25 papers · ranked by Valyu relevance
Stuart M. Marshall, Alastair R. G. Murray, Leroy Cronin
One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can…
Stuart M. Marshall, Alastair R. G. Murray, Leroy Cronin
One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random architecturesin a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can…
Tuan Nhon Dang, Paul Murray, Angus Graeme Forbes
Background Molecular activation pathways are inherently complex, and understanding relations across many biochemical reactions and reaction types is difficult. Visualizing and analyzing a pathway is a challenge due to the network size and the diversity of relations between proteins and molecules. Results In this paper…
Yuzhen Ye, Thomas G. Doak, Christos A. Ouzounis
A common biological pathway reconstruction approach-as implemented by many automatic biological pathway services (such as the KAAS and RAST servers) and the functional annotation of metagenomic sequences-starts with the identification of protein functions or families (e.g., KO families for the KEGG database and the FIG…
Erik Csikos
Directed networks arise across biological, social, informational, and engineered systems, yet most analyses treat directedness as a binary property: a network is either a directed acyclic graph (DAG) or it is not. This binary classification obscures the rich spectrum of hierarchical, recurrent, and modular structure…
Mona Arabzadeh, Morteza Saheb Zamani, Mehdi Sedighi, Sayed‐Amir Marashi
'Sayed‐Amir Marashi'] An Elementary Flux Mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find these flux-balanced pathways. In this paper, an approach to…
Neha Talluri, Tristan Figueroa-Reid, Justin Hiemstra, Chris S. Magnano + 19 more
Cells coordinate diverse biological processes through interactions among thousands of molecules, but mapping these interactions comprehensively and systematically remains an open problem. Pathway reconstruction algorithms address this problem by linking molecules of interest, identified from high-throughput omics…
Sarah M. Kim, Matthew I. Peña, Mark Moll, George N. Bennett + 1 more
'Lydia E. Kavraki'] Recent developments in metabolic engineering have led to the successful biosynthesis of valuable products, such as the precursor of the antimalarial compound, artemisinin, and opioid precursor, thebaine. Synthesizing these traditionally plant-derived compounds in genetically modified yeast cells…
Chathranee Jayathilaka, Robyn P. Araujo, Lan Anh Nguyen, Mark B. Flegg
'Mark B. Flegg'] Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions from the identification of topological features, for example…
Dan Vasilescu, James Greene, James C. Schaff, Ion I Moraru + 1 more
Rule-based modeling allows representation and simulation of biological systems where molecular features (such as protein domains) and feature-specific details of molecular interactions are accounted for. The rule-based description is precise and can define very fine molecular details (e.g. how phosphorylation status of…
Kevin Lim, Limsoon Wong
Background The metabolic network is an aggregation of enzyme catalyzed reactions that converts one compound to another. Paths in a metabolic network are a sequence of enzymes that describe how a chemical compound of interest can be produced in a biological system. As the number of such paths is quite large, many…
Allison Pon, Timothy Jewison, Yilu Su, Yongjie Liang + 4 more
'Adam Maciejewski' 'Michael Wilson' 'David S. Wishart'] PathWhiz ([http://smpdb.ca/pathwhiz]()) is a web server designed to create colourful, visually pleasing and biologically accurate pathway diagrams that are both machine-readable and interactive. As a web server, PathWhiz is accessible from almost any place and…
Sean M. Halper, Iman Farasat, Howard M. Salis
Engineered heterologous metabolic pathways can convert low-cost feedstock into high-value products, though it remains a significant challenge to reliably and efficiently maximize end-product biosynthesis, particularly when many enzymes must be co-expressed together. When current approaches are applied to many-enzyme…
Ganesh A Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman + 2 more
Pathway analysis refers to the computational approaches used to investigate network behavior as a system. Pathway analysis can be broadly classified into two types: topological/structural network analysis and dynamical analysis. Topological analysis of a pathway identifies the global qualitative properties of the…
Gianluca Mattei, Daniel C. Zielinski, Zhuohui Gan, Matteo Ramazzotti + 1 more
Analyzing biological data using pathways helps identify trends in data tied to the function of a network. A large number of pathway-based analysis tools have been developed toward this goal. These pathways are often manually curated and thus associations are subject to the biases of the curator. A potentially…
Melissa D. Walker, Gabrielle E. Giese, Amy D. Holdorf, Sushila Bhattacharya + 14 more
In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology and the response to therapeutic drugs. On March 15, 2020, a stay-at-home order was put into effect in the state of Massachusetts, USA, to flatten the curve of the spread of the…
Jasmin Hafner, Vassily Hatzimanikatis
Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in biosynthetic pathway design is the extraction of novel metabolic pathways…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Authors not listed
Selection of efficient multi-step synthesis routes is a fundamental challenge in organic synthesis. Comparing different routes involves numerous parameters, economic considerations, and integration of nuanced chemical knowledge. While computer-aided synthesis planning (CASP) tools can generate synthetic routes…
Merim Dzaferagic, Nicholas J. Kaminski, Neal McBride, Irene Macaluso + 1 more
'Nicola Marchetti'] Abstract The rapid evolution of network services demands new paradigms for studying and designing networks. We propose a framework to investigate the underlying mechanisms of wireless network functions. This framework isolates and analyses a network function as a complex system. We propose…
Ryan Miller, Sebastian Muraru, Ana Belén Malpartida, Josh Low + 7 more
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while…
ALESSANDRO ALIPRANDI, Dario Alessi, Luca Morgan, Elisa Pelorosso + 1 more
Self-organization is a key pathway to achieving high levels of matter complexity. However, an energy-consuming active process, such as a dissipative regime, is essential for adaptation and evolution to occur. In this study, we transform the passive self-organization of a luminescent square planar Pt(II) complex into an…
Ryan Suderman, Eshan D. Mitra, Yen Ting Lin, Keesha E. Erickson + 2 more
'Song Feng' 'William S. Hlavacek'] Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species that may arise in the system. In many cases, this is not…
Samuel Genheden, Esben Bjerrum
We introduce a framework for benchmarking multi-step retrosynthesis methods, i.e. route predictions, called PaRoutes. The framework consists of two sets of 10,000 synthetic routes extracted from the patent literature, a list of stock compounds, and a curated set of reactions on which one-step retrosynthesis models can…
Chonghuan Zhang, Qianyue Zhang, Alexei Lapkin
Biochemical transformations may allow significant improvements in synthetic efficiency of complex functional molecules through reduction in the number of synthetic steps or avoidance of harsh conditions and/or toxic solvents/reactants. Yet, there is a limited access to biochemical reaction data, which reduces the…