Publications

  1. Scalzitti N, Miralavy I, Korenchan DE, Farrar CT, Gilad A, Banzhaf W. Computational peptide discovery with a genetic programming approach. J Comput Aided Mol Des 2024;38(17):1-22. PMID: . doi.org/10.1007/s10822-024-00558-0.
  2. Nagar D, Vladimirov N, Farrar CT, Perlman O. Dynamic and rapid deep synthesis of molecular MRI signals. Sci Rep 2023;13(1):18291. PMID: 37880343, doi.org/10.1038/s41598-023-45548-8.
  3. Fillion A, Bricco AR, Lee HD, Korenchan D, Farrar CT, Gilad AA. Development of a synthetic biosensor for chemical exchange MRI utilizing in silico optimized peptides. NMR in Biomed. 2023; e5007. doi.org/10.1002/nbm.5007.
  4. Bricco AR, Miralavy I, Bo S, Perlman O, Korenchan D, Farrar CT, McMahon MT, Banzhaf W, Gilad AA. A genetic programming approach to engineering MRI reporter genes. ACS Synth Biol 2023;12(4):1154-1163. PMID: 36947694, doi.org/10.1021/acssynbio.2c00648.
  5. Kuruppu D, Bhere D, Farrar CT, Shah K, Brownell AL, Mahmood U, Tanabe KK. Oncolytic HSV1 targets different growth phases of breast cancer leptomeningeal metastases. Cancer Gene Therapy. 2023 Feb 1 (online ahead of print). PMID: 3621067, doi.org/10.1038/s41417-023-00588-0.
  6. Weigand-Whittier J, Sedykh M, Herz K, Coll-Font J, Foster AN, Gerstner ER, Nguyen C, Zaiss M, Farrar CT, Perlman O. Accelerated and quantitative three-dimensional molecular MRI using a generative adversarial network. Magn Reson Med 2023;89(5):1901-1914. PMID: 36585915, doi.org/10.1002/mrm.29574
  7. Cohen O, Yu VY, Tringale KR, Young RJ, Perlman O, Farrar CT, Otazo R. CEST MR Fingerprinting (CEST-MRF) for BrainTumor Quantification Using EPI Readout and Deep Learning Reconstruction. Magn Reson Med 2023;89(1):233-249. PMID: 36128888, doi.org/10.1002/mrm.29448.
  8. Yurista SR, Eder RA, Kwon DH, Farrar CT, Yen YF, Tang WHW, Nguyen CT. Magnetic resonance imaging of cardiac metabolism in heart failure: how far have we come? Eur Heart J – Cardiovasc Imaging 2022;23(10):1277-1289.  PMID: 35788836. doi.org/10.1093/ehjci/jeac121.
  9. Ni P, Farinelli WA, Cheng LL, Farrar CT, Motamarry A, Moradi Tuchayi S, Wang Y, Anderson RR, Garibyan L. Total ice content and lipid saturation determine adipose tissue cryolipolysis by injection of ice-slurry. Lasers Surg Med 2022;55(1):116-125. PMID: 35598082. doi:10.1002/lsm.23557. 
  10. Perlman O, Farrar CT, Heo HY.  MR fingerprinting for semisolid magnetization transfer and chemical exchange saturation transfer quantification. NMR Biomed 2022;e4710. doi.org/10.1002/nbm.4710.
  11. Perlman O, Zhu B, Zaiss M, Rosen MS, Farrar CT. An end-to-end AI-based framework for automated discovery of rapid CEST/MT MRI acquisition protocols and molecular parameter quantification (AutoCEST). Magn Reson Med 2022;87(6):2792-2810. PMID: 35092076. doi.org/10.1002/mrm.29173.
  12. Perlman O, Ito H, Herz K, Shono N, Nakashima H, Zaiss M, Chiocca EA, Cohen O, Rosen MS, Farrar CT. Quantitative imaging of tumor apoptosis by magnetic resonance fingerprinting aided by deep learning. Nature Bio Med Eng 2021;6(5):648-657. PMID: 34764440. https://rdcu.be/cBemp.
  13. Khalifa A, Weigand-Whittier J, Farrar CT, Cash S. Tracking the Migration of Injectable Microdevices in the Rodent Brain Using a 9.4T Magnetic Resonance Imaging Scanner. Front Neurosci. 2021;15:738589. PMCID: PMC8524135. DOI: 10.3389/fnins.2021.738589
  14. Herz K, Mueller S, Perlman O, Zaitsev M, Knutsson L, Sun PZ, Zhou J, van Zijl P, Heinecke K, Schuenke P, Farrar CT, Schmidt M, Dorfler A, Scheffler K, Zaiss M. Pulseq-CEST: Towards multi-site multi-vendor compatibility and reproducibility of CEST experiments using an open-source sequence standard. Magn Reson Med 2021. DOI: 10.1002/mrm.28825
  15. Perlman O, Ito H, Gilad AA, McMahon MT, Chiocca EA, Nakashima H, Farrar CT. Redesigned reporter gene for improved proton exchange-based molecular MRI contrast. Sci Rep 2020;10(1):20664. PMCID: PMC7692519
  16. Perlman O, Herz K, Zaiss M, Cohen O, Rosen MS, Farrar CT. CEST MR-Fingerprinting: practical considerations and insights for acquisition schedule design and improved reconstruction. Magn Reson Med 2019;epub:1-17. PMCID: PMC7190069. DOI: 10.1002/mrm.27937
  17. Kuruppu D, Bhere D, Farrar CT, Shah K, Brownell AL, Tanabe KK. A model of breast cancer meningeal metastasis: characterization with in vivo molecular imaging. Cancer Gene Therapy 2019; 26(5-6):145-156. DOI: 10.1038/s41417-018-0060-z
  18. Cohen O, Huang S, McMahon MT, Rosen MS, Farrar CT. Rapid and Quantitative Chemical Exchange Saturation Transfer (CEST) Imaging with Magnetic Resonance Fingerprinting (MRF). 2017:80(6);2449-2463. PMCID: PMC6234098. DOI: 10.1002/mrm.27221
  19. Erstad DJ, Farrar CT, Ghoshal S, Masia R, Ferreira DS, Chen YCI, Choi JK, Wei L, Waghorn PA, Rotile NJ, Tu C, Graham-O’Regan KA, Sojoodi M, Li S, Li Y, Wang G, Corey KE, Or YS, Jiang L, Tanabe KK, Caravan P, Fuchs BC. Molecular magnetic resonance imaging accurately measures the antifibrotic effect of EDP-305, a novel farnesoid X receptor agonist. Hepatology Comm 2018:2(7);821-835. PMCID: PMC6049071
  20. Dos Santos Ferreira D, Jesus de Oliveira Pinto BL, Kumar V, Cardoso VN, Fernandes SO, Souza CM, Cassali GD, Moore A, Sosnovik D, Farrar C, Leite EA, Alves RJ, de Oliveira MC, Guimarães AR, Caravan P. Evaluation of antitumor activity and cardiac toxicity of a bone-targeted ph-sensitive liposomal formulation in a bone metastasis tumor model in mice. Nano medicine 2017;13(5):1693-1701. PMCID: PMC5483199
  21. Wei H, Bruns OT, Kaul M, Barch M, Wisniowska A, Chen O, Cordero JM, Okada S, Heine M, Farrar CT, Chen Y, Montana D, Hansen E, Adam G, Ittrich H, Jasanoff AP, Bawendi MG. Exceedingly-Small Iron Oxide Nanoparticles as Positive MRI Contrast Agents. Proc Natl Acad Sci USA 2017;114(9):2325-2330. PMCID: PMC5338531
  22. Zhu B, Rotile N, Day H, Rietz T, Farrar CT, Lauwers GY, Tanabe KK, Rosen B, Fuchs BC, Caravan P. Combined MR elastography and collagen molecular MR imaging accurately stage liver fibrosis in a rat model. Hepatology 2017;65(3):1015-1025. PMCID: PMC5319882
  23. Gale E, Jones C, Ramsay I, Farrar CT, Caravan P. A Janus Chelator Enables Biochemically Responsive MRI Contrast With Exceptional Dynamic Range. J Am Chem Soc 2016;138(49);15861-15864. PMCID: PMC5328420
  24. Wang P, Ross A, Yoo B, Yang J, Farrar C, Ran C, Pantazopoulos P, Medarova Z, Moore A. Magnetic resonance imaging of intra-pancreatic ductal nanoparticle delivery to islet cells. Diabetes Metab Res Rev 2017;33{5):e2881. DOI: 10.1002/dmrr.2881
  25. Wang P, Yoo B, Sherman S, Mukherjee P, Ross A, Pantazopoulos P, Petkova V, Farrar CT, Medarova Z, Moore A. Predictive imaging of chemotherapeutic response in a transgenic mouse model of pancreatic cancer. Intl J Cancer 2016;139(3): 712-718. PMCID: PMC4925171
  26. Peterson TE, Kirkpatrick ND, Huang Y, Farrar CT, Marijt K, Kamoun WS, Seano G, Datta M, Vardam-Kaur T, Snuderl M, Goveia J, Muzikansky A, Leow CC, Xu L, Batchelor TT, Dudas DG, Fukumura D, Jain RK. Dual inhibition of Ang-2 and VEGF receptors normalizes tumor vasculature and prolongs survival in glioblastoma by altering macrophages. Proc Natl Acad Sci USA 2016;113(16):4470-4475. PMCID: PMC4843449
  27. Chen HH, Chen Y, Farrar CT, Gale EM, Caravan P, Liao R, Chen JW, Sosnovik DE. Molecular MRI of myocardial peroxidase activity in ischemic injury reveals a chemical milieu incompatible with stem cell survival. J Cardiovasc Magn Reson 2016;18(Suppl 1):O16.​
  28. Farrar CT, DePeralta D, Day H, Rietz T, Wei L, Lauwers GY, Keil B, Subramaniam A, Sinskey AJ, Tanabe KK, Fuchs BC, Caravan P. 3D molecular MR imaging of liver fibrosis and response to rapamycin therapy in a bile duct ligation rat model. J Hepatology 2015;63(3):689-696. PMCID: PMC4543390
  29. Farrar CT, Buhrman JS, Liu G, Kleijn A, Lamfers MLM, McMahon MT, Gilad AA, Fulci G. Establishing the lysine-rich protein (LRP) CEST reporter gene as a CEST-MRI detector for oncolytic virotherapy. Radiology 2015;275(3):746-754. PMCID: PMC4450912
  30. Emblem KE, Farrar CT, Gerstner ER, Batchelor TT, Borra RJH, Rosen BR, Sorensen AG, Jain RK. Vessel Caliber MRI – a potential biomarker for cancer imaging in clinical trials. Nature Rev Clin Oncol 2014;11(10):566-584. PMCID: PMC4445139
  31. Chen O, Riedemann L, Etoc F, Herrmann H, Coppey M, Barch M, Farrar CT, Zhao J, Bruns OT, Wei H, Guo P, Cui J, Jensen R, Chen Y, Harris DK, Cordero JM, Wang Z, Jasanoff A, Fukumura D, Reimer R, Dahan M, Jain RK, Bawendi MG. Magnetofluorescent core-shell supernanoparticles. Nature Comm 2014;5:5093(1-8). PMCID: PMC4264679
  32. Farrar CT, Williams CM, Hudry E, Hashimoto T, Hyman B. RNA aptamer probes as optical imaging agents for the detection of amyloid plaques. PLoS ONE 2014;9(2):e89901. PMCID: PMC3935954
  33. Emblem KE, Mouridsen K, Bjornerud A, Farrar CT, Jennings D, Borra RJH, Wen PY, Ivy P, Batchelor TT, Rosen BR, Jain RK, Sorensen AG. Vessel Architectural Imaging reveals cancer patient survival in response to anti-angiogenic therapy. Nature Med 2013 (advanced online publication). PMCID: PMC3769525
  34. Huang S, Kim JK, Atochin D, Farrar CT, Huang PL, Suh JY, Kwon SJ, Shim WH, Cho H, Cho G, Kim YR. Cerebral blood volume affects blood-brain barrier integrity in acute transient stroke model. J Cereb Blood Flow Metab 2013;33(6):898-905. PMCID: PMC3677109
  35. Snuderl M, Batista A, Kirkpatrick ND, de Almodovar CR, Riedemann L, Walsh EC, Anolik R, Huang Y, Martin JD, Kamoun W, Knevels E, Schmidt T, Farrar CT, Vakoc BJ, Mohan N, Chung E, Roberge S, Peterson T, Zhelyazkova BH, Yip S, Hasselblatt M, Rossig C, Niemeyer E, Klagsbrun M, Duda DG, Fukumura D, Xu L, Carmeliet P, Jain RK. Placental growth factor/neuropilin 1 signaling is a therapeutic target in pediatric medulloblastoma. Cell 2013;152:1065-1076. PMCID: PMC3587980
  36. Hingtgen S, Figueiredo JL, Farrar CT, Duebgen M, Martinez-Quintanilla J, Bhere D, Shah K. Real time multi-modality imaging of glioblastoma tumor resection and recurrence. J Neuro-Oncology 2013;111:153-161. PMCID: PMC3548430
  37. Kodack DP, Chung E, Yamashita H, Incio J, Duyverman A, Song Y, Ager E, Farrar CT, Huang Y, Lussiez A, Goel S, Snuderl M, Hiddingh L, Kamoun W, Tannos BA, Fukumura D, Engelman JA, Jain RK. Combined targeting of HER2 and VEGFR2 for effective treatment of HER2-amplified breast cancer brain metastases. Proc Natl Acad Sci USA 2012;109(45):E3119-E3127. PMCID: PMC3494882
  38. Huang S, Farrar CT, Dai G, Kwon SJ, Bogdanov AA, Rosen BR, Kim YR. Dynamic monitoring of blood-brain barrier integrity using Water Exchange Index (WEI) during mannitol and CO2 challenges in mouse brain. NMR Biomed 2012;26(4):376-385. PMCID: PMC4029920
  39. Uppal R, Medarova Z, Farrar CT, Dai G, Moore A, Caravan P. Molecular imaging of fibrin in a breast cancer xenograft mouse model. Invest Radiol 2012;47(10):553-558. PMCID: PMC3653620
  40. Koffie RM, Farrar CT, Saidi LJ, William CM, Hyman BT, Spires-Jones TL. Nanoparticles enhance brain delivery of blood-brain barrier-impermeable probes for in vivo optical and magnetic resonance imaging. Proc Natl Acad Sci USA 2011;108(46):18837-18842. PMCID: PMC3219113
  41. Farrar CT, Kamoun W, Ley CD, Kim YR, Catana C, Kwon SJ, Rosen BR, Jain RK, Sorensen AG. Sensitivity of MRI tumor biomarkers to VEGFR inhibitor therapy in an orthotopic mouse glioma model. PLoS ONE 2011;6(3):e17228. PMCID: PMC3048404
  42. Chae SS, Kamoun WS, Farrar CT, Kirkpatrick ND, Niemeyer E, de Graff AMA, Sorensen AG, Munn LL, Jain RK, Fukumura D. Angiopoietin-2 interferes with anti-VEGFR-2- induced vessel normalization and survival benefit in mice bearing gliomas. Clin Cancer Res 2010; 16(14):3618-3627. PMCID: PMC2905497
  43. Farrar CT, Kamoun W, Ley CD, Kim YR, Kwon SJ, Dai G, Rosen BR, di Tomasso E, Jain RK, Sorensen AG. In vivo validation of MRI vessel caliber index (VCI) measurement methods with intravital optical microscopy in a U87 mouse brain tumor model. Neuro-Oncology 2010; 12(4):341-350. PMCID: PMC2940602
  44. Kamoun WS,* Ley CD,* Farrar CT,* Duyverman AM, Lahdenranta J, Lacorre DA, Batchelor TT, di Tomaso E, Duda DG, Munn LL, Fukumura D, Sorensen AG, Jain RK. Edema control by cediranib, a VEGF targeted kinase inhibitor, prolongs survival despite persistent brain tumor growth in mice. J Clin Oncol 2009; 27:2542-2552.  *These authors contributed equally. PMCID: PMC2739611
  45. Blackwell ML, Farrar CT, Fischl B, Rosen BR. Target-selective contrast agents for magnetic resonance microscopy. NeuroImage 2009; 46:382-393. PMCID: PMC2762731
  46. Caravan P, Farrar CT, Frullano L, Uppal R. Influence of molecular parameters and increasing magnetic field strength on relaxivity of T1 contrast agents. Contrast Media Molec Imag 2009; 4:89-100. PMCID: PMC3995751
  47. Farrar CT, Dai G, Novikov M, Rosenzweig A, Weissleder R, Rosen BR, Sosnovik DE. Impact of field strength and iron-oxide nanoparticle concentration on the linearity and diagnostic accuracy of off-resonance imaging. NMR Biomed 2008; 21:453-463. PMCID: PMC2629945
  48. Medarova Z, Pham W, Farrar CT, Petkova V, Moore A. In vivo imaging of siRNA delivery and silencing in tumors.  Nature Med 2007; 13:372-377. DOI: https://aip.scitation.org/doi/10.1063/1.1346640
  49. Sun PZ, Farrar CT, Sorensen AG. Corrections for artifacts in chemical exchange saturation transfer (CEST) imaging from B0 and B1 field errors. Magn Reson Med 2007; 58:1207-1215. DOI: 10.1002/mrm.21398
  50. Liu CH, Huang S, Cui J, Kim YR, Farrar CT, Moskowitz MA, Rosen BR, Liu PK. MR contrast probes that trace gene transcripts for cerebral ischemia in live animals. FASEB 2007; 21:3004-3015. PMCID: PMC2657320
  51. Fleischman A, Johnsen S, Systrom DM, Hrovat M, Farrar CT, Frontera W, Fitch K, Thomas BJ, Torriani M, Côté HCF, Grinspoon SK. Effects of a nucleoside reverse transcriptase inhibitor, stavudine, on glucose disposal and mitochondrial function in muscle of healthy adults. Am J Physiol  Endocrinol Metab 2007; 292:E1666-E1673. PMCID: PMC3206591
  52. Farrar CT, Wedeen VL, Ackerman JL. The cylindrical meanderline radio frequency coil for intravascular magnetic resonance studies of atherosclerotic plaque. Magn Reson Med 2005; 53:226-230. DOI: 10.1002/mrm.20330
  53. Bajaj VS, Farrar CT, Hornstein MK, Mastovsky I, Vieregg J, Bryant J, Eléna B, Kreischer KE, Temkin RJ, Griffin RG. Dynamic nuclear polarization at 9 Tesla using a novel 250 GHz gyrotron microwave source. J Magn Reson 2003; 160(2):85-90. PMCID: PMC2914497
  54. Farrar CT, Hall DA, Gerfen GJ, Inati SJ, Griffin RG. Mechanism of dynamic nuclear polarization at high magnetic fields. J Chem Phys 2001; 114:4922-4933. DOI: 10.1063/1.1346640
  55. McNulty JC, Silapie JL, Carnevali M, Farrar CT, Griffin RG, Formaggio F, Crisma M, Toniolo C, Millhauser GL. Electron spin resonance of TOAC labeled peptides: Folding transitions and high frequency spectroscopy. Biopolymers (Peptide Science) 2000; 55:479-485.
  56. Farrar CT, Ma J, Singel DJ, Halkides CJ. Structural changes induced in p21Ras upon GAP-334 complexation as probed by ESEEM spectroscopy and molecular dynamics simulation. Structure 2000; 8(12):1279-1287.
  57. Farrar CT, Hall DA, Gerfen GJ, Rosay M, Griffin RG. High frequency dynamic nuclear polarization in the nuclear rotating frame. J Magn Reson 2000; 144:134-141.
  58. Bennati ML, Farrar CT, Bryant JA, Inati SJ, Weis V, Gerfen GJ, Riggs-Gelasco P, Stubbe J, Griffin RG. Pulsed electron nuclear double resonance (ENDOR) at 140 GHz. J Magn Reson 1999; 138:232-243.
  59. Halkides CJ, Farrar CT, Singel DJ. The effects of cryoprotectants on the structure and activity of p21 ras: Implications for electron spin-echo envelope modulation spectroscopy. J Magn Reson 1998; 134:142-153.
  60. Gerfen GJ, van der Donk WA, Yu G, McCarthy JR, Jarvi ET, Matthews DP, Farrar CT, Griffin RG, Stubbe J. Characterization of a substrate derived radical detected during the inactivation of ribonucleotide reductase from Escherichia coli by 2′-fluoromethylene-2′-deoxycytidine 5′-diphosphate. J Am Chem Soc 1998; 120(16):3823-3835.
  61. Farrar CT, Halkides CJ, Singel DJ. The frozen solution structure of p21 ras determined by ESEEM spectroscopy reveals weak coordination of Thr35 to the active site metal ion. Structure 1997; 5(8):1055-1066.
  62. Farrar CT, Gerfen GJ, Griffin RG, Force DA, Britt RD. Electronic structure of the YD tyrosyl radical in photosystem II: A high frequency EPR spectroscopic and density functional theoretical study. J Phys Chem B 1997; 101:6634-6641.
  63. Halkides CJ, Bellew BF, Gerfen GJ, Farrar CT, Carter PH, Ruoll B, Evans DA, Griffin RG, Singel DJ. High frequency (139.5 GHz) electron paramagnetic resonance spectroscopy of the GTP form of p21 ras with selective 17O-labeling of threonine. Biochemistry 1996; 35(37):12194-12200.
  64. Braddock-Wilking J, Leman JT, Farrar CT, Larsen SC, Singel DJ, Barron AR. Radical anion complexes of tris-(1,3-diphenyltriazenido)aluminum. J Am Chem Soc 1995; 117:1736-1745.
  65. Farrar CT, Leman JT, Larsen SC, Braddock-Wilking J, Singel DJ, Barron AR. Electronic structure of the tris-(1,3-diphenyltriazenido)aluminum radical anion: A theoretical and experimental  EPR and ESEEM study. J Am Chem Soc 1995; 117:1746-1753.
  66. Halkides CJ, Farrar CT, Larsen RG, Redfield AG, Singel DJ. Characterization of the active site of p21 ras by electron spin-echo envelope modulation spectroscopy with selective labeling; Comparison between GDP and GTP forms. Biochemistry 1994; 33(13):4019-4035.