A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass
- Soyeon Choi, Pradeep K Prabhakar, Ratul Chowdhury, …, Breeanna R Urbanowicz, Costas Maranas, Katrien M Devos
- J Exp Bot, 10.1093/jxb/erad255
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network
- Vikas Upadhyay, Veda Sheersh Boorla, Costas D Maranas, …, Vikas Upadhyay, Veda Sheersh Boorla, Costas D Maranas
- Metab Eng, 10.1016/j.ymben.2023.06.001
Little Brown Bats ( Myotis lucifugus ) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection
- Shubhada K Chothe, Padmaja Jakka, Veda Sheersh Boorla, …, Meera Surendran Nair, Costas D Maranas, Suresh V Kuchipudi
- Viruses, 10.3390/v15051103
A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis
- Wheaton L Schroeder, Teun Kuil, Antonius J A van Maris, …, Daniel G Olson, Lee R Lynd, Costas D Maranas
- Metab Eng, 10.1016/j.ymben.2023.04.003
Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis , for production of citramalate
- Zong-Yen Wu, Wan Sun, Yihui Shen, …, Costas D Maranas, Zengyi Shao, Yasuo Yoshikuni
- Metab Eng, 10.1016/j.mec.2023.e00220
SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City
- Kurt J Vandegrift, Michele Yon, Meera Surendran Nair, …, Peter J Hudson, Vivek Kapur, Suresh V Kuchipudi
- Viruses, 10.3390/v14122770
Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken
- Abhinay Gontu, Erika A Marlin, Santhamani Ramasamy, …, Costas D Maranas, Meera Surendran Nair, Suresh V Kuchipudi
- Viruses, 10.3390/v14071358
A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues
- Chen Chen, Veda Sheersh Boorla, Ratul Chowdhury, …, Meera Surendran Nair, Suresh V Kuchipudi, Costas D Maranas
- None, 10.1101/2022.03.22.485413
Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity
- Chunliu Zhuo, Xin Wang, Maite Docampo-Palacios, …, Costas D Maranas, Fang Chen, Richard A Dixon
- Sci Adv, 10.1126/sciadv.abm8145
Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media
- J Carl Schultz, Shekhar Mishra, Emily Gaither, …, Hoang Dinh, Costas Maranas, Huimin Zhao
- Microb Cell Fact, 10.1186/s12934-022-01750-3
Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer
- Suresh V Kuchipudi, Meera Surendran-Nair, Rachel M Ruden, …, James M Musser, Peter J Hudson, Vivek Kapur
- Proc Natl Acad Sci U S A, 10.1073/pnas.2121644119
Quantifying the propagation of parametric uncertainty on flux balance analysis
- Hoang V Dinh, Debolina Sarkar, Costas D Maranas
- Metab Eng, 10.1016/j.ymben.2021.10.012
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2
- Juan Ángel Patiño-Galindo, Ioan Filip, Ratul Chowdhury, …, Peter K Sorger, Mohammed AlQuraishi, Raul Rabadan
- Genome Med, 10.1186/s13073-021-00943-6
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling
- Debolina Sarkar, Marine Landa, Anindita Bandyopadhyay, Himadri B Pakrasi, Jonathan P Zehr, Costas D Maranas
- PLoS Comput Biol, 10.1371/journal.pcbi.1008983
Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds
- Lin Wang, Costas D Maranas
- ACS Synth Biol, 10.1021/acssynbio.0c00598
A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers
- John I Hendry, Hoang V Dinh, Debolina Sarkar, …, Anindita Bandyopadhyay, Himadri B Pakrasi, Costas D Maranas
- None, 10.3390/metabo11030168
Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture
- Charles Foster, Kamil Charubin, Eleftherios T Papoutsakis, Costas D Maranas
- mSystems, 10.1128/msystems.01325-20
Building kinetic models for metabolic engineering
- Charles J Foster, Lin Wang, Hoang V Dinh, Patrick F Suthers, Costas D Maranas
- Curr Opin Biotechnol, 10.1016/j.copbio.2020.11.010
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms
- Patrick F Suthers, Charles J Foster, Debolina Sarkar, Lin Wang, Costas D Maranas
- Metab Eng, 10.1016/j.ymben.2020.11.013
Engineering biology approaches for food and nutrient production by cyanobacteria
- Deng Liu, Michelle Liberton, John I Hendry, Javad Aminian-Dehkordi, Costas D Maranas, Himadri B Pakrasi
- Curr Opin Biotechnol, 10.1016/j.copbio.2020.09.011
Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity
- Ratul Chowdhury, Veda Sheersh Boorla, Costas D Maranas
- None, 10.1016/j.csbj.2020.09.019
In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13 C and 2 H Tracers
- Tyler B Jacobson, Travis K Korosh, David M Stevenson, …, Daniel G Olson, Lee R Lynd, Daniel Amador-Noguez
- mSystems, 10.1128/msystems.00736-19
SNPeffect: identifying functional roles of SNPs using metabolic networks
- Debolina Sarkar, Costas D Maranas
- Plant J, 10.1111/tpj.14746
Author Correction: Artificial water channels enable fast and selective water permeation through water-wire networks
- Woochul Song, Himanshu Joshi, Ratul Chowdhury, …, Jun-Li Hou, Aleksei Aksimentiev, Manish Kumar
- Nat Nanotechnol, 10.1038/s41565-020-0640-6
7 Log Virus Removal in a Simple Functionalized Sand Filter
- Laxmicharan Samineni, Boya Xiong, Ratul Chowdhury, …, Darrell Velegol, Manish Kumar, Stephanie Velegol
- Environ Sci Technol, 10.1021/acs.est.9b03734
Metabolic model guided strain design of cyanobacteria
- John I Hendry, Anindita Bandyopadhyay, Shyam Srinivasan, Himadri B Pakrasi, Costas D Maranas
- Curr Opin Biotechnol, 10.1016/j.copbio.2019.08.011
Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code
- Kurt Throckmorton, Vladimir Vinnik, Ratul Chowdhury, …, Costas Maranas, Brian Pfleger, Michael George Thomas
- ACS Chem Biol, 10.1021/acschembio.9b00532
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
- Karsten Zengler, Kirsten Hofmockel, Nitin S Baliga, …, Matthew D Wallenstein, Elizabeth A Shank, Trent R Northen
- Nat Methods, 10.1038/s41592-019-0465-0
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism
- Debolina Sarkar, Thomas J Mueller, Deng Liu, Himadri B Pakrasi, Costas D Maranas
- PLoS Comput Biol, 10.1371/journal.pcbi.1006692