| Year |
Citation |
Score |
| 2023 |
Chowdhury NB, Simons-Senftle M, Decouard B, Quillere I, Rigault M, Sajeevan KA, Acharya B, Chowdhury R, Hirel B, Dellagi A, Maranas C, Saha R. A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation. Iscience. 26: 108400. PMID 38077131 DOI: 10.1016/j.isci.2023.108400 |
0.61 |
|
| 2022 |
Boorla VS, Chowdhury R, Ramasubramanian R, Ameglio B, Frick R, Gray JJ, Maranas CD. De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD). Proteins. PMID 36111441 DOI: 10.1002/prot.26422 |
0.753 |
|
| 2022 |
Chen C, Boorla VS, Chowdhury R, Nissly RH, Gontu A, Chothe SK, LaBella L, Jakka P, Ramasamy S, Vandegrift KJ, Nair MS, Kuchipudi SV, Maranas CD. A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues. Biorxiv : the Preprint Server For Biology. PMID 35350198 DOI: 10.1101/2022.03.22.485413 |
0.739 |
|
| 2021 |
Chen C, Boorla VS, Banerjee D, Chowdhury R, Cavener VS, Nissly RH, Gontu A, Boyle NR, Vandegrift K, Nair MS, Kuchipudi SV, Maranas CD. Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34588290 DOI: 10.1073/pnas.2106480118 |
0.741 |
|
| 2021 |
Chowdhury NB, Schroeder WL, Sarkar D, Amiour N, Quilleré I, Hirel B, Maranas CD, Saha R. Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen-Deficient Stress Condition. Journal of Experimental Botany. PMID 34554248 DOI: 10.1093/jxb/erab435 |
0.631 |
|
| 2021 |
Patiño-Galindo JÁ, Filip I, Chowdhury R, Maranas CD, Sorger PK, AlQuraishi M, Rabadan R. Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2. Genome Medicine. 13: 124. PMID 34362430 DOI: 10.1186/s13073-021-00943-6 |
0.752 |
|
| 2020 |
Wang Z, Doshi A, Chowdhury R, Wang Y, Maranas CD, Cirino PC. Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid. Protein Engineering, Design & Selection : Peds. 33. PMID 33215672 DOI: 10.1093/protein/gzaa027 |
0.735 |
|
| 2020 |
Chowdhury R, Boorla VS, Maranas CD. Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity. Computational and Structural Biotechnology Journal. 18: 2573-2582. PMID 32983400 DOI: 10.1016/j.csbj.2020.09.019 |
0.732 |
|
| 2020 |
Chowdhury R, Grisewood MJ, Boorla VS, Yan Q, Pfleger BF, Maranas CD. IPRO+/-: Computational Protein Design Tool Allowing for Insertions and Deletions. Structure (London, England : 1993). PMID 32857964 DOI: 10.1016/J.Str.2020.08.003 |
0.746 |
|
| 2020 |
Gopalakrishnan S, Dash S, Maranas C. K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data. Metabolic Engineering. PMID 32173504 DOI: 10.1016/J.Ymben.2020.03.001 |
0.361 |
|
| 2020 |
Song W, Joshi H, Chowdhury R, Najem JS, Shen YX, Lang C, Henderson CB, Tu YM, Farell M, Pitz ME, Maranas CD, Cremer PS, Hickey RJ, Sarles SA, Hou JL, et al. Author Correction: Artificial water channels enable fast and selective water permeation through water-wire networks. Nature Nanotechnology. PMID 31980744 DOI: 10.1038/S41565-020-0640-6 |
0.692 |
|
| 2019 |
Song W, Joshi H, Chowdhury R, Najem JS, Shen YX, Lang C, Henderson CB, Tu YM, Farell M, Pitz ME, Maranas CD, Cremer PS, Hickey RJ, Sarles SA, Hou JL, et al. Artificial water channels enable fast and selective water permeation through water-wire networks. Nature Nanotechnology. PMID 31844288 DOI: 10.1038/S41565-019-0586-8 |
0.7 |
|
| 2019 |
Samineni L, Xiong B, Chowdhury R, Pei A, Kuehster L, Wang H, Dickey R, Soto PE, Massenburg L, Nguyen TH, Maranas C, Velegol D, Kumar M, Velegol SB. 7-log virus removal in a simple functionalized sand filter. Environmental Science & Technology. PMID 31593449 DOI: 10.1021/Acs.Est.9B03734 |
0.722 |
|
| 2018 |
Chowdhury R, Allan MF, Maranas CD. OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes. Antibodies (Basel, Switzerland). 7. PMID 31544875 DOI: 10.3390/antib7030023 |
0.736 |
|
| 2018 |
Chowdhury R, Ren T, Shankla M, Decker K, Grisewood M, Prabhakar J, Baker C, Golbeck JH, Aksimentiev A, Kumar M, Maranas CD. PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore. Nature Communications. 9: 3661. PMID 30202038 DOI: 10.1038/S41467-018-06097-1 |
0.71 |
|
| 2018 |
Hernandez-Lozada NJ, Lai RY, Simmons T, Thomas KA, Chowdhury R, Maranas CD, Pfleger BF. Highly active C8-acyl-ACP thioesterase variant isolated by a synthetic selection strategy. Acs Synthetic Biology. PMID 30064208 DOI: 10.1021/Acssynbio.8B00215 |
0.732 |
|
| 2017 |
Tiller KE, Chowdhury R, Li T, Ludwig SD, Sen S, Maranas CD, Tessier PM. Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis. Frontiers in Immunology. 8: 986. PMID 28928732 DOI: 10.3389/Fimmu.2017.00986 |
0.733 |
|
| 2017 |
Entzminger KC, Hyun JM, Pantazes RJ, Patterson-Orazem AC, Qerqez AN, Frye ZP, Hughes RA, Ellington AD, Lieberman RL, Maranas CD, Maynard JA. De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide. Scientific Reports. 7: 10295. PMID 28860479 DOI: 10.1038/S41598-017-10737-9 |
0.761 |
|
| 2016 |
Saha R, Liu D, Hoynes-O'Connor A, Liberton M, Yu J, Bhattacharyya-Pakrasi M, Balassy A, Zhang F, Moon TS, Maranas CD, Pakrasi HB. Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses. Mbio. 7. PMID 27143387 DOI: 10.1128/Mbio.00464-16 |
0.611 |
|
| 2015 |
Berla BM, Saha R, Maranas CD, Pakrasi HB. Cyanobacterial Alkanes Modulate Photosynthetic Cyclic Electron Flow to Assist Growth under Cold Stress. Scientific Reports. 5: 14894. PMID 26459862 DOI: 10.1038/Srep14894 |
0.604 |
|
| 2015 |
Chowdhury R, Chowdhury A, Maranas CD. Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models. Metabolites. 5: 536-70. PMID 26426067 DOI: 10.3390/metabo5040536 |
0.735 |
|
| 2015 |
Pantazes RJ, Grisewood MJ, Li T, Gifford NP, Maranas CD. The Iterative Protein Redesign and Optimization (IPRO) suite of programs. Journal of Computational Chemistry. 36: 251-63. PMID 25448866 DOI: 10.1002/jcc.23796 |
0.768 |
|
| 2015 |
Chowdhury A, Zomorrodi AR, Maranas CD. Bilevel optimization techniques in computational strain design Computers and Chemical Engineering. 72: 363-372. DOI: 10.1016/J.Compchemeng.2014.06.007 |
0.718 |
|
| 2014 |
Simons M, Saha R, Amiour N, Kumar A, Guillard L, Clément G, Miquel M, Li Z, Mouille G, Lea PJ, Hirel B, Maranas CD. Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. Plant Physiology. 166: 1659-74. PMID 25248718 DOI: 10.1104/Pp.114.245787 |
0.65 |
|
| 2014 |
Li T, Pantazes RJ, Maranas CD. OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes. Plos One. 9: e105954. PMID 25153121 DOI: 10.1371/journal.pone.0105954 |
0.763 |
|
| 2014 |
Khodayari A, Zomorrodi AR, Liao JC, Maranas CD. A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data. Metabolic Engineering. 25: 50-62. PMID 24928774 DOI: 10.1016/J.Ymben.2014.05.014 |
0.736 |
|
| 2014 |
Simons M, Saha R, Guillard L, Clément G, Armengaud P, Cañas R, Maranas CD, Lea PJ, Hirel B. Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling Journal of Experimental Botany. 65: 5657-5671. PMID 24863438 DOI: 10.1093/Jxb/Eru227 |
0.649 |
|
| 2014 |
Zomorrodi AR, Islam MM, Maranas CD. d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. Acs Synthetic Biology. 3: 247-57. PMID 24742179 DOI: 10.1021/Sb4001307 |
0.708 |
|
| 2014 |
Saha R, Chowdhury A, Maranas CD. Recent advances in the reconstruction of metabolic models and integration of omics data. Current Opinion in Biotechnology. 29: 39-45. PMID 24632194 DOI: 10.1016/J.Copbio.2014.02.011 |
0.634 |
|
| 2014 |
Chowdhury A, Zomorrodi AR, Maranas CD. k-OptForce: integrating kinetics with flux balance analysis for strain design. Plos Computational Biology. 10: e1003487. PMID 24586136 DOI: 10.1371/Journal.Pcbi.1003487 |
0.717 |
|
| 2014 |
Zomorrodi AR, Maranas CD. Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits European Journal of Operational Research. 237: 665-676. DOI: 10.1016/J.Ejor.2014.01.054 |
0.719 |
|
| 2013 |
Grisewood MJ, Gifford NP, Pantazes RJ, Li Y, Cirino PC, Janik MJ, Maranas CD. OptZyme: computational enzyme redesign using transition state analogues. Plos One. 8: e75358. PMID 24116038 DOI: 10.1371/Journal.Pone.0075358 |
0.731 |
|
| 2013 |
Berla BM, Saha R, Immethun CM, Maranas CD, Moon TS, Pakrasi HB. Synthetic biology of cyanobacteria: unique challenges and opportunities. Frontiers in Microbiology. 4: 246. PMID 24009604 DOI: 10.3389/Fmicb.2013.00246 |
0.64 |
|
| 2013 |
Pantazes RJ, Maranas CD. MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. Bmc Bioinformatics. 14: 168. PMID 23718826 DOI: 10.1186/1471-2105-14-168 |
0.758 |
|
| 2013 |
Zomorrodi AR, Lafontaine Rivera JG, Liao JC, Maranas CD. Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks. Biotechnology Journal. 8: 1090-104. PMID 23450699 DOI: 10.1002/Biot.201200270 |
0.747 |
|
| 2012 |
Saha R, Verseput AT, Berla BM, Mueller TJ, Pakrasi HB, Maranas CD. Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. Plos One. 7: e48285. PMID 23133581 DOI: 10.1371/Journal.Pone.0048285 |
0.647 |
|
| 2012 |
Ranganathan S, Tee TW, Chowdhury A, Zomorrodi AR, Yoon JM, Fu Y, Shanks JV, Maranas CD. An integrated computational and experimental study for overproducing fatty acids in Escherichia coli. Metabolic Engineering. 14: 687-704. PMID 23036703 DOI: 10.1016/J.Ymben.2012.08.008 |
0.72 |
|
| 2012 |
Zomorrodi AR, Suthers PF, Ranganathan S, Maranas CD. Mathematical optimization applications in metabolic networks. Metabolic Engineering. 14: 672-86. PMID 23026121 DOI: 10.1016/J.Ymben.2012.09.005 |
0.737 |
|
| 2012 |
Zomorrodi AR, Maranas CD. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. Plos Computational Biology. 8: e1002363. PMID 22319433 DOI: 10.1371/Journal.Pcbi.1002363 |
0.719 |
|
| 2011 |
Saha R, Suthers PF, Maranas CD. Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. Plos One. 6: e21784. PMID 21755001 DOI: 10.1371/Journal.Pone.0021784 |
0.648 |
|
| 2011 |
Pantazes RJ, Grisewood MJ, Maranas CD. Recent advances in computational protein design. Current Opinion in Structural Biology. 21: 467-72. PMID 21600758 DOI: 10.1016/j.sbi.2011.04.005 |
0.763 |
|
| 2010 |
Zomorrodi AR, Maranas CD. Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. Bmc Systems Biology. 4: 178. PMID 21190580 DOI: 10.1186/1752-0509-4-178 |
0.733 |
|
| 2010 |
Pantazes RJ, Maranas CD. OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding. Protein Engineering, Design & Selection : Peds. 23: 849-58. PMID 20847101 DOI: 10.1093/protein/gzq061 |
0.768 |
|
| 2009 |
Khoury GA, Fazelinia H, Chin JW, Pantazes RJ, Cirino PC, Maranas CD. Computational design of Candida boidinii xylose reductase for altered cofactor specificity. Protein Science : a Publication of the Protein Society. 18: 2125-38. PMID 19693930 DOI: 10.1002/Pro.227 |
0.771 |
|
| 2009 |
Suthers PF, Zomorrodi A, Maranas CD. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Molecular Systems Biology. 5: 301. PMID 19690570 DOI: 10.1038/msb.2009.56 |
0.723 |
|
| 2009 |
Suthers PF, Kumar VS, Zomorrodi A, Ranganathan S, Maranas CD. Using systems engineering to reconstruct, analyze And redesign metabolism Computer Aided Chemical Engineering. 27: 113-115. DOI: 10.1016/S1570-7946(09)70239-1 |
0.701 |
|
| 2007 |
Pantazes RJ, Saraf MC, Maranas CD. Optimal protein library design using recombination or point mutations based on sequence-based scoring functions. Protein Engineering, Design & Selection : Peds. 20: 361-73. PMID 17686879 DOI: 10.1093/protein/gzm030 |
0.756 |
|
| 1999 |
Camarda KV, Bonnell BW, Maranas CD, Nagarajan R. Design of surfactant solutions with optimal macroscopic properties Computers and Chemical Engineering. 23. DOI: 10.1016/S0098-1354(99)80115-X |
0.657 |
|
| 1999 |
Camarda KV, Maranas CD. Optimization in polymer design using connectivity indices Industrial and Engineering Chemistry Research. 38: 1884-1892. |
0.666 |
|
| 1997 |
Androulakis I, Maranas C, Floudas C. Journal of Global Optimization. 11: 1-34. DOI: 10.1023/A:1008224308626 |
0.604 |
|
| 1997 |
Harding ST, Maranas CD, McDonald CM, Floudas CA. Locating All Homogeneous Azeotropes in Multicomponent Mixtures Industrial & Engineering Chemistry Research. 36: 160-178. DOI: 10.1021/Ie960305F |
0.414 |
|
| 1997 |
Maranas C, Androulakis I, Floudas C, Berger A, Mulvey J. Solving long-term financial planning problems via global optimization Journal of Economic Dynamics and Control. 21: 1405-1425. DOI: 10.1016/S0165-1889(97)00032-8 |
0.588 |
|
| 1997 |
Maranas CD, Floudas CA. Global optimization in generalized geometric programming Computers & Chemical Engineering. 21: 351-369. DOI: 10.1016/S0098-1354(96)00282-7 |
0.429 |
|
| 1996 |
Adjiman C, Androulakis I, Maranas C, Floudas C. A global optimization method, αBB, for process design Computers & Chemical Engineering. 20: S419-S424. DOI: 10.1016/0098-1354(96)00080-4 |
0.705 |
|
| 1996 |
Maranas C, McDonald C, Harding S, Floudas C. Locating all azeotropes in homogeneous azeotropic systems Computers & Chemical Engineering. 20: S413-S418. DOI: 10.1016/0098-1354(96)00079-8 |
0.449 |
|
| 1995 |
Maranas CD, Floudas CA, Pardalos PM. New results in the packing of equal circles in a square Discrete Mathematics. 142: 287-293. DOI: 10.1016/0012-365X(93)E0230-2 |
0.372 |
|
| 1995 |
Androulakis IP, Maranas CD, Floudas CA. ?BB: A global optimization method for general constrained nonconvex problems Journal of Global Optimization. 7: 337-363. DOI: 10.1007/Bf01099647 |
0.599 |
|
| 1995 |
Maranas CD, Floudas CA. Finding all solutions of nonlinearly constrained systems of equations Journal of Global Optimization. 7: 143-182. DOI: 10.1007/Bf01097059 |
0.43 |
|
| 1994 |
Maranas CD, Floudas CA. A deterministic global optimization approach for molecular structure determination The Journal of Chemical Physics. 100: 1247-1261. DOI: 10.1063/1.467236 |
0.446 |
|
| 1994 |
Maranas CD, Floudas CA. Global minimum potential energy conformations of small molecules Journal of Global Optimization. 4: 135-170. DOI: 10.1007/Bf01096720 |
0.444 |
|
| 1993 |
Maranas CD, Floudas CA. Global optimization for molecular conformation problems Annals of Operations Research. 42: 85-117. DOI: 10.1007/Bf02023173 |
0.458 |
|
| 1992 |
Maranas CD, Floudas CA. A global optimization approach for Lennard‐Jones microclusters The Journal of Chemical Physics. 97: 7667-7678. DOI: 10.1063/1.463486 |
0.46 |
|
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