang; Samuels, David C. (Public Library of Science, 2011-11-17)
    The activity of polymerase gamma is complicated, involving both correct and incorrect DNA polymerization events, exonuclease activity, and the disassociation of the polymerase: DNA complex. Pausing of pol-gamma might ...
  • Memory Switches in Chemical Reaction Space 

    Ramakrishnan, Naren; Upinder, S. Bhalla (Public Library of Science, 2008-07-18)
    Just as complex electronic circuits are built from simple Boolean gates, diverse biological functions, including signal transduction, differentiation, and stress response, frequently use biochemical switches as a functional ...
  • Network-Based Prediction and Analysis of HIV Dependency Factors 

    Murali, T. M.; Dyer, Matthew D.; Badger, David; Tyler, Brett M.; Katze, Michael G. (Public Library of Science, 2011-09-22)
    HIV Dependency Factors (HDFs) are a class of human proteins that are essential for HIV replication, but are not lethal to the host cell when silenced. Three previous genome-wide RNAi experiments identified HDF sets with ...
  • Protecting the communication structure in sensor networks 

    Olariu, S.; Xu, Q.; Eltoweissy, M.; Wadaa, A.; Zomaya, A. Y. (Hindawi Publishing Corporation, 2005)
    In the near future wireless sensor networks will be employed in a wide variety of applications establishing ubiquitous networks that will pervade society. The inherent vulnerability of these massively deployed networks to ...
  • Technical note: Simulating chemical systems in Fortran90 and Matlab with the Kinetic PreProcessor KPP-2.1 

    Sandu, Adrian; Sander, Rolf (Copernicus Publications, 2006-01-01)
    This paper presents the new version 2.1 of the Kinetic PreProcessor (KPP). Taking a set of chemical reactions and their rate coefficients as input, KPP generates Fortran90, Fortran77, Matlab, or C code for the temporal ...
  • Global estimates of CO sources with high resolution by adjoint inversion of multiple satellite datasets (MOPITT, AIRS, SCIAMACHY, TES) 

    Kopacz, M.; Jacob, D. J.; Fisher, J. A.; Logan, J. A.; Zhang, L.; Megretskaia, I. A.; Yantosca, R. M.; Singh, K.; Henze, D. K.; Burrows, J. P.; Buchwitz, M.; Khlystova, I.; McMillan, W. W.; Gille, J. C.; Edwards, D. P.; Eldering, A.; Thouret, V.; Nedelec, P. (Copernicus Publications, 2010)
    We combine CO column measurements from the MOPITT, AIRS, SCIAMACHY, and TES satellite instruments in a full-year (May 2004-April 2005) global inversion of CO sources at 4 degrees x 5 degrees spatial resolution and monthly ...
  • Origin and radiative forcing of black carbon transported to the Himalayas and Tibetan Plateau 

    Kopacz, M.; Mauzerall, D. L.; Wang, J.; Leibensperger, E. M.; Henze, D. K.; Singh, K. (Copernicus Publications, 2011)
    The remote and high elevation regions of central Asia are influenced by black carbon (BC) emissions from a variety of locations. BC deposition contributes to melting of glaciers and questions exist, of both scientific and ...
  • Chemical Mechanism Solvers in Air Quality Models 

    Zhang, Hong; Linford, John C.; Sandu, Adrian; Sander, Rolf (MDPI AG, 2011-09-01)
    The solution of chemical kinetics is one of the most computationally intensive tasks in atmospheric chemical transport simulations. Due to the stiff nature of the system, implicit time stepping algorithms which repeatedly ...

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