Publications

1. Raval K, Jamshidi N, Seyran B, Salwinski L, Pillai R, Yang L, Ma F, Pellegrini M, Shin J, Yang X, Tudzarova S. Dysfunctional β-cell longevity in diabetes relies on energy conservation and positive epistasis.. Life science alliance, 2024.
2. Wang J, Ashraf Ganjouei A, Romero-Hernandez F, Foroutani L, Bahceci D, Deranteriassian A, Casey M, Li PY, Houshmand S, Behr S, Jamshidi N, Majumdar S, Donahue T, Kim GE, Wang ZJ, Thornblade LW, Adam M, Alseidi A. A Computer Vision Algorithm to Predict Superior Mesenteric Artery Margin Status for Patients with Pancreatic Ductal Adenocarcinoma.. Annals of surgery, 2024.
3. Jamshidi N, Feizi A, Sirlin CB, Lavine JE, Kuo MD. Multi-Modality, Multi-Dimensional Characterization of Pediatric Non-Alcoholic Fatty Liver Disease.. Metabolites, 2023.
4. Jamshidi N, Nigam KB, Nigam SK. Loss of the Kidney Urate Transporter, Urat1, Leads to Disrupted Redox Homeostasis in Mice.. Antioxidants (Basel, Switzerland), 2023.
5. Jamshidi N, Senthilvelan J, Dawson DW, Donahue TR, Kuo MD. Construction of a radiogenomic association map of pancreatic ductal adenocarcinoma.. BMC cancer, 2023.
6. Jamshidi N, Nigam SK. Drug transporters OAT1 and OAT3 have specific effects on multiple organs and gut microbiome as revealed by contextualized metabolic network reconstructions.. Scientific reports, 2022.
7. Granados JC, Falah K, Koo I, Morgan EW, Perdew GH, Patterson AD, Jamshidi N, Nigam SK. AHR is a master regulator of diverse pathways in endogenous metabolism.. Scientific reports, 2022.
8. Senthilvelan J, Jamshidi N. A pipeline for automated deep learning liver segmentation (PADLLS) from contrast enhanced CT exams.. Scientific reports, 2022.
9. Kao SD, Srinivasa RN, Callese T, Jamshidi N, Plotnik A. Looking beyond the gunsight: A potential bailout technique for arterial and venous recanalization.. Diagnostic and interventional radiology (Ankara, Turkey), 2022.
10. Jamshidi N, Tan W, Foote D, Reardon L, Lluri G, Aboulhosn J, Moriarty J, Lin J. Mechanical thrombectomy of COVID-19 DVT with congenital heart disease leading to phlegmasia cerulea dolens: a case report.. BMC cardiovascular disorders, 2021.
11. Cipollari S, Jamshidi N, Du L, Sung K, Huang D, Margolis DJ, Huang J, Reiter RE, Kuo MD. Tissue clearing techniques for three-dimensional optical imaging of intact human prostate and correlations with multi-parametric MRI.. The Prostate, 2021.
12. Cipollari S, Jamshidi N, Du L, Sung K, Huang D, Margolis DJ, Huang J, Reiter RE, Kuo MD. Tissue clearing techniques for three-dimensional optical imaging of intact human prostate and correlations with multi-parametric MRI.. The Prostate, 2021.
13. Granados JC, Nigam AK, Bush KT, Jamshidi N, Nigam SK. A key role for the transporter OAT1 in systemic lipid metabolism.. The Journal of biological chemistry, 2021.
14. Ranganayaki S, Jamshidi N, Aiyaz M, Rashmi SK, Gayathri N, Harsha PK, Padmanabhan B, Srinivas Bharath MM. Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration.. Scientific reports, 2021.
15. Jamshidi N, Chiang J. Inline balloon-assisted vascular sheath fragment removal.. CVIR endovascular, 2020.
16. Jamshidi N, Xu X, von Löhneysen K, Soldau K, Mohney RP, Karoly ED, Scott M, Friedman JS. Metabolome Changes during In Vivo Red Cell Aging Reveal Disruption of Key Metabolic Pathways.. iScience, 2020.
17. Jamshidi N, Kee ST. Transcatheter Embolization of Renal-Splenic Shunt to Treat Hematemesis.. Cardiovascular and interventional radiology, 2020.
18. Jamshidi N. PK Papyrus Coronary Stent for the Treatment of Diminutive and Tortuous Visceral Artery Pseudoaneurysms.. Cardiovascular and interventional radiology, 2020.
19. Jamshidi N, Chang J, Mock K, Nguyen B, Dauphine C, Kuo MD. Correction: Evaluation of the predictive ability of ultrasound-based assessment of breast cancer using BI-RADS natural language reporting against commercial transcriptome-based tests.. PloS one, 2020.
20. Mostolizadeh R, Dräger A, Jamshidi N. Insights into Dynamic Network States Using Metabolomic Data.. Methods in molecular biology (Clifton, N.J.), 2019.
21. Jeong WK, Jamshidi N, Felker ER, Raman SS, Lu DS. Radiomics and radiogenomics of primary liver cancers.. Clinical and molecular hepatology, 2018.
22. Jamshidi N, Yamamoto S, Gornbein J, Kuo MD. Receptor-based Surrogate Subtypes and Discrepancies with Breast Cancer Intrinsic Subtypes: Implications for Image Biomarker Development.. Radiology, 2018.
23. Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.. PLoS computational biology, 2018.
24. Raghunathan A, Jamshidi N. Integrated Host-Pathogen Metabolic Reconstructions.. Methods in molecular biology (Clifton, N.J.), 2018.
25. Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T. The Emerging Facets of Non-Cancerous Warburg Effect.. Frontiers in endocrinology, 2017.
26. Jamshidi N, Margolis DJ, Raman S, Huang J, Reiter RE, Kuo MD. Multiregional Radiogenomic Assessment of Prostate Microenvironments with Multiparametric MR Imaging and DNA Whole-Exome Sequencing of Prostate Glands with Adenocarcinoma.. Radiology, 2017.
27. Lee M, Woo B, Kuo MD, Jamshidi N, Kim JH. Quality of Radiomic Features in Glioblastoma Multiforme: Impact of Semi-Automated Tumor Segmentation Software.. Korean journal of radiology, 2017.
28. Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.. Scientific reports, 2017.
29. Jamshidi N, Huang D, Abtin FG, Loh CT, Kee ST, Suh RD, Yamamoto S, Das K, Dry S, Binder S, Enzmann DR, Kuo MD. Genomic Adequacy from Solid Tumor Core Needle Biopsies of ex Vivo Tissue and in Vivo Lung Masses: Prospective Study.. Radiology, 2016.
30. Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SY, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO, Nigam SK. An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network.. The Journal of biological chemistry, 2016.
31. Du L, Yamamoto S, Burnette BL, Huang D, Gao K, Jamshidi N, Kuo MD. Transcriptome profiling reveals novel gene expression signatures and regulating transcription factors of TGFβ-induced epithelial-to-mesenchymal transition.. Cancer medicine, 2016.
32. Yamamoto S, Huang D, Du L, Korn RL, Jamshidi N, Burnette BL, Kuo MD. Radiogenomic Analysis Demonstrates Associations between (18)F-Fluoro-2-Deoxyglucose PET, Prognosis, and Epithelial-Mesenchymal Transition in Non-Small Cell Lung Cancer.. Radiology, 2016.
33. Jamshidi N, Jonasch E, Zapala M, Korn RL, Brooks JD, Ljungberg B, Kuo MD. The radiogenomic risk score stratifies outcomes in a renal cell cancer phase 2 clinical trial.. European radiology, 2015.
34. Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, Jamshidi N, Palsson BO. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics.. Cell systems, 2015.
35. Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I. Do genome-scale models need exact solvers or clearer standards?. Molecular systems biology, 2015.
36. Jamshidi N, Raghunathan A. Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods.. Frontiers in microbiology, 2015.
37. Eraly SA, Liu HC, Jamshidi N, Nigam SK. Transcriptome-based reconstructions from the murine knockout suggest involvement of the urate transporter, URAT1 (slc22a12), in novel metabolic pathways.. Biochemistry and biophysics reports, 2015.
38. Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions.. Wiley interdisciplinary reviews. Systems biology and medicine, 2015.
39. Jamshidi N, Jonasch E, Zapala M, Korn RL, Aganovic L, Zhao H, Tumkur Sitaram R, Tibshirani RJ, Banerjee S, Brooks JD, Ljungberg B, Kuo MD. The Radiogenomic Risk Score: Construction of a Prognostic Quantitative, Noninvasive Image-based Molecular Assay for Renal Cell Carcinoma.. Radiology, 2015.
40. Yamamoto S, Han W, Kim Y, Du L, Jamshidi N, Huang D, Kim JH, Kuo MD. Breast Cancer: Radiogenomic Biomarker Reveals Associations among Dynamic Contrast-enhanced MR Imaging, Long Noncoding RNA, and Metastasis.. Radiology, 2015.
41. Kuo MD, Jamshidi N. Behind the numbers: Decoding molecular phenotypes with radiogenomics--guiding principles and technical considerations.. Radiology, 2014.
42. Thomas A, Rahmanian S, Bordbar A, Palsson BØ, Jamshidi N. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.. Scientific reports, 2014.
43. Jamshidi N, Diehn M, Bredel M, Kuo MD. Illuminating radiogenomic characteristics of glioblastoma multiforme through integration of MR imaging, messenger RNA expression, and DNA copy number variation.. Radiology, 2013.
44. Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson BO, Nigam SK. Multispecific drug transporter Slc22a8 (Oat3) regulates multiple metabolic and signaling pathways.. Drug metabolism and disposition: the biological fate of chemicals, 2013.
45. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. A community-driven global reconstruction of human metabolism.. Nature biotechnology, 2013.
46. Slayden RA, Jackson M, Zucker J, Ramirez MV, Dawson CC, Crew R, Sampson NS, Thomas ST, Jamshidi N, Sisk P, Caspi R, Crick DC, McNeil MR, Pavelka MS, Niederweis M, Siroy A, Dona V, McFadden J, Boshoff H, Lew JM. Updating and curating metabolic pathways of TB.. Tuberculosis (Edinburgh, Scotland), 2013.
47. Hathout G, Jamshidi N. Parameter optimization for quantitative signal-concentration mapping using spoiled gradient echo MRI.. Radiology research and practice, 2012.
48. Jamshidi N, Miller FJ, Mandel J, Evans T, Kuo MD. Individualized therapy of HHT driven by network analysis of metabolomic profiles.. BMC systems biology, 2011.
49. Ahn SY, Jamshidi N, Mo ML, Wu W, Eraly SA, Dnyanmote A, Bush KT, Gallegos TF, Sweet DH, Palsson BØ, Nigam SK. Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis.. The Journal of biological chemistry, 2011.
50. Bordbar A, Jamshidi N, Palsson BO. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states.. BMC systems biology, 2011.
51. Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.. BMC systems biology, 2010.
52. Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology, 2010.
53. Obrzut S, Tiongson J, Jamshidi N, Phan HM, Hoh C, Birgersdotter-Green U. Assessment of metabolic phenotypes in patients with non-ischemic dilated cardiomyopathy undergoing cardiac resynchronization therapy.. Journal of cardiovascular translational research, 2010.
54. Obrzut S, Jamshidi N, Karimi A, Birgersdotter-Green U, Hoh C. Imaging and modeling of myocardial metabolism.. Journal of cardiovascular translational research, 2010.
55. Jamshidi N, Palsson BØ. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal, 2010.
56. de Graaf AA, Freidig AP, De Roos B, Jamshidi N, Heinemann M, Rullmann JA, Hall KD, Adiels M, van Ommen B. Nutritional systems biology modeling: from molecular mechanisms to physiology.. PLoS computational biology, 2009.
57. Jamshidi N, Palsson BØ. Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal, 2009.
58. Jamshidi N, Palsson BO. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.. BMC systems biology, 2009.
59. Thiele I, Jamshidi N, Fleming RM, Palsson BØ. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.. PLoS computational biology, 2009.
60. Li F, Thiele I, Jamshidi N, Palsson BØ. Identification of potential pathway mediation targets in Toll-like receptor signaling.. PLoS computational biology, 2009.
61. Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BO. Genome-scale network analysis of imprinted human metabolic genes.. Epigenetics, 2009.
62. Jamshidi N, Palsson BØ. Top-down analysis of temporal hierarchy in biochemical reaction networks.. PLoS computational biology, 2008.
63. Jamshidi N, Palsson BØ. Formulating genome-scale kinetic models in the post-genome era.. Molecular systems biology, 2008.
64. Mo ML, Jamshidi N, Palsson BØ. A genome-scale, constraint-based approach to systems biology of human metabolism.. Molecular bioSystems, 2007.
65. Jamshidi N, Palsson BØ. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.. BMC systems biology, 2007.
66. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ. Global reconstruction of the human metabolic network based on genomic and bibliomic data.. Proceedings of the National Academy of Sciences of the United States of America, 2007.
67. Jamshidi N, Vo TD, Palsson BO. In silico analysis of SNPs and other high-throughput data.. Methods in molecular biology (Clifton, N.J.), 2007.
68. Jamshidi N, Palsson BØ. Systems biology of SNPs.. Molecular systems biology, 2006.
69. Jamshidi N, Palsson BØ. Systems biology of the human red blood cell.. Blood cells, molecules & diseases, 2006.
70. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.. Nucleic acids research, 2005.
71. Jamshidi N, Wiback SJ, Palsson B BØ. In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism.. Genome research, 2002.
72. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BO, Edwards JS. Description and analysis of metabolic connectivity and dynamics in the human red blood cell.. Biophysical journal, 2002.
73. Gurtner C, Tu E, Jamshidi N, Haigis RW, Onofrey TJ, Edman CF, Sosnowski R, Wallace B, Heller MJ. Microelectronic array devices and techniques for electric field enhanced DNA hybridization in low-conductance buffers.. Electrophoresis, 2002.
74. Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. Dynamic simulation of the human red blood cell metabolic network.. Bioinformatics (Oxford, England), 2001.
75. Suzuki H, Delano FA, Jamshidi N, Katz D, Mori M, Kosaki K, Gottlieb RA, Ishii H, Schmid-Schönbein GW. Enhanced DNA fragmentation in the thymus of spontaneously hypertensive rats.. The American journal of physiology, 1999.
76. Suzuki H, DeLano FA, Parks DA, Jamshidi N, Granger DN, Ishii H, Suematsu M, Zweifach BW, Schmid-Schönbein GW. Xanthine oxidase activity associated with arterial blood pressure in spontaneously hypertensive rats.. Proceedings of the National Academy of Sciences of the United States of America, 1998.