Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production

S Jagadevan, A Banerjee, C Banerjee, C Guria… - Biotechnology for …, 2018 - Springer
In the wake of the uprising global energy crisis, microalgae have emerged as an alternate
feedstock for biofuel production. In addition, microalgae bear immense potential as bio-cell …

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

Machine learning for the advancement of genome-scale metabolic modeling

P Kundu, S Beura, S Mondal, AK Das, A Ghosh - Biotechnology Advances, 2024 - Elsevier
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the
interrelations between genotype, phenotype, and external environment. The recent …

VANTED v2: a framework for systems biology applications

H Rohn, A Junker, A Hartmann, E Grafahrend-Belau… - BMC systems …, 2012 - Springer
Background Experimental datasets are becoming larger and increasingly complex,
spanning different data domains, thereby expanding the requirements for respective tool …

Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi‐omics perspective

M Kohlstedt, PK Sappa, H Meyer… - Environmental …, 2014 - Wiley Online Library
The Gram‐positive bacterium B acillus subtilis encounters nutrient limitations and osmotic
stress in its natural soil ecosystem. To ensure survival and sustain growth, highly integrated …

A Genome-Scale Metabolic Model of Soybean (Glycine max) Highlights Metabolic Fluxes in Seedlings

TB Moreira, R Shaw, X Luo, O Ganguly, HS Kim… - Plant …, 2019 - academic.oup.com
Until they become photoautotrophic juvenile plants, seedlings depend upon the reserves
stored in seed tissues. These reserves must be mobilized and metabolized, and their …

Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering

K Baghalian, MR Hajirezaei, F Schreiber - The Plant Cell, 2014 - academic.oup.com
Abstract Models are used to represent aspects of the real world for specific purposes, and
mathematical models have opened up new approaches in studying the behavior and …

Toward the role of interaction in visual analytics

A Kerren, F Schreiber - Proceedings of the 2012 Winter …, 2012 - ieeexplore.ieee.org
This paper firstly provides a general introduction in the most important aspects and ideas of
Visual Analytics. This multidisciplinary field focuses on the analytical reasoning of typically …

Integrated network analysis and effective tools in plant systems biology

A Fukushima, S Kanaya, K Nishida - Frontiers in plant science, 2014 - frontiersin.org
One of the ultimate goals in plant systems biology is to elucidate the genotype-phenotype
relationship in plant cellular systems. Integrated network analysis that combines omics data …

ReactionFlow: an interactive visualization tool for causality analysis in biological pathways

TN Dang, P Murray, J Aurisano, AG Forbes - BMC proceedings, 2015 - Springer
Background Molecular and systems biologists are tasked with the comprehension and
analysis of incredibly complex networks of biochemical interactions, called pathways, that …