RNA-seq is now the technology of choice for genome-wide differential gene expression experiments, but it is not clear how many biological replicates are needed to ensure valid biological interpretation of the results or which statistical tools are best for analyzing the data. An RNA-seq experiment with 48 biological replicates in each of two conditions was performed to answer these questions an...

The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models u...

Dedicated to my parents Sabitri Das (late) and Balaram Das For their love and courage iv ACKNOWLEDGEMENTS I am deeply grateful for the guidance and support of my advisor Prof. Joshua S. insightful comments and prompt advice made my graduate-student life a fascinating and enriching experience. I thank him for his support, for sharing his endless supply of ideas, and for being my philosopher and ...

The purpose of this project is to deliver fast and collaborative image processing to the biology laboratory bench. This will be achieved in the context of spatial data mapping, reconstruction, analysis and database query by developing GRID-enabled tools based on the existing tools developed as part of the Mouse Atlas Program at the MRC Human Genetics Unit. The Mouse Atlas Program at the MRC Hum...

∗Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY, 10027, USA, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, 10027, USA, and New York Genome Center, New York, 10013, USA ,†Department of Mathematics, University of Michigan, 530 S. Church Street, Ann Arbor, MI 48109,‡Department of Computer Science and ...

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently contains biological test results for more than 700 000 compounds. The goal of PubChem is to make this information easily accessible to biomedical researchers. In this work, we present a set of web ...

Huge volume of biological data, which is heterogeneous, autonomous and dynamic in nature, is being produced at a rapid pace throughout the community. Along with the increase in biological data, many tools are being designed to analyze them by different research groups. Integration of these biological data and tools is becoming one of the major topics in the bioinformatics community. Grid comput...

Stakeholders of petroleum hydrocarbon-contaminated (PHC) sites aim to meet remediation goals cost-effectively. But contaminated are typically complex, and when inefficient strategies implemented, time money wasted. Various can be implemented for site almost all at some point involve a biological component. Therefore, during characterization, seeing the complete picture by obtaining multiple lin...