Search results for "genome-scale"

Hits ?▲	Authors	Title	Venue	Year	Link	Author keywords
62	Benjarath Phoophakdee, Mohammed J. Zaki	Genome-scale disk-based suffix tree indexing.	SIGMOD Conference	2007	DBLP DOI BibTeX RDF	disk-based, genome-scale, sequence indexing, suffix tree, external memory
60	Xinghua Shi, Rick Stevens	SWARM: a scientific workflow for supporting bayesian approaches to improve metabolic models.	CLADE	2008	DBLP DOI BibTeX RDF	metabolic models, scientific workflow, bayesian approaches
55	José P. Pinto, Oscar Días, Anália Lourenço, Sónia Carneiro, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha 0001	Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis.	IWPACBB	2008	DBLP DOI BibTeX RDF	Genome-scale model reconstruction, Zymomonas mobillis, data integration, data quality
41	Yun Zhang 0013, Faisal N. Abu-Khzam, Nicole E. Baldwin, Elissa J. Chesler, Michael A. Langston, Nagiza F. Samatova	Genome-Scale Computational Approaches to Memory-Intensive Applications in Systems Biology.	SC	2005	DBLP DOI BibTeX RDF
38	Marcin Imielinski, Niels Klitgord, Calin Belta	Investigating the genomic basis of metabolic robustness through in silico flux analysis.	CDC	2008	DBLP DOI BibTeX RDF
38	Zheng Fu, Xin Chen 0037, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang 0001	A Parsimony Approach to Genome-Wide Ortholog Assignment.	RECOMB	2006	DBLP DOI BibTeX RDF
37	Zemin Ning, Mario Cáccamo, James C. Mullikin	ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale.	CSB Workshops	2005	DBLP DOI BibTeX RDF
36	Xinghua Shi, Rick L. Stevens	A Bayesian Approach to High-Throughput Biological Model Generation.	BICoB	2009	DBLP DOI BibTeX RDF
31	Manesh J. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang 0008, Inna Vokler, Philip F. LoCascio, Dong Xu 0002, Ying Xu 0001	A Computational Pipeline for Protein Structure Prediction and Analysis at Genome Scale.	BIBE	2003	DBLP DOI BibTeX RDF
31	Tao Jiang 0001	A Combinatorial Approach to Genome-Wide Ortholog Assignment: Beyond Sequence Similarity Search.	CPM	2007	DBLP DOI BibTeX RDF
31	Xin Chen 0037, Jie Zheng 0002, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi, Tao Jiang 0001	Assignment of Orthologous Genes via Genome Rearrangement.	IEEE ACM Trans. Comput. Biol. Bioinform.	2005	DBLP DOI BibTeX RDF	Ortholog, paralog, reversal, comparative genomics, genome rearrangement, gene duplication
23	Meili Chen, Yingke Ma, Song Wu, Xinchang Zheng, Hongen Kang, Jian Sang, Xingjian Xu, Lili Hao, Zhaohua Li, Zheng Gong, Jing-Fa Xiao, Zhang Zhang 0002, Wenming Zhao, Yiming Bao	Genome Warehouse: A Public Repository Housing Genome-scale Data.	Genom. Proteom. Bioinform.	2021	DBLP DOI BibTeX RDF
23	Giancarlo Croce	Towards a genome-scale coevolutionary analysis. (Vers une analyse co-évolutive à l'échelle du génome).		2019	RDF
23	Risa Kawaguchi, Hisanori Kiryu	Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.	BMC Bioinform.	2016	DBLP DOI BibTeX RDF
23	John W. Nicol, Gregg A. Helt, Steven G. Blanchard Jr., Archana Raja, Ann E. Loraine	The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.	Bioinform.	2009	DBLP DOI BibTeX RDF
22	Nagiza F. Samatova, Al Geist, George Ostrouchov, Anatoli V. Melechko	Parallel Out-of-Core Algorithm for Genome-Scale Enumeration of Metabolic Systemic Pathways.	IPDPS	2002	DBLP DOI BibTeX RDF
20	Margaret J. Eppstein, Paul Haake	Very large scale ReliefF for genome-wide association analysis.	CIBCB	2008	DBLP DOI BibTeX RDF
18	Adrianto Wirawan, Bertil Schmidt	Parallel Discovery of Transcription Factor Binding Sites.	APCCAS	2006	DBLP DOI BibTeX RDF
17	Bin Du, Laurence Yang 0001, Colton J. Lloyd, Xin Fang, Bernhard O. Palsson	Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.	PLoS Comput. Biol.	2019	DBLP DOI BibTeX RDF
16	Anna V. Anagnostopoulos, Judith A. Blake, Carol J. Bult, Martin Ringwald, Joel E. Richardson, James A. Kadin, Janan T. Eppig	Using bio-ontologies as data annotation, integration & analytical tools at the Mouse Genome Informatics resource.	BIBE	2008	DBLP DOI BibTeX RDF
16	Tsai-Hung Fan, Shufen Lee, Hsueh-I Lu, Tsung-Shan Tsou, Tsai-Cheng Wang, Adam Yao	An Optimal Algorithm for Maximum-Sum Segment and Its Application in Bioinformatics Extended Abstract.	CIAA	2003	DBLP DOI BibTeX RDF
13	Fernando Cruz, João Capela, Eugénio C. Ferreira, Miguel Rocha 0001, Oscar Días	BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models.	IEEE ACM Trans. Comput. Biol. Bioinform.	2024	DBLP DOI BibTeX RDF
13	Patrick E. Gelbach, Handan Cetin, Stacey D. Finley	Flux sampling in genome-scale metabolic modeling of microbial communities.	BMC Bioinform.	2024	DBLP DOI BibTeX RDF
13	Juliette Cooke, Maxime Delmas, Cecilia Wieder, Pablo Rodríguez-Mier, Clément Frainay, Florence Vinson, Timothy M. D. Ebbels, Nathalie Poupin, Fabien Jourdan	Genome scale metabolic network modelling for metabolic profile predictions.	PLoS Comput. Biol.	2024	DBLP DOI BibTeX RDF
13	Takeyuki Tamura	MetNetComp: Database for Minimal and Maximal Gene-Deletion Strategies for Growth-Coupled Production of Genome-Scale Metabolic Networks.	IEEE ACM Trans. Comput. Biol. Bioinform.	2023	DBLP DOI BibTeX RDF
13	Feiran Li, Yu Chen, Johan Gustafsson, Hao Wang, Yi Wang, Chong Zhang, Xinhui Xing	Genome-scale metabolic models applied for human health and biopharmaceutical engineering.	Quant. Biol.	2023	DBLP DOI BibTeX RDF
13	Huan Du, Meng Li, Yang Liu	Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities.	Quant. Biol.	2023	DBLP DOI BibTeX RDF
13	Thummarat Paklao, Apichat Suratanee, Kitiporn Plaimas	ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology.	BMC Bioinform.	2023	DBLP DOI BibTeX RDF
13	Jakob P. Pettersen, Sandra Castillo, Paula Jouhten, Eivind Almaas	Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts.	BMC Bioinform.	2023	DBLP DOI BibTeX RDF
13	Enes Fahri Tezcan, Yigit Demirtas, Zeynep Petek Cakar, Kutlu Ö. Ülgen	Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets.	Frontiers Bioinform.	2023	DBLP DOI BibTeX RDF
13	Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, Defne G. Ozgulbas, Natalia Vassilieva, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian T. Foster, James J. Davis 0002, Michael E. Papka, Thomas S. Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan	GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics.	Int. J. High Perform. Comput. Appl.	2023	DBLP DOI BibTeX RDF
13	Gaofei Jiang, Jiaxuan Zhang, Yaozhong Zhang, Xinrun Yang, Tingting Li, Ningqi Wang, Xingjian Chen, Fang-Jie Zhao, Zhong Wei, Yangchun Xu, Qirong Shen, Wei Xue	DCiPatho: deep cross-fusion networks for genome scale identification of pathogens.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
13	Elena Lucy Carter, Chrystala Constantinidou, Mohammad Tauqeer Alam	Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.	Briefings Bioinform.	2023	DBLP DOI BibTeX RDF
13	Alexandru Oarga, Bridget Bannerman, Jorge Júlvez	CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities.	Bioinform.	2023	DBLP DOI BibTeX RDF
13	Pooya Borzou, Jafar Ghaisari, Iman Izadi, Yasin Eshraghi, Yousof Gheisari	A novel strategy for dynamic modeling of genome-scale interaction networks.	Bioinform.	2023	DBLP DOI BibTeX RDF
13	Lun Ai 0001, Shi-Shun Liang, Wang-Zhou Dai, Liam Hallett, Stephen H. Muggleton, Geoff S. Baldwin	Human Comprehensible Active Learning of Genome-Scale Metabolic Networks.	CoRR	2023	DBLP DOI BibTeX RDF
13	Ashka Shah, Arvind Ramanathan, Valérie Hayot-Sasson, Rick Stevens	Causal Discovery and Optimal Experimental Design for Genome-Scale Biological Network Recovery.	CoRR	2023	DBLP DOI BibTeX RDF
13	Jinyi Qian, Yuzhou Wang, Xiner Liu, Zijian Hu, Nan Xu, Yuetong Wang, Tianqiong Shi, Chao Ye	Improving acetoin production through construction of a genome-scale metabolic model.	Comput. Biol. Medicine	2023	DBLP DOI BibTeX RDF
13	Pritam Kundu, Amit Ghosh	Genome-scale community modeling for deciphering the inter-microbial metabolic interactions in fungus-farming termite gut microbiome.	Comput. Biol. Medicine	2023	DBLP DOI BibTeX RDF
13	Maxwell Neal, Deepan Thiruppathy, Karsten Zengler	Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	Diego Tec-Campos, Camila Posadas, Juan D. Tibocha-Bonilla, Deepan Thiruppathy, Nathan Glonek, Cristal Zuñiga, Alejandro Zepeda, Karsten Zengler	The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	Tareian A. Cazares, Faiz W. Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T. Bejjani, Joseph A. Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C. Kottyan, Artem Barski, Matthew T. Weirauch, V. B. Surya Prasath, Emily R. Miraldi	maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	Tyler W. H. Backman, Christina Schenk, Tijana Radivojevic, David Ando, Jahnavi Singh, Jeffrey J. Czajka, Zak Costello, Jay D. Keasling, Yinjie Tang, Elena V. Akhmatskaya, Héctor García Martín	BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	Emanuel Cunha, Miguel Silva, Inês Chaves, Hüseyin Demirci, Davide Lagoa, Diogo Lima, Miguel Rocha 0001, Isabel Rocha, Oscar Días	The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	Alina Rekena, Marina J. Pinheiro, Nemailla Bonturi, Isma Belouah, Eliise Tammekivi, Koit Herodes, Eduard J. Kerkhoven, Petri-Jaan Lahtvee	Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	William T. Scott Jr., Sara Benito-Vaquerizo, Johannes Zimmermann, Djordje Bajic, Almut Heinken, María Suárez-Diez, Peter J. Schaap	A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia.	PLoS Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	Puhua Niu, Maria J. Soto, Shuai Huang 0001, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian	Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction.	J. Comput. Biol.	2023	DBLP DOI BibTeX RDF
13	Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu	Genome-Scale Algorithm Design: Bioinformatics in the Era of High-Throughput Sequencing (2nd edition).		2023	RDF
13	Ashka Shah, Arvind Ramanathan, Valérie Hayot-Sasson, Rick Stevens	Causal Discovery and Optimal Experimental Design for Genome-Scale Biological Network Recovery.	PASC	2023	DBLP DOI BibTeX RDF
13	Teresa Joven, Jorge Lázaro, Jorge Júlvez	Modeling Uncertain Biomass Composition in Genome-Scale Metabolic Models with Flexible Nets.	QEST	2023	DBLP DOI BibTeX RDF
13	Gautham Dharuman, Arvind Ramanathan	Protein Generation via Genome-scale Language Models with Bio-physical Scoring.	SC Workshops	2023	DBLP DOI BibTeX RDF
13	Kowshika Sarker, Ruoqing Zhu, Hannah D. Holscher, ChengXiang Zhai	Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intake.	BCB	2023	DBLP DOI BibTeX RDF
13	Miria Bernardino, Robert G. Beiko	Genome-scale prediction of bacterial promoters.	Biosyst.	2022	DBLP DOI BibTeX RDF
13	Ying Ji 0002, Rui Chen 0021, Quan Wang 0004, Qiang Wei, Ran Tao, Bingshan Li	A Bayesian framework to integrate multi-level genome-scale data for Autism risk gene prioritization.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
13	Max van 't Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson, Morten O. A. Sommer	High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917.	BMC Bioinform.	2022	DBLP DOI BibTeX RDF
13	Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hong-Yu Ou	T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model.	Briefings Bioinform.	2022	DBLP DOI BibTeX RDF
13	Xinxin Peng, Xiaoyu Wang, Yuming Guo, Zongyuan Ge, Fuyi Li, Xin Gao 0001, Jiangning Song	RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.	Briefings Bioinform.	2022	DBLP DOI BibTeX RDF
13	Gianvito Pio, Paolo Mignone, Giuseppe Magazzù, Guido Zampieri, Michelangelo Ceci, Claudio Angione	Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction.	Bioinform.	2022	DBLP DOI BibTeX RDF
13	Rebecca L. Rubinstein, Mikayla A. Borton, Haiyan Zhou, Michael Shaffer, David W. Hoyt, James Stegen, Christopher S. Henry, Kelly C. Wrighton, Roelof Versteeg	ORT: a workflow linking genome-scale metabolic models with reactive transport codes.	Bioinform.	2022	DBLP DOI BibTeX RDF
13	Ines Thiele, German A. Preciat Gonzalez, Ronan M. T. Fleming	MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions.	Bioinform.	2022	DBLP DOI BibTeX RDF
13	Tadeja Rezen, Alexandre Martins, Miha Mraz, Nikolaj Zimic, Damjana Rozman, Miha Moskon	Integration of omics data to generate and analyse COVID-19 specific genome-scale metabolic models.	Comput. Biol. Medicine	2022	DBLP DOI BibTeX RDF
13	Abhijit Paul, Salman Azhar, Phonindra Nath Das, Nandadulal Bairagi, Samrat Chatterjee	Elucidating the metabolic characteristics of pancreatic β-cells from patients with type 2 diabetes (T2D) using a genome-scale metabolic modeling.	Comput. Biol. Medicine	2022	DBLP DOI BibTeX RDF
13	Tânia Barata, Vítor Vieira, Rúben Rodrigues, Ricardo Pires das Neves, Miguel Rocha 0001	Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells.	Comput. Biol. Medicine	2022	DBLP DOI BibTeX RDF
13	Giuseppe Magazzù, Guido Zampieri, Claudio Angione	Clinical stratification improves the diagnostic accuracy of small omics datasets within machine learning and genome-scale metabolic modelling methods.	Comput. Biol. Medicine	2022	DBLP DOI BibTeX RDF
13	Alexandre Oliveira, Emanuel Cunha, Fernando Cruz, João Capela, João Carlos Sequeira, Marta Sampaio, Cláudia Sampaio, Oscar Días	Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool.	J. Integr. Bioinform.	2022	DBLP DOI BibTeX RDF
13	Maureen A. Carey, Gregory L. Medlock, Michal Stolarczyk, William A. Petri Jr., Jennifer L. Guler, Jason A. Papin	Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models.	PLoS Comput. Biol.	2022	DBLP DOI BibTeX RDF
13	Verónica S. Martínez, Pedro A. Saa, Jason Jooste, Kanupriya Tiwari, Lake-Ee Quek, Lars Keld Nielsen	The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility.	PLoS Comput. Biol.	2022	DBLP DOI BibTeX RDF
13	Nicole Pearcy, Marco Garavaglia, Thomas Millat, James P. Gilbert, Yoseb Song, Hassan Hartman, Craig Woods, Claudio Tomi-Andrino, Rajesh Reddy Bommareddy, Byung-Kwan Cho, David A. Fell, Mark Poolman, John R. King, Klaus Winzer, Jamie Twycross, Nigel P. Minton	A genome-scale metabolic model of Cupriavidus necator H16 integrated with TraDIS and transcriptomic data reveals metabolic insights for biotechnological applications.	PLoS Comput. Biol.	2022	DBLP DOI BibTeX RDF
13	Matteo N. Amaradio, Giorgio Jansen, Varun Ojha 0001, Jole Costanza, Giuseppe Di Fatta, Giuseppe Nicosia	Inferring Pathological Metabolic Patterns in Breast Cancer Tissue from Genome-Scale Models.	LOD (1)	2022	DBLP DOI BibTeX RDF
13	Kiumars Badr, Q. Peter He, Jin Wang	Understanding the evolution of interspecies metabolic interactions using dynamic genome-scale metabolic modeling*.	ACC	2022	DBLP DOI BibTeX RDF
13	Yunfeng Shan, Guo Li, Xiu-Qing Li, Robin Gras, Youjun Zhou	Data-Mining with Three Genome-Scale Approaches Supports that Lungfish is the Closest Living Relative of Land Vertebrate, but not Coelacanth.	CSCI	2022	DBLP DOI BibTeX RDF
13	Payal Gaggar, Manish Kumar, Kunal Mukhopadhyay	Genome-Scale Identification, in Silico Characterization and Interaction Study Between Wheat SNARE and NPSN Gene Families Involved in Vesicular Transport.	IEEE ACM Trans. Comput. Biol. Bioinform.	2021	DBLP DOI BibTeX RDF
13	Sudip Sharma, Sudhir Kumar 0001	Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps.	Nat. Comput. Sci.	2021	DBLP DOI BibTeX RDF
13	Qi Wang, Zhaoqian Liu, Bo Yan, Wen-Chi Chou, Laurence Ettwiller, Qin Ma 0003, Bingqiang Liu	A novel computational framework for genome-scale alternative transcription units prediction.	Briefings Bioinform.	2021	DBLP DOI BibTeX RDF
13	Wei Du 0002, Gaoyang Li, Nicholas Ho, Landon Jenkins, Drew Hockaday, Jiankang Tan, Huansheng Cao	CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms.	Briefings Bioinform.	2021	DBLP DOI BibTeX RDF
13	Sisheng Liu, Jinpeng Liu, Yanqi Xie, Tingting Zhai, Eugene W. Hinderer, Arnold J. Stromberg, Nathan L. Vanderford, Jill M. Kolesar, Hunter N. B. Moseley, Li Chen, Chunming Liu, Chi Wang 0003	MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations.	Bioinform.	2021	DBLP DOI BibTeX RDF
13	Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele	DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.	Bioinform.	2021	DBLP DOI BibTeX RDF
13	Mahim Mahbub, Zahin Wahab, Rezwana Reaz, Mohammad Saifur Rahman, Md. Shamsuzzoha Bayzid	wQFM: highly accurate genome-scale species tree estimation from weighted quartets.	Bioinform.	2021	DBLP DOI BibTeX RDF
13	Sylwester Swat, Artur Laskowski, Jan Badura, Wojciech Frohmberg, Pawel Wojciechowski, Aleksandra Swiercz, Marta Kasprzak, Jacek Blazewicz	Genome-scale de novo assembly using ALGA.	Bioinform.	2021	DBLP DOI BibTeX RDF
13	Ewelina Weglarz-Tomczak, Jakub M. Tomczak, Stanley Brul	M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models.	Bioinform.	2021	DBLP DOI BibTeX RDF
13	Giuseppe Cattaneo, Umberto Ferraro Petrillo, Raffaele Giancarlo, Francesco Palini, Chiara Romualdi	The Power of Alignment-Free Histogram-based Functions: a Comprehensive Genome Scale Experimental Analysis - Version 1.	CoRR	2021	DBLP BibTeX RDF
13	Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan	Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism.	PLoS Comput. Biol.	2021	DBLP DOI BibTeX RDF
13	Christian Schulz 0011, Tjasa Kumelj, Emil Karlsen, Eivind Almaas	Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition.	PLoS Comput. Biol.	2021	DBLP DOI BibTeX RDF
13	Piyush Nanda, Amit Ghosh	Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection.	PLoS Comput. Biol.	2021	DBLP DOI BibTeX RDF
13	Chaitra Sarathy, Marian Breuer, Martina Kutmon, Michiel E. Adriaens, Chris T. A. Evelo, Ilja C. W. Arts	Comparison of metabolic states using genome-scale metabolic models.	PLoS Comput. Biol.	2021	DBLP DOI BibTeX RDF
13	Sudharshan Ravi, Rudiyanto Gunawan	ΔFBA - Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data.	PLoS Comput. Biol.	2021	DBLP DOI BibTeX RDF
13	Alexandre Oliveira, Emanuel Cunha, Fernando Cruz, João Capela, João Carlos Sequeira, Marta Sampaio, Oscar Días	Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database.	PACBB	2021	DBLP DOI BibTeX RDF
13	Miria Bernardino, Robert G. Beiko	Genome-scale prediction of bacterial promoters.	CIBCB	2021	DBLP DOI BibTeX RDF
13	Mu Gao, Peik Lund-Andersen, Alex Morehead, Sajid Mahmud, Chen Chen, Xiao Chen, Nabin Giri, Raj S. Roy, Farhan Quadir, T. Chad Effler, Ryan Prout, Subil Abraham, Wael R. Elwasif, Nicholas Quentin Haas, Jeffrey Skolnick, Jianlin Cheng, Ada Sedova	High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function.	MLHPC@SC	2021	DBLP DOI BibTeX RDF
13	Mojtaba Tefagh, Stephen P. Boyd	SWIFTCORE: a tool for the context-specific reconstruction of genome-scale metabolic networks.	BMC Bioinform.	2020	DBLP DOI BibTeX RDF
13	Hanen Mhamdi, Jérémie Bourdon, Abdelhalim Larhlimi, Mourad Elloumi	Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks.	Informatics	2020	DBLP DOI BibTeX RDF
13	Archana Hari, Daniel Lobo	Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.	Nucleic Acids Res.	2020	DBLP DOI BibTeX RDF
13	Marco Passaro, Martina Martinovic, Valeria Bevilacqua, Elliot A. Hershberg, Grazisa Rossetti, Brian J. Beliveau, Raoul Jean Pierre Bonnal, Massimiliano Pagani	OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment.	Nucleic Acids Res.	2020	DBLP DOI BibTeX RDF
13	Charles J. Norsigian, Neha Pusarla, John Luke McConn, James T. Yurkovich, Andreas Dräger, Bernhard O. Palsson, Zachary A. King	BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.	Nucleic Acids Res.	2020	DBLP DOI BibTeX RDF
13	Vittorio Fortino, Giovanni Scala, Dario Greco	Feature set optimization in biomarker discovery from genome-scale data.	Bioinform.	2020	DBLP DOI BibTeX RDF
13	Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi	GEMtractor: extracting views into genome-scale metabolic models.	Bioinform.	2020	DBLP DOI BibTeX RDF
13	Francisco Guil, José F. Hidalgo, José M. García 0001	Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach.	Bioinform.	2020	DBLP DOI BibTeX RDF
13	Nikolay Martyushenko, Eivind Almaas	ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models.	Bioinform.	2020	DBLP DOI BibTeX RDF
13	Claude Pasquier, Alain Robichon	Computational prediction of miRNA/mRNA duplexomes at the whole human genome scale reveals functional subnetworks of interacting genes with embedded miRNA annealing motifs.	Comput. Biol. Chem.	2020	DBLP DOI BibTeX RDF
13	Andrea Cabbia, Peter A. J. Hilbers, Natal A. W. van Riel	A Distance-Based Framework for the Characterization of Metabolic Heterogeneity in Large Sets of Genome-Scale Metabolic Models.	Patterns	2020	DBLP DOI BibTeX RDF