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| [[Image:Pano1.jpg|750px]] | | My name is [http://www3.abhishek-tiwari.com/ Abhishek Tiwari] and I am PhD student in Bioengineering at [http://www.abi.auckland.ac.nz/uoa/ Auckland Bioengineering Institute], the [http://www.auckland.ac.nz/ University of Auckland]. I am condcuting my doctoral research on modelling of hormone dynamics. This wiki is the new home of my PhD research activities and it will provide models, results, experiments, or any other insights related to the project. I also maintain the [http://www.abhishek-tiwari.com/ Fisheye Perspective] blog which aggregates my random thoughts and speculations about science, systems biology, synthetic biology and technology. |
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| [[Abhishek Tiwari | <font face="trebuchet ms" style="color:#ffffff"> '''Home''' </font>]]
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| [[Abhishek Tiwari:Contact | <font face="trebuchet ms" style="color:#ffffff"> '''Contact''' </font>]] | |
| [[Abhishek Tiwari:iCODONS | <font face="trebuchet ms" style="color:#ffffff"> '''iCODONS''' </font>]]
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| [[Abhishek Tiwari:Reprints | <font face="trebuchet ms" style="color:#ffffff"> '''Publications''' </font>]]
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| [[Abhishek Tiwari:Research | <font face="trebuchet ms" style="color:#ffffff"> '''Research''' </font>]] | |
| [[Abhishek Tiwari:Projects | <font face="trebuchet ms" style="color:#ffffff"> '''Projects''' </font>]]
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| [[Abhishek Tiwari:Softwares | <font face="trebuchet ms" style="color:#ffffff"> '''Softwares''' </font>]]
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| [[Abhishek Tiwari:Links | <font face="trebuchet ms" style="color:#ffffff"> '''Links''' </font>]]
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| | ==Project content== |
| | *Table of content-[[Modelling Hormone Dynamics]] |
| | *Publications-[[Manuscripts Modelling Hormone Dynamics]] |
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| | ==Quick Links== |
| | | *[[Curated HPA-Axis Models]] |
| =Welcome to webpage of Abhishek Tiwari= | | *[[Modelling ACTH-induced steroidogenesis]] |
| | | *[[Multicellular simulation using CellML]] |
| The current focus of my research is the application of computational methods and tools to solve biological problems of fundamental significance. More details can be found in [[Abhishek Tiwari:Research|Research]] section. Recently I completed my BS Bioinformatics from VIT, Vellore, India and currently working as Jr. Research Associate with Informatics Group at GVK Biosciences.
| | *[[Hormone Dynamics of HAC15/Y1 Cells]] |
| I am also a member of Prof Gautam R. Desiraju Research Group at School of Chemistry at University
| | *[http://openwetware.org/wiki/OpenWetWare:Information_management/PubgetNotes Referring DOI and PMID] |
| of Hyderabad. My research network is known as [[Abhishek Tiwari:iCODONS|iCODONS]].
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| =Latest Articles by Abhishek Tiwari= | |
| * [[Abhishek Tiwari:Biological Text Mining|Biological Text Mining]] | |
| * [[Abhishek Tiwari:Hot Computational Biology Papers-By Category|Hot Computational Biology Papers-By Category]] | |
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| =Hot Computational Biology Papers=
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| '''Powered by''' [[Image:footer_logo.gif]] [[Image:bmc_logo.gif]] [[Image:Oxford_logo.gif]]
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| '''''PLoS Computational Biology''''' Volume 2 | Issue 8 | AUGUST 2006
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| *'''An Integrative Method for Accurate Comparative Genome Mapping''' | |
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| '''Synopsis'''
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| Comparative genomics is an important discipline with applications in evolutionary, genetic, and ge
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| nome rearrangement studies. When comparing genomes, one is usually interested in investigating the relation between the genomic segments to establish their evolutionary origin: are the segments orthologous, and hence inherited from their most recent common ancestor? Are they paralogs, and hence duplicated from an ancestral segment? Did the segments undergo reordering? Were the segments deleted or inserted and—if so—how (insertion sequence, prophage, horizontal gene transfer)?
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| In this paper, Swidan et al. present MAGIC, a new approach for comparative genome mapping. The main novelty of this approach is the biologically intuitive clustering step, which aims towards both calculating reorder-free segments and identifying orthologous segments. The authors demonstrate MAGIC's robustness, relative to both its initial input and to its parameters' values. MAGIC's scalability is demonstrated by running it on distantly related organisms and on large genomes. In addition, Swidan et al. provide a detailed analysis of the differences between MAGIC and other comparative mapping methods.
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| Applying MAGIC to several prokaryotic pairs enabled the authors to address the aforementioned questions and to quantitatively study the different evolutionary forces shaping the prokaryotic genome as well as to investigate their breakpoint distribution.
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| '''''PLoS Computational Biology''''' Volume 2 | Issue 8 | AUGUST 2006
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| *'''The Ion Channel Inverse Problem: Neuroinformatics Meets Biophysics'''
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| '''Synopsis'''
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| Ion channels are the building blocks of the information processing capability of neurons: any realistic computational model of a neuron must include reliable and effective ion channel components. With the growing availability of computational resources, numerical inverse approaches are increasingly used across a range of disciplines. In this review paper authors suggest same type of inverse methodology for the study of ion channels. Inverse Problem approach address the question “what system gave rise to these observations?” usually by starting with a parameterized model that is expected to correspond to the real system for some point in its parameter space. A computational model of the recording process is built so that it can take any set of parameters and generate the data that they would have given rise to in exactly the same format as the experimental data. The model can then be compared to the real system in the space—that of the real data—where the most information is present. The forward calculation is then repeated over and over for different parameter sets guided by an optimization process to find the model or models that best represent the data.
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