Omics-Driven Biotechnology for Industrial Applications

Amer, Bashar; Baidoo, Edward K.

doi:10.3389/fbioe.2021.613307

Omics-Driven Biotechnology for Industrial Applications

Journal Article · Tue Feb 23 00:00:00 EST 2021 · Frontiers in Bioengineering and Biotechnology

DOI:https://doi.org/10.3389/fbioe.2021.613307· OSTI ID:1798751

Amer, Bashar ^[1]; Baidoo, Edward K. ^[2]

Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Agile BioFoundry, Emeryville, CA (United States)

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on “omics” driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in “omics” technologies, compare the pros and cons of the different “omics” technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of “omics” technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of “omics” technologies to agricultural and food biotechnology, and review the impact of “omics” on current COVID-19 research.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1798751

Journal Information:: Frontiers in Bioengineering and Biotechnology, Journal Name: Frontiers in Bioengineering and Biotechnology Vol. 9; ISSN 2296-4185

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (177)

Probability-based protein identification by searching sequence databases using mass spectrometry data Perkins, David N.; Pappin, Darryl J. C.; Creasy, David M. Electrophoresis, Vol. 20, Issue 18 https://doi.org/10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2	journal	December 1999
The KEGG Database Kanehisa, Minoru In Silico’ Simulation of Biological Processes: Novartis Foundation Symposium 247 https://doi.org/10.1002/0470857897.ch8	book	November 2002
Targeted Metabolomics Roberts, Lee D.; Souza, Amanda L.; Gerszten, Robert E. Current Protocols in Molecular Biology, Vol. 98, Issue 1 https://doi.org/10.1002/0471142727.mb3002s98	journal	April 2012
A Review on Quantitative Multiplexed Proteomics Pappireddi, Nishant; Martin, Lance; Wühr, Martin ChemBioChem, Vol. 20, Issue 10 https://doi.org/10.1002/cbic.201800650	journal	April 2019
Combining Genomics, Metabolome Analysis, and Biochemical Modelling to Understand Metabolic Networks Fiehn, Oliver Comparative and Functional Genomics, Vol. 2, Issue 3 https://doi.org/10.1002/cfg.82	journal	January 2001
Development of a solid phase extraction protocol coupled with liquid chromatography mass spectrometry to analyze central carbon metabolites in lake sediment microcosms: Sample Preparation Yang, Song; Synovec, Robert E.; Kalyuzhnaya, Marina G. Journal of Separation Science, Vol. 34, Issue 24 https://doi.org/10.1002/jssc.201100533	journal	November 2011
A decade of metaproteomics: Where we stand and what the future holds: PROTEOMICS Wilmes, Paul; Heintz-Buschart, Anna; Bond, Philip L. PROTEOMICS, Vol. 15, Issue 20 https://doi.org/10.1002/pmic.201500183	journal	September 2015
High-resolution gas chromatography/mass spectrometry metabolomics of non-human primate serum Misra, Biswapriya B.; Bassey, Ekong; Bishop, Andrew C. Rapid Communications in Mass Spectrometry, Vol. 32, Issue 17 https://doi.org/10.1002/rcm.8197	journal	July 2018
Elucidation of chemical modifier reactivity towards peptides and proteins and the analysis of specific fragmentation by matrix‐assisted laser desorption/ionization collision‐induced dissociation tandem mass spectrometry Rühl, Michael; Kühn, Benjamin; Roos, Jessica Rapid Communications in Mass Spectrometry, Vol. 33, Issue S1 https://doi.org/10.1002/rcm.8223	journal	August 2018
Rice starch biotechnology: Rice endosperm as a model of cereal endosperms: Rice starch biotechnology Nakamura, Yasunori Starch - Stärke, Vol. 70, Issue 1-2 https://doi.org/10.1002/star.201600375	journal	July 2017
Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria Babele, Piyoosh Kumar; Young, Jamey D. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 12, Issue 3 https://doi.org/10.1002/wsbm.1472	journal	December 2019
Mechanisms and improvement of acid resistance in lactic acid bacteria Wang, Chao; Cui, Yanhua; Qu, Xiaojun Archives of Microbiology, Vol. 200, Issue 2 https://doi.org/10.1007/s00203-017-1446-2	journal	October 2017
Critical steps in carbon metabolism affecting lipid accumulation and their regulation in oleaginous microorganisms Dourou, Marianna; Aggeli, Dimitra; Papanikolaou, Seraphim Applied Microbiology and Biotechnology, Vol. 102, Issue 6 https://doi.org/10.1007/s00253-018-8813-z	journal	February 2018
Biomanufacturing: history and perspective Zhang, Yi-Heng Percival; Sun, Jibin; Ma, Yanhe Journal of Industrial Microbiology & Biotechnology, Vol. 44, Issue 4-5 https://doi.org/10.1007/s10295-016-1863-2	journal	November 2016
Recent progress and new challenges in metagenomics for biotechnology Chistoserdova, Ludmila Biotechnology Letters, Vol. 32, Issue 10 https://doi.org/10.1007/s10529-010-0306-9	journal	May 2010
Luxury phosphorus uptake in microalgae Solovchenko, Alexei E.; Ismagulova, Tatiana T.; Lukyanov, Alexandr A. Journal of Applied Phycology, Vol. 31, Issue 5 https://doi.org/10.1007/s10811-019-01831-8	journal	July 2019
Understanding and engineering alcohol-tolerant bacteria using OMICS technology Horinouchi, Takaaki; Maeda, Tomoya; Furusawa, Chikara World Journal of Microbiology and Biotechnology, Vol. 34, Issue 11 https://doi.org/10.1007/s11274-018-2542-4	journal	October 2018
Harnessing microbial metabolomics for industrial applications Zhao, Jiachen; Wang, Guan; Chu, Ju World Journal of Microbiology and Biotechnology, Vol. 36, Issue 1 https://doi.org/10.1007/s11274-019-2775-x	journal	December 2019
Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research Scalbert, Augustin; Brennan, Lorraine; Fiehn, Oliver Metabolomics, Vol. 5, Issue 4 https://doi.org/10.1007/s11306-009-0168-0	journal	June 2009
Metabolomics in pesticide research and development: review and future perspectives Aliferis, Konstantinos A.; Chrysayi-Tokousbalides, Maria Metabolomics, Vol. 7, Issue 1 https://doi.org/10.1007/s11306-010-0231-x	journal	August 2010
COVAIN: a toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data Sun, Xiaoliang; Weckwerth, Wolfram Metabolomics, Vol. 8, Issue S1 https://doi.org/10.1007/s11306-012-0399-3	journal	February 2012
Evaluation of quenching and extraction procedures for performing metabolomics in Acidithiobacillus ferrooxidans Doran, Marney L.; Mykytczuk, Nadia; Bieniek, Arielle Metabolomics, Vol. 13, Issue 12 https://doi.org/10.1007/s11306-017-1298-4	journal	November 2017
NMR-based metabolomics in real-time monitoring of treatment induced toxicity and cachexia in head and neck cancer: a method for early detection of high risk patients Boguszewicz, Ł.; Bieleń, A.; Mrochem-Kwarciak, J. Metabolomics, Vol. 15, Issue 8 https://doi.org/10.1007/s11306-019-1576-4	journal	August 2019
Rhizosphere microbiome: revisiting the synergy of plant-microbe interactions Mohanram, Saritha; Kumar, Praveen Annals of Microbiology, Vol. 69, Issue 4 https://doi.org/10.1007/s13213-019-01448-9	journal	February 2019
The Role of Advanced Magnetic Resonance Imaging Techniques in Multiple Sclerosis Clinical Trials Mahajan, Kedar R.; Ontaneda, Daniel Neurotherapeutics, Vol. 14, Issue 4 https://doi.org/10.1007/s13311-017-0561-8	journal	August 2017
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database Eng, Jimmy K.; McCormack, Ashley L.; Yates, John R. Journal of the American Society for Mass Spectrometry, Vol. 5, Issue 11 https://doi.org/10.1016/1044-0305(94)80016-2	journal	November 1994
Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial Folegatti, Pedro M.; Ewer, Katie J.; Aley, Parvinder K. The Lancet, Vol. 396, Issue 10249 https://doi.org/10.1016/S0140-6736(20)31604-4	journal	August 2020
Development of high throughput 96-blade solid phase microextraction-liquid chromatrography-mass spectrometry protocol for metabolomics Mousavi, Fatemeh; Bojko, Barbara; Pawliszyn, Janusz Analytica Chimica Acta, Vol. 892 https://doi.org/10.1016/j.aca.2015.08.016	journal	September 2015
Top Down proteomics: Facts and perspectives Catherman, Adam D.; Skinner, Owen S.; Kelleher, Neil L. Biochemical and Biophysical Research Communications, Vol. 445, Issue 4 https://doi.org/10.1016/j.bbrc.2014.02.041	journal	March 2014
Leveraging knowledge engineering and machine learning for microbial bio-manufacturing Oyetunde, Tolutola; Bao, Forrest Sheng; Chen, Jiung-Wen Biotechnology Advances, Vol. 36, Issue 4 https://doi.org/10.1016/j.biotechadv.2018.04.008	journal	July 2018
UHPLC high resolution orbitrap metabolomic fingerprinting of the unique species Ophryosporus triangularis Meyen from the Atacama Desert, Northern Chile Simirgiotis, Mario J.; Quispe, Cristina; Mocan, Andrei Revista Brasileira de Farmacognosia, Vol. 27, Issue 2 https://doi.org/10.1016/j.bjp.2016.10.002	journal	March 2017
Proteomic and Metabolomic Characterization of COVID-19 Patient Sera Shen, Bo; Yi, Xiao; Sun, Yaoting Cell, Vol. 182, Issue 1 https://doi.org/10.1016/j.cell.2020.05.032	journal	July 2020
Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge Cell Systems, Vol. 2, Issue 5 https://doi.org/10.1016/j.cels.2016.04.004	journal	May 2016
Omics Meets Metabolic Pathway Engineering Chen, Guo-Qiang Cell Systems, Vol. 2, Issue 6 https://doi.org/10.1016/j.cels.2016.05.005	journal	June 2016
A novel approach to the simultaneous extraction and non-targeted analysis of the small molecules metabolome and lipidome using 96-well solid phase extraction plates with column-switching technology Li, Yubo; Zhang, Zhenzhu; Liu, Xinyu Journal of Chromatography A, Vol. 1409 https://doi.org/10.1016/j.chroma.2015.07.048	journal	August 2015
Omics-Driven Systems Interrogation of Metabolic Dysregulation in COVID-19 Pathogenesis Song, Jin-Wen; Lam, Sin Man; Fan, Xing Cell Metabolism, Vol. 32, Issue 2 https://doi.org/10.1016/j.cmet.2020.06.016	journal	August 2020
How adaptive evolution reshapes metabolism to improve fitness: recent advances and future outlook Long, Christopher P.; Antoniewicz, Maciek R. Current Opinion in Chemical Engineering, Vol. 22 https://doi.org/10.1016/j.coche.2018.11.001	journal	December 2018
The future of analytical chemistry in foodomics Ferranti, Pasquale Current Opinion in Food Science, Vol. 22 https://doi.org/10.1016/j.cofs.2018.02.005	journal	August 2018
Integrating genomics and metabolomics for engineering plant metabolic pathways Oksman-Caldentey, Kirsi-Marja; Saito, Kazuki Current Opinion in Biotechnology, Vol. 16, Issue 2 https://doi.org/10.1016/j.copbio.2005.02.007	journal	April 2005
Metabolomics-assisted synthetic biology Ellis, David I.; Goodacre, Royston Current Opinion in Biotechnology, Vol. 23, Issue 1 https://doi.org/10.1016/j.copbio.2011.10.014	journal	February 2012
Increasing carbon source uptake rates to improve chemical productivity in metabolic engineering Yan, Qiang; Fong, Stephen S. Current Opinion in Biotechnology, Vol. 53 https://doi.org/10.1016/j.copbio.2018.06.001	journal	October 2018
Advanced MALDI mass spectrometry imaging in pharmaceutical research and drug development Schulz, Sandra; Becker, Michael; Groseclose, M. Reid Current Opinion in Biotechnology, Vol. 55 https://doi.org/10.1016/j.copbio.2018.08.003	journal	February 2019
Multi-omics and potential applications in wine production Sirén, Kimmo; Mak, Sarah Siu Tze; Fischer, Ulrich Current Opinion in Biotechnology, Vol. 56 https://doi.org/10.1016/j.copbio.2018.11.014	journal	April 2019
Recent trends in metabolic engineering of microbial chemical factories Liu, Yi; Nielsen, Jens Current Opinion in Biotechnology, Vol. 60 https://doi.org/10.1016/j.copbio.2019.05.010	journal	December 2019
Combining omics technologies with CRISPR-based genome editing to study food microbes Pan, Meichen; Barrangou, Rodolphe Current Opinion in Biotechnology, Vol. 61 https://doi.org/10.1016/j.copbio.2019.12.027	journal	February 2020
Metabolomics and systems biology: making sense of the soup Kell, D. Current Opinion in Microbiology, Vol. 7, Issue 3 https://doi.org/10.1016/j.mib.2004.04.012	journal	June 2004
Recent advances in mass spectrometry-based approaches for proteomics and biologics: Great contribution for developing therapeutic antibodies Iwamoto, Noriko; Shimada, Takashi Pharmacology & Therapeutics, Vol. 185 https://doi.org/10.1016/j.pharmthera.2017.12.007	journal	May 2018
Analytical Approaches to Metabolomics and Applications to Systems Biology Wang, Jeffrey H.; Byun, Jaeman; Pennathur, Subramaniam Seminars in Nephrology, Vol. 30, Issue 5 https://doi.org/10.1016/j.semnephrol.2010.07.007	journal	September 2010
Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast Jakočiūnas, Tadas; Klitgaard, Andreas K.; Kontou, Eftychia Eva Synthetic and Systems Biotechnology, Vol. 5, Issue 1 https://doi.org/10.1016/j.synbio.2020.01.004	journal	March 2020
Advances in Computational Methods in Systems Biology Gilbert, David; Heiner, Monika Theoretical Computer Science, Vol. 599 https://doi.org/10.1016/j.tcs.2015.08.013	journal	September 2015
Dynamic Metabolomics for Engineering Biology: Accelerating Learning Cycles for Bioproduction Vavricka, Christopher J.; Hasunuma, Tomohisa; Kondo, Akihiko Trends in Biotechnology, Vol. 38, Issue 1 https://doi.org/10.1016/j.tibtech.2019.07.009	journal	January 2020
New advances in analytical methods for mass spectrometry-based large-scale metabolomics study Liu, Xinyu; Zhou, Lina; Shi, Xianzhe TrAC Trends in Analytical Chemistry, Vol. 121 https://doi.org/10.1016/j.trac.2019.115665	journal	December 2019
Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for isopentenol production Kang, Aram; George, Kevin W.; Wang, George Metabolic Engineering, Vol. 34 https://doi.org/10.1016/j.ymben.2015.12.002	journal	March 2016
Biosynthesis of monoethylene glycol in Saccharomyces cerevisiae utilizing native glycolytic enzymes Uranukul, Boonsom; Woolston, Benjamin M.; Fink, Gerald R. Metabolic Engineering, Vol. 51 https://doi.org/10.1016/j.ymben.2018.09.012	journal	January 2019
Exceptional solvent tolerance in Yarrowia lipolytica is enhanced by sterols Walker, Caleb; Ryu, Seunghyun; Trinh, Cong T. Metabolic Engineering, Vol. 54 https://doi.org/10.1016/j.ymben.2019.03.003	journal	July 2019
The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology Sandberg, Troy E.; Salazar, Michael J.; Weng, Liam L. Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.08.004	journal	December 2019
Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli Kang, Aram; Mendez-Perez, Daniel; Goh, Ee-Been Metabolic Engineering, Vol. 56 https://doi.org/10.1016/j.ymben.2019.09.003	journal	December 2019
Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers Robinson, Christopher J.; Carbonell, Pablo; Jervis, Adrian J. Metabolic Engineering, Vol. 60 https://doi.org/10.1016/j.ymben.2020.04.008	journal	July 2020
SALSA: A Pattern Recognition Algorithm To Detect Electrophile-Adducted Peptides by Automated Evaluation of CID Spectra in LC−MS−MS Analyses Hansen, Beau T.; Jones, Juliet A.; Mason, Daniel E. Analytical Chemistry, Vol. 73, Issue 8 https://doi.org/10.1021/ac001172h	journal	April 2001
An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics Wolters, Dirk A.; Washburn, Michael P.; Yates, John R. Analytical Chemistry, Vol. 73, Issue 23 https://doi.org/10.1021/ac010617e	journal	December 2001
Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags Dayon, Loïc; Hainard, Alexandre; Licker, Virginie Analytical Chemistry, Vol. 80, Issue 8 https://doi.org/10.1021/ac702422x	journal	April 2008
Capillary Electrophoresis–Nanoelectrospray Ionization–Selected Reaction Monitoring Mass Spectrometry via a True Sheathless Metal-Coated Emitter Interface for Robust and High-Sensitivity Sample Quantification Guo, Xuejiang; Fillmore, Thomas L.; Gao, Yuqian Analytical Chemistry, Vol. 88, Issue 8 https://doi.org/10.1021/acs.analchem.5b04912	journal	April 2016
Real-Time In-Organism NMR Metabolomics Reveals Different Roles of AMP-Activated Protein Kinase Catalytic Subunits Nguyen, Tin Tin Manh; An, Yong Jin; Cha, Jin Wook Analytical Chemistry, Vol. 92, Issue 11 https://doi.org/10.1021/acs.analchem.9b05670	journal	May 2020
The Omics Revolution in Agricultural Research Van Emon, Jeanette M. Journal of Agricultural and Food Chemistry, Vol. 64, Issue 1 https://doi.org/10.1021/acs.jafc.5b04515	journal	November 2015
Computational Immune Proteomics Approach to Target COVID-19 Tilocca, Bruno; Britti, Domenico; Urbani, Andrea Journal of Proteome Research, Vol. 19, Issue 11 https://doi.org/10.1021/acs.jproteome.0c00553	journal	September 2020
Optimization and Application of Direct Infusion Nanoelectrospray HRMS Method for Large-Scale Urinary Metabolic Phenotyping in Molecular Epidemiology Chekmeneva, Elena; dos Santos Correia, Gonçalo; Chan, Queenie Journal of Proteome Research, Vol. 16, Issue 4 https://doi.org/10.1021/acs.jproteome.6b01003	journal	March 2017
Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes Chen, Yan; Guenther, Joel M.; Gin, Jennifer W. Journal of Proteome Research, Vol. 18, Issue 10 https://doi.org/10.1021/acs.jproteome.9b00455	journal	August 2019
Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid Hagen, Andrew; Poust, Sean; Rond, Tristan de ACS Synthetic Biology, Vol. 5, Issue 1 https://doi.org/10.1021/acssynbio.5b00153	journal	November 2015
Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol Rohlhill, Julia; Sandoval, Nicholas R.; Papoutsakis, Eleftherios T. ACS Synthetic Biology, Vol. 6, Issue 8, p. 1584-1595 https://doi.org/10.1021/acssynbio.7b00114	journal	May 2017
Lessons from Two Design–Build–Test–Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning Opgenorth, Paul; Costello, Zak; Okada, Takuya ACS Synthetic Biology, Vol. 8, Issue 6 https://doi.org/10.1021/acssynbio.9b00020	journal	May 2019
Metabolomics – the link between genotypes and phenotypes Fiehn, Oliver Plant Molecular Biology, Vol. 48, Issue 1/2, p. 155-171 https://doi.org/10.1023/A:1013713905833	journal	January 2002
MALDI Imaging mass spectrometry: current frontiers and perspectives in pathology research and practice Aichler, Michaela; Walch, Axel Laboratory Investigation, Vol. 95, Issue 4 https://doi.org/10.1038/labinvest.2014.156	journal	January 2015
Genome‐scale engineering for systems and synthetic biology Esvelt, Kevin M.; Wang, Harris H. Molecular Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1038/msb.2012.66	journal	January 2013
Environmental Breviatea harbour mutualistic Arcobacter epibionts Hamann, Emmo; Gruber-Vodicka, Harald; Kleiner, Manuel Nature, Vol. 534, Issue 7606 https://doi.org/10.1038/nature18297	journal	June 2016
Nanopore development at Oxford Nanopore Brown, Clive G.; Clarke, James Nature Biotechnology, Vol. 34, Issue 8 https://doi.org/10.1038/nbt.3622	journal	August 2016
Targeted proteomics Marx, Vivien Nature Methods, Vol. 10, Issue 1 https://doi.org/10.1038/nmeth.2285	journal	December 2012
Real-time metabolome profiling of the metabolic switch between starvation and growth Link, Hannes; Fuhrer, Tobias; Gerosa, Luca Nature Methods, Vol. 12, Issue 11 https://doi.org/10.1038/nmeth.3584	journal	September 2015
A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics Southam, Andrew D.; Weber, Ralf J. M.; Engel, Jasper Nature Protocols, Vol. 12, Issue 2 https://doi.org/10.1038/nprot.2016.156	journal	January 2017
Functional analysis of natural microbial consortia using community proteomics VerBerkmoes, Nathan C.; Denef, Vincent J.; Hettich, Robert L. Nature Reviews Microbiology, Vol. 7, Issue 3 https://doi.org/10.1038/nrmicro2080	journal	March 2009
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O. Nature Reviews Microbiology, Vol. 10, Issue 4 https://doi.org/10.1038/nrmicro2737	journal	February 2012
Assessing species biomass contributions in microbial communities via metaproteomics Kleiner, Manuel; Thorson, Erin; Sharp, Christine E. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01544-x	journal	November 2017
Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS Bian, Yangyang; Zheng, Runsheng; Bayer, Florian P. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-13973-x	journal	January 2020
New frontiers for the materials genome initiative de Pablo, Juan J.; Jackson, Nicholas E.; Webb, Michael A. npj Computational Materials, Vol. 5, Issue 1 https://doi.org/10.1038/s41524-019-0173-4	journal	April 2019
Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly Zhalnina, Kateryna; Louie, Katherine B.; Hao, Zhao Nature Microbiology, Vol. 3, Issue 4 https://doi.org/10.1038/s41564-018-0129-3	journal	March 2018
RNA sequencing: the teenage years Stark, Rory; Grzelak, Marta; Hadfield, James Nature Reviews Genetics, Vol. 20, Issue 11 https://doi.org/10.1038/s41576-019-0150-2	journal	July 2019
Complete biosynthesis of cannabinoids and their unnatural analogues in yeast Luo, Xiaozhou; Reiter, Michael A.; d’Espaux, Leo Nature, Vol. 567, Issue 7746 https://doi.org/10.1038/s41586-019-0978-9	journal	February 2019
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing Gordon, David E.; Jang, Gwendolyn M.; Bouhaddou, Mehdi Nature, Vol. 583, Issue 7816 https://doi.org/10.1038/s41586-020-2286-9	journal	April 2020
ChAdOx1 nCoV-19 vaccine prevents SARS-CoV-2 pneumonia in rhesus macaques van Doremalen, Neeltje; Lambe, Teresa; Spencer, Alexandra Nature, Vol. 586, Issue 7830 https://doi.org/10.1038/s41586-020-2608-y	journal	July 2020
Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults Mulligan, Mark J.; Lyke, Kirsten E.; Kitchin, Nicholas Nature, Vol. 586, Issue 7830 https://doi.org/10.1038/s41586-020-2639-4	journal	August 2020
SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information Dührkop, Kai; Fleischauer, Markus; Ludwig, Marcus Nature Methods, Vol. 16, Issue 4 https://doi.org/10.1038/s41592-019-0344-8	journal	March 2019
DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family Batrakou, Dzmitry G.; Müller, Carolin A.; Wilson, Rosemary H. C. Nature Protocols, Vol. 15, Issue 3 https://doi.org/10.1038/s41596-019-0287-7	journal	February 2020
Transcriptome analysis for phosphorus starvation-induced lipid accumulation in Scenedesmus sp Yang, Fangfang; Xiang, Wenzhou; Li, Tao Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-34650-x	journal	November 2018
Untargeted metabolomics by high resolution mass spectrometry coupled to normal and reversed phase liquid chromatography as a tool to study the in vitro biotransformation of new psychoactive substances Manier, Sascha K.; Keller, Andreas; Schäper, Jan Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-39235-w	journal	February 2019
An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals Carbonell, Pablo; Jervis, Adrian J.; Robinson, Christopher J. Communications Biology, Vol. 1, Issue 1 https://doi.org/10.1038/s42003-018-0076-9	journal	June 2018
Proteomics technology in systems biology Smith, Jeffrey C.; Figeys, Daniel Molecular BioSystems, Vol. 2, Issue 8 https://doi.org/10.1039/b606798k	journal	January 2006
Advances in mass spectrometry-based metabolomics for investigation of metabolites Ren, Jun-Ling; Zhang, Ai-Hua; Kong, Ling RSC Advances, Vol. 8, Issue 40 https://doi.org/10.1039/c8ra01574k	journal	January 2018
NMR-based metabolomics and fluxomics: developments and future prospects Giraudeau, Patrick The Analyst, Vol. 145, Issue 7 https://doi.org/10.1039/d0an00142b	journal	January 2020
An mRNA Vaccine against SARS-CoV-2 — Preliminary Report Jackson, Lisa A.; Anderson, Evan J.; Rouphael, Nadine G. New England Journal of Medicine, Vol. 383, Issue 20 https://doi.org/10.1056/nejmoa2022483	journal	November 2020
Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use Kleiner, M.; Wentrup, C.; Lott, C. Proceedings of the National Academy of Sciences, Vol. 109, Issue 19 https://doi.org/10.1073/pnas.1121198109	journal	April 2012
Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities Kleiner, Manuel; Dong, Xiaoli; Hinzke, Tjorven Proceedings of the National Academy of Sciences, Vol. 115, Issue 24 https://doi.org/10.1073/pnas.1722325115	journal	May 2018
Online Peptide Fractionation Using a Multiphasic Microfluidic Liquid Chromatography Chip Improves Reproducibility and Detection Limits for Quantitation in Discovery and Targeted Proteomics* Krisp, Christoph; Yang, Hao; van Soest, Remco Molecular & Cellular Proteomics, Vol. 14, Issue 6 https://doi.org/10.1074/mcp.M114.046425	journal	June 2015
Interpretation of Shotgun Proteomic Data: The Protein Inference Problem Nesvizhskii, Alexey I.; Aebersold, Ruedi Molecular & Cellular Proteomics, Vol. 4, Issue 10 https://doi.org/10.1074/mcp.R500012-MCP200	journal	July 2005
ModifiComb, a New Proteomic Tool for Mapping Substoichiometric Post-translational Modifications, Finding Novel Types of Modifications, and Fingerprinting Complex Protein Mixtures Savitski, Mikhail M.; Nielsen, Michael L.; Zubarev, Roman A. Molecular & Cellular Proteomics, Vol. 5, Issue 5 https://doi.org/10.1074/mcp.T500034-MCP200	journal	January 2006
Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction Doellinger, Joerg; Schneider, Andy; Hoeller, Marcell Molecular & Cellular Proteomics, Vol. 19, Issue 1 https://doi.org/10.1074/mcp.TIR119.001616	journal	January 2020
Metagenomics for taxonomy profiling: tools and approaches Kumar Awasthi, Mukesh; Ravindran, B.; Sarsaiya, Surendra Bioengineered, Vol. 11, Issue 1 https://doi.org/10.1080/21655979.2020.1736238	journal	January 2020
Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar OMICS: A Journal of Integrative Biology, Vol. 17, Issue 11 https://doi.org/10.1089/omi.2013.0025	journal	November 2013
Analysis of matched mRNA measurements from two different microarray technologies Kuo, W. P.; Jenssen, T. -K.; Butte, A. J. Bioinformatics, Vol. 18, Issue 3 https://doi.org/10.1093/bioinformatics/18.3.405	journal	March 2002
TANDEM: matching proteins with tandem mass spectra Craig, R.; Beavis, R. C. Bioinformatics, Vol. 20, Issue 9 https://doi.org/10.1093/bioinformatics/bth092	journal	February 2004
CRONOS: the cross-reference navigation server Waegele, Brigitte; Dunger-Kaltenbach, Irmtraud; Fobo, Gisela Bioinformatics, Vol. 25, Issue 1 https://doi.org/10.1093/bioinformatics/btn590	journal	November 2008
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments MacLean, Brendan; Tomazela, Daniela M.; Shulman, Nicholas Bioinformatics, Vol. 26, Issue 7 https://doi.org/10.1093/bioinformatics/btq054	journal	February 2010
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model Yizhak, K.; Benyamini, T.; Liebermeister, W. Bioinformatics, Vol. 26, Issue 12 https://doi.org/10.1093/bioinformatics/btq183	journal	June 2010
UniNovo: a universal tool for de novo peptide sequencing Jeong, Kyowon; Kim, Sangtae; Pevzner, Pavel A. Bioinformatics, Vol. 29, Issue 16 https://doi.org/10.1093/bioinformatics/btt338	journal	June 2013
Outreach and online training services at the Saccharomyces Genome Database MacPherson, Kevin A.; Starr, Barry; Wong, Edith D. Database, Vol. 2017 https://doi.org/10.1093/database/bax002	journal	January 2017
Nuclear Magnetic Resonance Spectroscopy and Imaging in Animal Research Chatham, J. C.; Blackband, S. J. ILAR Journal, Vol. 42, Issue 3 https://doi.org/10.1093/ilar.42.3.189	journal	January 2001
Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples Smith, A. M.; Heisler, L. E.; St. Onge, R. P. Nucleic Acids Research, Vol. 38, Issue 13 https://doi.org/10.1093/nar/gkq368	journal	May 2010
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata Pagani, I.; Liolios, K.; Jansson, J. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1100	journal	December 2011
GenBank Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1195	journal	November 2012
SIGNOR: a database of causal relationships between biological entities Perfetto, Livia; Briganti, Leonardo; Calderone, Alberto Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1048	journal	October 2015
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli Sajed, Tanvir; Marcu, Ana; Ramirez, Miguel Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1060	journal	October 2015
YMDB 2.0: a significantly expanded version of the yeast metabolome database Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1058	journal	November 2016
KEGG: new perspectives on genomes, pathways, diseases and drugs Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1092	journal	November 2016
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Szklarczyk, Damian; Gable, Annika L.; Lyon, David Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1131	journal	November 2018
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis Chong, Jasmine; Soufan, Othman; Li, Carin Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky310	journal	May 2018
Bacillus pumilus LZP02 Promotes Rice Root Growth by Improving Carbohydrate Metabolism and Phenylpropanoid Biosynthesis Liu, Hong; Wang, Zhigang; Xu, Weihui Molecular Plant-Microbe Interactions®, Vol. 33, Issue 10 https://doi.org/10.1094/MPMI-04-20-0106-R	journal	October 2020
Quantitative phenotyping via deep barcode sequencing Smith, A. M.; Heisler, L. E.; Mellor, J. Genome Research, Vol. 19, Issue 10 https://doi.org/10.1101/gr.093955.109	journal	July 2009
Nanopore sequencing: Review of potential applications in functional genomics Kono, Nobuaki; Arakawa, Kazuharu Development, Growth & Differentiation, Vol. 61, Issue 5 https://doi.org/10.1111/dgd.12608	journal	April 2019
The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms Wilmes, Paul; Bond, Philip L. Environmental Microbiology, Vol. 6, Issue 9 https://doi.org/10.1111/j.1462-2920.2004.00687.x	journal	September 2004
Genome-scale models of bacterial metabolism: reconstruction and applications Durot, Maxime; Bourguignon, Pierre-Yves; Schachter, Vincent FEMS Microbiology Reviews, Vol. 33, Issue 1 https://doi.org/10.1111/j.1574-6976.2008.00146.x	journal	January 2009
Industrial biomanufacturing: The future of chemical production Clomburg, James M.; Crumbley, Anna M.; Gonzalez, Ramon Science, Vol. 355, Issue 6320 https://doi.org/10.1126/science.aag0804	journal	January 2017
An Integrated Clinico-Metabolomic Model Improves Prediction of Death in Sepsis Langley, R. J.; Tsalik, E. L.; Velkinburgh, J. C. v. Science Translational Medicine, Vol. 5, Issue 195 https://doi.org/10.1126/scitranslmed.3005893	journal	July 2013
Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution Van den Bergh, Bram; Swings, Toon; Fauvart, Maarten Microbiology and Molecular Biology Reviews, Vol. 82, Issue 3 https://doi.org/10.1128/MMBR.00008-18	journal	July 2018
Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton Bryson, Samuel; Li, Zhou; Pett-Ridge, Jennifer mSystems, Vol. 1, Issue 2 https://doi.org/10.1128/msystems.00027-15	journal	April 2016
Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities Kleiner, Manuel mSystems, Vol. 4, Issue 3 https://doi.org/10.1128/msystems.00115-19	journal	May 2019
Integrative clinical, genomics and metabolomics data analysis for mainstream precision medicine to investigate COVID-19 Ahmed, Zeeshan; Zeeshan, Saman; Foran, David J. BMJ Innovations, Vol. 7, Issue 1 https://doi.org/10.1136/bmjinnov-2020-000444	journal	September 2020
Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology Cox, Jürgen; Mann, Matthias Annual Review of Biochemistry, Vol. 80, Issue 1 https://doi.org/10.1146/annurev-biochem-061308-093216	journal	July 2011
Biomanufacturing of Therapeutic Cells: State of the Art, Current Challenges, and Future Perspectives Roh, Kyung-Ho; Nerem, Robert M.; Roy, Krishnendu Annual Review of Chemical and Biomolecular Engineering, Vol. 7, Issue 1 https://doi.org/10.1146/annurev-chembioeng-080615-033559	journal	June 2016
Use of Natural Selection and Evolution to Develop New Starter Cultures for Fermented Foods Johansen, Eric Annual Review of Food Science and Technology, Vol. 9, Issue 1 https://doi.org/10.1146/annurev-food-030117-012450	journal	March 2018
Adaptive Laboratory Evolution of Ale and Lager Yeasts for Improved Brewing Efficiency and Beer Quality Gibson, B.; Dahabieh, M.; Krogerus, K. Annual Review of Food Science and Technology, Vol. 11, Issue 1 https://doi.org/10.1146/annurev-food-032519-051715	journal	March 2020
Metabolomics for Functional Genomics, Systems Biology, and Biotechnology Saito, Kazuki; Matsuda, Fumio Annual Review of Plant Biology, Vol. 61, Issue 1 https://doi.org/10.1146/annurev.arplant.043008.092035	journal	June 2010
Bridging the Gap between Fluxomics and Industrial Biotechnology Feng, Xueyang; Page, Lawrence; Rubens, Jacob Journal of Biomedicine and Biotechnology, Vol. 2010 https://doi.org/10.1155/2010/460717	journal	January 2010
Integrative “Omic” Analysis of Experimental Bacteremia Identifies a Metabolic Signature That Distinguishes Human Sepsis from Systemic Inflammatory Response Syndromes Langley, Raymond J.; Tipper, Jennifer L.; Bruse, Shannon American Journal of Respiratory and Critical Care Medicine, Vol. 190, Issue 4 https://doi.org/10.1164/rccm.201404-0624OC	journal	August 2014
Metabolomics to Predict Antiviral Drug Efficacy in COVID-19 Migaud, Marie; Gandotra, Sheetal; Chand, Hitendra S. American Journal of Respiratory Cell and Molecular Biology, Vol. 63, Issue 3 https://doi.org/10.1165/rcmb.2020-0206LE	journal	September 2020
Multi-omics Data Integration, Interpretation, and Its Application Subramanian, Indhupriya; Verma, Srikant; Kumar, Shiva Bioinformatics and Biology Insights, Vol. 14 https://doi.org/10.1177/1177932219899051	journal	January 2020
Evaluation and validation of an analytical approach for high-throughput metabolomic fingerprinting using direct introduction–high-resolution mass spectrometry: Applicability to classification of urine of scrapie-infected ewes Rathahao-Paris, Estelle; Alves, Sandra; Boussaid, Nawel European Journal of Mass Spectrometry, Vol. 25, Issue 2 https://doi.org/10.1177/1469066718806450	journal	October 2018
Adaptive laboratory evolution – principles and applications for biotechnology Dragosits, Martin; Mattanovich, Diethard Microbial Cell Factories, Vol. 12, Issue 1 https://doi.org/10.1186/1475-2859-12-64	journal	January 2013
SECIMTools: a suite of metabolomics data analysis tools Kirpich, Alexander S.; Ibarra, Miguel; Moskalenko, Oleksandr BMC Bioinformatics, Vol. 19, Issue 1 https://doi.org/10.1186/s12859-018-2134-1	journal	April 2018
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity Phaneuf, Patrick V.; Yurkovich, James T.; Heckmann, David BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-06920-4	journal	July 2020
Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis Volke, Daniel Christoph; Rohwer, Johann; Fischer, Rainer Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1235-5	journal	November 2019
Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation Wehrs, Maren; Thompson, Mitchell G.; Banerjee, Deepanwita Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01423-z	journal	August 2020
Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides Geiselman, Gina M.; Zhuang, Xun; Kirby, James Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-1293-8	journal	February 2020
Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation Sun, Xiao-Man; Ren, Lu-Jing; Zhao, Quan-Yu Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1275-9	journal	October 2018
Improvement of sabinene tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies Wu, Tong; Liu, Jinfeng; Li, Meijie Biotechnology for Biofuels, Vol. 13, Issue 1 https://doi.org/10.1186/s13068-020-01715-x	journal	April 2020
Liquid chromatography mass spectrometry-based proteomics: Biological and technological aspects Karpievitch, Yuliya V.; Polpitiya, Ashoka D.; Anderson, Gordon A. The Annals of Applied Statistics, Vol. 4, Issue 4 https://doi.org/10.1214/10-AOAS341	journal	December 2010
Recent technical advances in proteomics Yates, III, John R. F1000Research, Vol. 8 https://doi.org/10.12688/f1000research.16987.1	journal	January 2019
Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data Guo, Yan; Sheng, Quanhu; Li, Jiang PLoS ONE, Vol. 8, Issue 8 https://doi.org/10.1371/journal.pone.0071462	journal	August 2013
Insights gained into respiratory infection pathogenesis using lung tissue metabolomics Bernatchez, Jean A.; McCall, Laura-Isobel PLOS Pathogens, Vol. 16, Issue 7 https://doi.org/10.1371/journal.ppat.1008662	journal	July 2020
Design and Analysis of Bar-seq Experiments Robinson, David G.; Chen, Wei; Storey, John D. G3: Genes\|Genomes\|Genetics, Vol. 4, Issue 1 https://doi.org/10.1534/g3.113.008565	journal	November 2013
Biotechnological, genomics and systems–synthetic biology revolution: redesigning genetic code for a pragmatic systems medicine Roukos, Dimitrios H. Expert Review of Medical Devices, Vol. 9, Issue 2 https://doi.org/10.1586/erd.11.68	journal	March 2012
Principles and Applications of Soil Microbiology, Second Edition Cupples, Alison M. Journal of Environmental Quality, Vol. 34, Issue 2 https://doi.org/10.2134/JEQ2005.0731DUP	journal	March 2005
Lignocellulosic Biomass: A Sustainable Bioenergy Source for the Future Fatma, Shabih; Hameed, Amir; Noman, Muhammad Protein & Peptide Letters, Vol. 25, Issue 2 https://doi.org/10.2174/0929866525666180122144504	journal	May 2018
Microbial Metabolomics Tang, Jane Current Genomics, Vol. 12, Issue 6 https://doi.org/10.2174/138920211797248619	journal	September 2011
Toward Reproducible Results from Targeted Metabolomic Studies: Perspectives for Data Pre-processing and a Basis for Analytic Pipeline Development Gross, Thomas; Mapstone, Mark; Miramontes, Ricardo Current Topics in Medicinal Chemistry, Vol. 18, Issue 11 https://doi.org/10.2174/1568026618666180711144323	journal	August 2018
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data Roumpeka, Despoina D.; Wallace, R. John; Escalettes, Frank Frontiers in Genetics, Vol. 8 https://doi.org/10.3389/fgene.2017.00023	journal	March 2017
Genome to Phenome: Improving Animal Health, Production, and Well-Being – A New USDA Blueprint for Animal Genome Research 2018–2027 Rexroad, Caird; Vallet, Jeffrey; Matukumalli, Lakshmi Kumar Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00327	journal	May 2019
Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse Gardinassi, Luiz G.; Souza, Camila O. S.; Sales-Campos, Helioswilton Frontiers in Immunology, Vol. 11 https://doi.org/10.3389/fimmu.2020.01636	journal	June 2020
More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics Hinzke, Tjorven; Kouris, Angela; Hughes, Rebecca-Ayme Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00238	journal	February 2019
Evaluation of Sample Preparation Methods for Fast Proteotyping of Microorganisms by Tandem Mass Spectrometry Hayoun, Karim; Gouveia, Duarte; Grenga, Lucia Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01985	journal	September 2019
Next-Generation Sequencing: From Understanding Biology to Personalized Medicine Frese, Karen; Katus, Hugo; Meder, Benjamin Biology, Vol. 2, Issue 1 https://doi.org/10.3390/biology2010378	journal	March 2013
Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics Duong, Van-An; Park, Jong-Moon; Lee, Hookeun International Journal of Molecular Sciences, Vol. 21, Issue 4 https://doi.org/10.3390/ijms21041524	journal	February 2020
Metabolomics Benefits from Orbitrap GC–MS—Comparison of Low- and High-Resolution GC–MS Stettin, Daniel; Poulin, Remington X.; Pohnert, Georg Metabolites, Vol. 10, Issue 4 https://doi.org/10.3390/metabo10040143	journal	April 2020
Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community Pinu, Farhana R.; Beale, David J.; Paten, Amy M. Metabolites, Vol. 9, Issue 4 https://doi.org/10.3390/metabo9040076	journal	April 2019
WebSpecmine: A Website for Metabolomics Data Analysis and Mining Cardoso, Sara; Afonso, Telma; Maraschin, Marcelo Metabolites, Vol. 9, Issue 10 https://doi.org/10.3390/metabo9100237	journal	October 2019
Post-translational modifications and their applications in eye research Chen, Bing-Jie; Lam, Thomas Chuen; Liu, Long-Qian Molecular Medicine Reports, Vol. 15, Issue 6 https://doi.org/10.3892/mmr.2017.6529	journal	April 2017
Current Status and Applications of Adaptive Laboratory Evolution in Industrial Microorganisms Lee, SuRin; Kim, Pil Journal of Microbiology and Biotechnology, Vol. 30, Issue 6 https://doi.org/10.4014/jmb.2003.03072	journal	June 2020
Use of Metatranscriptomics in Microbiome Research Bashiardes, Stavros; Zilberman-Schapira, Gili; Elinav, Eran Bioinformatics and Biology Insights, Vol. 10 https://doi.org/10.4137/BBI.S34610	journal	January 2016
Nano-LC in proteomics: recent advances and approaches Wilson, Steven Ray; Vehus, Tore; Berg, Henriette Sjaanes Bioanalysis, Vol. 7, Issue 14 https://doi.org/10.4155/bio.15.92	journal	August 2015
SWPepNovo: An Efficient De Novo Peptide Sequencing Tool for Large-scale MS/MS Spectra Analysis Li, Chuang; Li, Kenli; Li, Keqin International Journal of Biological Sciences, Vol. 15, Issue 9 https://doi.org/10.7150/ijbs.32142	journal	January 2019

Similar Records

Biotransformation of Pesticides across Biological Systems: Molecular Mechanisms, Omics Insights, and Biotechnological Advances for Environmental Sustainability

Journal Article · Thu Oct 23 20:00:00 EDT 2025 · ACS Omega · OSTI ID:3001259

Chapter 3: Omics Advances of Biosynthetic Pathways of Isoprenoid Production in Microalgae

Book · Sat Dec 31 23:00:00 EST 2016 · OSTI ID:1340647

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

Journal Article · Fri Jan 20 19:00:00 EST 2023 · Materials Today Bio · OSTI ID:1958544

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
biotechnology
genomics
metabolic engineering
metabolomics
multi-omics
proteomics
systems biology
transcriptomics

Omics-Driven Biotechnology for Industrial Applications

Citation Formats

References (177)

Similar Records

Related Subjects