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Research articles, presentations, and other scholarship

Recent Submissions

  • A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs 

    Liu, Mingming; Adelman, Zach N.; Myles, Kevin M.; Zhang, Liqing (Hindawi Publishing Corp, 2014-05-28)
    With the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. Sequence assembly approaches have been modified to meet the requirements for ...
  • Trust Management of Smart Service Communities 

    Al-Hamadi, Hamid; Chen, Ing-Ray; Cho, Jin-Hee (IEEE, 2019)
    In this paper, the notion of a smart service community is proposed to address the grand challenge of a huge number of the Internet-of-Things (IoT) devices providing similar services in a smart city environment (e.g., ...
  • Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum 

    Getz, Eric W.; Tithi, Saima Sultana; Zhang, Liqing; Aylward, Frank O. (American Society for Microbiology, 2018-09)
    Diverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track ...
  • Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis) 

    Grene, Ruth; Klumas, Curtis; Suren, Haktan; Yang, Kuan; Collakova, Eva; Myers, Elijah; Heath, Lenwood S.; Holliday, Jason A. (Frontiers, 2012)
    Microarray gene expression profiling is a powerful technique to understand complex developmental processes, but making biologically meaningful inferences from such studies has always been challenging. We previously reported ...
  • H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules 

    Gordon, JC; Myers, JB; Folta, T; Shoja, V; Heath, LS; Onufriev, A (2005-07-01)
    The structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. A number of existing practical methods predict protonation equilibrium pK constants ...
  • VMD: a community annotation database for oomycetes and microbial genomes 

    Tripathy, Sucheta; Pandey, Varun N.; Fang, Bing; Salas, Fidel; Tyler, Brett M. (2006-01-01)
    The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae ...
  • VIRGO: computational prediction of gene functions 

    Massjouni, Naveed; Rivera, Corban G.; Murali, T. M. (2006-07-01)
    Dramatic advances in sequencing technology and sophisticated experimental assays that interrogate the cell, combined with the public availability of the resulting data, herald the era of systems biology. However, the ...
  • Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction 

    Yang, Kuan; Zhang, Liqing (2008-03)
    Phylogenetic tree reconstruction requires construction of a multiple sequence alignment (MSA) from sequences. Computationally, it is difficult to achieve an optimal MSA for many sequences. Moreover, even if an optimal MSA ...
  • PIG-the pathogen interaction gateway 

    Driscoll, Tim; Dyer, Matthew D.; Murali, T. M.; Sobral, Bruno W. (2009-01)
    Protein-protein interactions (PPIs) play a vital role in initiating infection in a number of pathogens. Identifying which interactions allow a pathogen to infect its host can help us to understand methods of pathogenesis ...
  • Sexy gene conversions: locating gene conversions on the X-chromosome 

    Lawson, Mark J.; Zhang, Liqing (2009-08)
    Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan ...
  • H++3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations 

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V. (2012-07)
    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, ...
  • Why double-stranded RNA resists condensation 

    Tolokh, Igor S.; Pabit, Suzette A.; Katz, Andrea M.; Chen, Yujie; Drozdetski, Aleksander; Baker, Nathan; Pollack, Lois; Onufriev, Alexey V. (2014-09-15)
    The addition of small amounts of multivalent cations to solutions containing double-stranded DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the condensation is suppressed in double-stranded RNA, ...
  • XTALKDB: a database of signaling pathway crosstalk 

    Sam, Sarah A.; Teel, Joelle; Tegge, Allison N.; Bharadwaj, Aditya; Murali, T. M. (2017-01-04)
    Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents ...
  • CAGm: A repository of germline microsatellite variations in the 1000 genomes project 

    Kinney, N.; Titus-Glover, K.; Wren, J.D.; Varghese, R.T.; Michalak, P.; Liao, H.; Anandakrishnan, R.; Pulenthiran, A.; Kang, L.; Garner, H.R. (Oxford University Press, 2019-01-08)
    The human genome harbors an abundance of repetitive DNA; however, its function continues to be debated. Microsatellites-a class of short tandem repeat-are established as an important source of genetic variation. Array ...
  • Differentiating between cancer and normal tissue samples using multi-hit combinations of genetic mutations 

    Dash, S.; Kinney, N.A.; Varghese, R.T.; Garner, H.R.; Feng, W.-C.; Anandakrishnan, R. (Nature Publishing Group, 2019-01-30)
    Cancer is known to result from a combination of a small number of genetic defects. However, the specific combinations of mutations responsible for the vast majority of cancers have not been identified. Current computational ...
  • The pattern of DNA cleavage intensity around indels 

    Chen, Wei; Zhang, Liqing (Springer Nature, 2015-02-09)
    Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular ...
  • Identification and analysis of the N-6-methyladenosine in the Saccharomyces cerevisiae transcriptome 

    Chen, Wei; Tran, Hong; Liang, Zhiyong; Lin, Hao; Zhang, Liqing (Springer Nature, 2015-09-07)
    Knowledge of the distribution of N-6-methyladenosine (m(6)A) is invaluable for understanding RNA biological functions. However, limitation in experimental methods impedes the progress towards the identification of m(6)A ...
  • Cyber War Game in Temporal Networks 

    Cho, Jin-Hee; Gao, Jianxi (PLOS, 2016-02-09)
    In a cyber war game where a network is fully distributed and characterized by resource constraints and high dynamics, attackers or defenders often face a situation that may require optimal strategies to win the game with ...
  • Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models 

    Tegge, Allison N.; Rodrigues, Richard R.; Larkin, Adam L.; Vu, Lucas; Murali, T. M.; Rajagopalan, Padmavathy (Springer Nature, 2018-07-27)
    Liver homeostasis requires the presence of both parenchymal and non-parenchymal cells (NPCs). However, systems biology studies of the liver have primarily focused on hepatocytes. Using an organotypic three-dimensional (3D) ...
  • EpiViewer: an epidemiological application for exploring time series data 

    Thorve, Swapna; Wilson, Mandy L.; Lewis, Bryan L.; Swarup, Samarth; Vullikanti, Anil Kumar S.; Marathe, Madhav V. (2018-11-22)
    Abstract Background Visualization plays an important role in epidemic time series analysis and forecasting. Viewing time series data plotted on a graph can help researchers ...

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