Abstract:
:Cell type identification from an unknown sample can often be done by comparing its gene expression profile against a gene expression database containing profiles of a large number of cell-types. This type of compendium-based cell-type identification strategy is particularly successful for human and mouse samples because a large volume of data exists for these organisms. However, such rich data repositories often do not exist for most non-model organisms. This makes transcriptome-based sample classification in these species challenging. We propose to overcome this challenge by performing a cross-species compendium comparison. The key is to utilise a recently published cross-species gene set analysis (XGSA) framework to correct for biases that may arise due to potentially complex homologous gene mapping between two species. The framework is implemented as an open source R package called C3. We have evaluated the performance of C3 using a variety of public data in NCBI Gene Expression Omnibus. We also compared the functionality and performance of C3 against some similar gene expression profile matching tools. Our evaluation shows that C3 is a simple and effective method for cell type identification. C3 is available at https://github.com/VCCRI/C3.
journal_name
Comput Biol Chemjournal_title
Computational biology and chemistryauthors
Kabir MH,Djordjevic D,O'Connor MD,Ho JWKdoi
10.1016/j.compbiolchem.2018.10.003subject
Has Abstractpub_date
2018-12-01 00:00:00pages
187-192eissn
1476-9271issn
1476-928Xpii
S1476-9271(18)30159-2journal_volume
77pub_type
杂志文章abstract::MODULEWRITER is a PERL object relational mapping (ORM) tool that automatically generates database specific application programming interfaces (APIs) for SQL databases. The APIs consist of a package of modules providing access to each table row and column. Methods for retrieving, updating and saving entries are provide...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/s1476-9271(03)00021-5
更新日期:2003-05-01 00:00:00
abstract::The potential of using sole respirometric CO2 labeling measurement for 13C metabolic flux analysis was investigated by metabolic simulations. For this purpose a model was created, considering all CO2 forming and consuming reactions in the central catabolic and anabolic pathways. To facilitate the interpretation of the...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2005.02.005
更新日期:2005-04-01 00:00:00
abstract::Optimally weighted fuzzy k-nearest neighbors (OWFKNN) algorithm has been used to predict proteins' subcellular locations based on their amino acid composition, in this paper. The datasets used consists of two species which are 997 prokaryotic and 2427 eukaryotic protein sequences. The overall prediction accuracy achie...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2008.07.011
更新日期:2008-12-01 00:00:00
abstract::3CL proteases (3CLpro) are only found in RNA viruses and have a central role in polyprotein processing during replication. Therefore, 3CLpro has emerged as promising drug target for therapeutic treatment of infections caused by Coronaviruses. In the light of the recent major outbreak of the SARS-CoV-2 virus and the co...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107351
更新日期:2020-10-01 00:00:00
abstract::The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational cha...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2007.02.005
更新日期:2007-04-01 00:00:00
abstract::The electrostatic (ES) energy of each residue was for the first time quantitatively evaluated in a flavin mononucleotide binding protein (FBP). A residue electrostatic energy (RES) was obtained as the sum of the ES energies between atoms in each residue and all other atoms in the FBP dimer using atomic coordinates obt...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.01.001
更新日期:2018-02-01 00:00:00
abstract::The shortest common supersequence (SCS) problem is a classical NP-hard problem, which is normally solved by heuristic algorithms. One important heuristic that is inspired by the process of chemical reactions in nature is the chemical reaction optimization (CRO) and its algorithm known as CRO_SCS. In this paper we prop...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107327
更新日期:2020-10-01 00:00:00
abstract::Nicotinamidase is a key enzyme for the salvage pathway catalyzing the first step for the conversion of nicotinamide (NAm) to nicotinic acid (NA) required for the synthesis of Nicotinamide Adenine Dinucleotide (NAD+) in the subsequent steps. Leishmania protozoan parasites are NAD+ auxotrophs and need precursors (nicoti...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107150
更新日期:2019-12-01 00:00:00
abstract::Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core prot...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.02.017
更新日期:2018-06-01 00:00:00
abstract::Up to this date, there has been an ongoing debate about the mode of action of general anesthetics, which have postulated many biological sites as targets for their action. However, postoperative nausea and vomiting are common problems in which inhalational agents may have a role in their development. When a mode of ac...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2018.04.009
更新日期:2018-08-01 00:00:00
abstract::The induced pluripotent cells (iPSCs) are derived from somatic cells by reprogramming their genetic profiles. Such a process requires coordinated dynamic expression of hundreds of genes and proteins. As both deterministic and stochastic elements control the reprogramming process, it is not easy to have a way to reflec...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2011.05.002
更新日期:2011-08-10 00:00:00
abstract::G protein-coupled receptors (GPCRs), a large eukaryotic protein family, have proved difficult to comprehensively detect and functionally identify by homology searches and domain detection, because they are highly divergent and their sequences share strikingly little similarity. Transmembrane (TM) topology pattern anal...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2003.11.003
更新日期:2004-02-01 00:00:00
abstract::In this work we have studied the interaction of zervamicin IIB (ZrvIIB) with the model membranes of eukaryotes and prokaryotes using all-atom molecular dynamics. In all our simulations zervamicin molecule interacted only with lipid headgroups but did not penetrate the hydrophobic core of the bilayers. During the inter...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2010.12.005
更新日期:2011-02-01 00:00:00
abstract::Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglut...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2006.01.003
更新日期:2006-06-01 00:00:00
abstract::The single-stranded transfer DNA from the Ti plasmid of the soil bacteria Agrobacterium nonspecifically integrates into the plant chromosome and is inherited at subsequent cell divisions. How it is transferred across host membranes is unknown, but it is believed that VirE2 proteins form a membrane-spanning pore or cha...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.01.016
更新日期:2017-06-01 00:00:00
abstract::Currently Alzheimer's disease (AD) is a devastating neurological disorder that mainly affects the elderly. The treatment of AD has as main objective to increase the levels of ACh in the synaptic cleft by inhibiting the cholinesterase enzymes, which are responsible for the degradation of ACh. Twenty one synthesized cou...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107293
更新日期:2020-05-29 00:00:00
abstract::In this study, the structural and antioxidant behavior of the three lichen-derived natural compounds such as atranorin (AT), evernic acid (EV) and diffractaic acid (DF) has been investigated in the gas and water phase using both B3LYP and M06-2X functional level of density functional theory (DFT) with two different ba...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.03.009
更新日期:2019-06-01 00:00:00
abstract::The channel blocker picrotoxinin has been studied with GABAA-ρ1 and GABAA-ρ2 homology models based on the GluCl crystal structure. Picrotoxinin is tenfold more potent for GABAA-ρ2 than for GABAA-ρ1 homomeric channels. This intra-subunit selectivity arises from the unconserved residues at the 2' sites, which are the es...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.07.003
更新日期:2016-10-01 00:00:00
abstract::We have formulated the ab-initio prediction of the 3D-structure of proteins as a probabilistic programming problem where the inter-residue 3D-distances are treated as random variables. Lower and upper bounds for these random variables and the corresponding probabilities are estimated by nonparametric statistical metho...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/s0097-8485(02)00074-8
更新日期:2003-07-01 00:00:00
abstract::We present the mechanism of interaction of Wnt network module, which is responsible for periodic somitogenesis, with p53 regulatory network, which is one of the main regulators of various cellular functions, and switching of various oscillating states by investigating p53-Wnt model. The variation in Nutlin concentrati...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2015.07.014
更新日期:2015-12-01 00:00:00
abstract::The Egyptian flora is rich with a large number of Triticum plants, which are very difficult to discriminate between in the early developmental stages. This study assesses the significance of using two DNA Barcoding loci (matK and rbcL) in distinguishing between 18 different Triticum accessions in Egypt. We isolated an...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.09.003
更新日期:2017-12-01 00:00:00
abstract::The P-type ATPases (P-ATPases) are present in all living cells where they mediate ion transport across membranes on the expense of ATP hydrolysis. Different ions which are transported by these pumps are protons like calcium, sodium, potassium, and heavy metals such as manganese, iron, copper, and zinc. Maintenance of ...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.04.006
更新日期:2017-06-01 00:00:00
abstract::Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disorder, and its pathogenesis in males and in cases without accompanying lupus nephritis (LN-) is not fully understood. In this study, we identified 90 (82 up- and 8 downregulated) differentially expressed genes (DEGs) common to female LN-, female LN+ a...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107135
更新日期:2019-12-01 00:00:00
abstract::With the development of cancer research, various gene expression datasets containing cancer information show an explosive growth trend. In addition, due to the continuous maturity of single-cell RNA sequencing (scRNA-seq) technology, the protein information and pedigree information of a single cell are also continuous...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2020.107368
更新日期:2020-12-01 00:00:00
abstract::Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile level is presented, namely, the profile domain linker propensit...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2006.01.001
更新日期:2006-04-01 00:00:00
abstract::Prefoldin is a molecular chaperone and acts as a nano-actuator in cargo carriage and drug delivery for disease treatment. Investigating the mechanical properties of nano-actuator helps predict its behavior and measure its performance under various environmental conditions, like external forces that are applied. Accord...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.107133
更新日期:2019-12-01 00:00:00
abstract::Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2017.04.002
更新日期:2017-06-01 00:00:00
abstract::The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Usi...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2019.05.011
更新日期:2019-10-01 00:00:00
abstract::Human intestinal absorption (HIA) of the drugs administered through the oral route constitutes an important criterion for the candidate molecules. The computational approach for predicting the HIA of molecules may potentiate the screening of new drugs. In this study, ensemble learning (EL) based qualitative and quanti...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.01.005
更新日期:2016-04-01 00:00:00
abstract::Protein structure prediction is considered as one of the most challenging and computationally intractable combinatorial problem. Thus, the efficient modeling of convoluted search space, the clever use of energy functions, and more importantly, the use of effective sampling algorithms become crucial to address this pro...
journal_title:Computational biology and chemistry
pub_type: 杂志文章
doi:10.1016/j.compbiolchem.2016.01.008
更新日期:2016-04-01 00:00:00