Publications

2023

  • Jamshidi N, Feizi A, Sirlin CB, Lavine JE, Kuo MD. Multi-Modality, Multi-Dimensional Characterization of Pediatric Non-Alcoholic Fatty Liver Disease. Metabolites. 2023 Aug 8;13(8):929. PMID: 37623872
  • Jamshidi N, Nigam KB, Nigam SK. Loss of the Kidney Urate Transporter, Urat1, Leads to Disrupted Redox Homeostasis in Mice. Antioxidants (Basel). 2023 Mar 22;12(3):780. PMID: 36979028
  • Jamshidi N, Senthilvelan J, Dawson DW, Donahue TR, Kuo MD. Construction of a radiogenomic association map of pancreatic ductal adenocarcinoma. BMC Cancer. 2023 Feb 27;23(1):189. PMID: 36843111

2022

  • Jamshidi N and Nigam SK. Drug transporters OAT1 and OAT3 have specific effects on multiple organs and gut microbiome as revealed by contextualized metabolic network reconstructions. Nature Scientific Reports. 2022 Oct 31;12(1):18308. PMID: 36316339
  • Senthilvelan J and Jamshidi N. A pipeline for automated deep learning liver segmentation (PADLLS) from contrast enhanced CT exams. Nature Scientific Reports. 2022 Sep 22;12(1):15794. PMID: 36138084
  • 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. Nature Scientific Reports. 2022 Oct 5;12(1):16625. PMID: 36198709
  • Kao SD, Srinivasa RN, Callese T, Jamshidi N, Plotnik A. Looking beyond the gunsight: A potential bailout technique for arterial and venous recanalization. Diagn Interv Radiol. 2022 May;28(3):260-263. PMID: 35748210

2021

  • 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 Cardiovasc Disord. 2021 Dec 9;21(1):592. PMID: 34886795
  • Granados JC, Nigam AK, Bush KT, Jamshidi N, Nigam SK. A key role for the transporter OAT1 in systemic lipid metabolism. Journal of Biological Chemistry. 2021:100603. PMID: 33785360
  • †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. Prostate. 2021;81(9):521-9. PMID: 33876838
  • Ranganayaki S, Jamshidi N, Aiyaz M, Rashmi SK, Gayathri N, Harsha PK, Padmanabhan B, Bharath MMMS. Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration. Nature Scientific Reports. 2021 Jan 15;11(1):1483. PMID: 33452321

2020

  • Jamshidi N, Xu X, von L ̈ohneysen 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 Sep 29;23(10):101630. PMID: 33103072
  • Jamshidi N, Chiang J. Inline balloon-assisted vascular sheath fragment removal. CVIR Endovascular. 2020 Oct; 3(1):53. PMID: 32886241
  • Jamshidi N, Kee ST. Transcatheter Embolization of Renal-Splenic Shunt to Treat Hematemesis. CardioVascular and Interventional Radiology. 2020 Jul 24. PMID: 32710128
  • Jamshidi N. PK Papyrus Coronary Stent for the Treatment of Diminutive and Tortuous Visceral Artery Pseudoaneurysms. CardioVascular and Interventional Radiology. 2020 Mar; 43:1097–1098. PMID: 32133552
  • Jamshidi N, Chang J, Mock K, Nguyen B, Dauphine C, Kuo MD. 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 Jan 10;15(1):e0226634. PMID: 31923222

2019

  • Chiang J, *Jamshidi N. Radiogenomics of Oncology: Current Trends and Future Directions. Advances in Clinical Radiology. 2019 1, p71-82.
  • Jeong WK, *Jamshidi N, Felker ER, Raman SS, Lu DS. Radiomics and radiogenomics of primary liver cancers. Clin Mol Hepatol. 2019 Mar;25(1):21-29. PMID: 30441889

2018

  • 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 Jul 24:171118. PMID: 30040052
  • Raghunathan A, Jamshidi N. Integrated Host-Pathogen Metabolic Reconstructions. Methods Mol Biol. 2018 1716:197-217. PMID: 29222755
  • Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BØ, 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 Jan 4;14(1):e1005895. PMID: 29300748

2017

  • 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 Oct 23;8:279. PMID: 29109698
  • 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 Apr 28:162827. PMID: 28453432
  • 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 J Radiol. 2017 May- Jun;18(3):498-509. PMID: 28458602
  • Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BØ. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism. Nature Scientific Reports. 2017 Jan 25;7:41241. PMID: 28120890
  • 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. 2017 Mar;282(3):903-912. PMID: 27755912

2016

  • 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. Journal of Biological Chemistry. 2016 Sep 9;291(37):19474-86. PMID: 27440044
  • 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 Aug;5(8):1962-72. PMID: 27318801
  • Yamamoto S, Huang D, Du L, Korn RL, Jamshidi N, Burnette BL, Kuo MD. Radiogenomic Analysis Demonstrates Associations between 18F-Fluoro-2-Deoxyglucose PET, Prognosis, and Epithelial- Mesenchymal Transition in Non-Small Cell Lung Cancer. Radiology. 2016 Apr 15:160259. PMID: 27082783

2015

  • Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, *Jamshidi N, Palsson BØ. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems. 2015 Oct 28;1(4):283-92. PMID: 27136057
  • 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 Nov 11. PMID: 26560727
  • Jamshidi N, Raghunathan A. Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Frontiers in Microbiology 2015; 6:1032. 2015. PMID: 26500611
  • Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dr ̈ager A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrg ̊ard MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Nov`ere 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 BØ, 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. 201511(10):831. PMID: 26467284
  • 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 Oct;277(1):114-23. 2015 Aug 19. PMID: 26402495
  • Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. Wiley Interdiscip Rev Syst Biol Med. 2015 Nov;7(6):381-400. 2015 Aug 26. PMID: 26306749
  • 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. Biochem Biophys Rep. 2015 Sep 1;3:51-61. PMID: 26251846
  • Kim J, Kim Y, Yang Z, Hong B, Kuo MD, Han W, Yamamoto S, Jamshidi N. A Spatiotemporal Image Phenotyping Pipeline for Radiogenomic Profiling of Breast Cancer with DCE MRI. Med Phys. 2015 Jun;42(6):3605.
  • 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. 2015:142698. PMID: 25734557.

2014

  • Thomas A, Rahmanian S, Bordbar A, Palsson BØ, *Jamshidi N. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance. Nature Scientific Reports. 2014;4:3925. PMID: 24473230.
  • Kuo MD, Jamshidi N. Behind the numbers: Decoding molecular phenotypes with radiogenomics– guiding principles and technical considerations. Radiology. 2014;270(2):320-5. PMID: 24471381.

2013

  • 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 Sep 20. PMID: 24056404.
  • Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson BØ, Nigam SK. Multispecific Drug Transporter Oat3 (Slc22a8) Regulates Multiple Metabolic Pathways. Drug Metab Dispos. 2013 Aug 6. PMID: 23920220
  • 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 (Edinb). 2013 Jan;93(1):47-59. PMID:: 23375378
  • Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, B ̈olling 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 Nov`ere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, 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 Mar 3. PMID: 23455439

2012

  • Hathout G, Jamshidi N. Parameter optimization for quantitative signal-concentration mapping using spoiled gradient echo MRI. Radiol Res Pract. 2012;2012:815729. PMID: 23213523

2011

  • 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; 5(1):200. PMID: 22185482
  • Ahn SY, Jamshidi N, Mo ML, Wu W, Eraly SA, Dnyanmote A, Bush KT, Gallegos TF, Sweet DH, Palsson BØ, and Nigam SK. Linkage of organic anion transporter-1 to metabolic pathways through integrated ”omics”-driven network and functional analysis. Journal of Biological Chemistry. 2011; 286(36):31522-31. PMID: 21757732

2010

  • Obrzut S, Jamshidi N, Karimi A, Birgersdotter-Green U, Hoh C. Imaging and modeling of myocardial metabolism. Journal of Cardiovascular Translational Research. 2010 Aug; 3(4):384-96. PMID: 20559785
  • 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 Dec;3 (6):643-51. PMID: 20842468
  • 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 Oct 19; 6:422. PMID: 20959820
  • 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; 4:140. PMID: 20959003
  • Jamshidi N, Palsson BØ. Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models. Biophysical Journal. 2010 Jan 2; 98(2):175-185. PMID: 20338839

2009

  • Jamshidi N, Palsson BØ. Flux-concentration duality in dynamic nonequilibrium biological networks. Biophysical Journal. 2009; 97(5):L11-3. PMID: 19720010
  • 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 Nov 5(11): e1000554. PMID: 19956660
  • Jamshidi N, Palsson BØ. Using In Silico Models to Simulate Dual Perturbation Experiments: Procedure Development and interpretation of outcomes. BMC Systems Biology. 2009 Apr 30;3:44. PMID: 19405968
  • Thiele I, Jamshidi N, Fleming RMT, Palsson BØ. Genome-Scale Reconstruction of the transcription and translation machinery in Escherichia coli: A knowledge-database and mathematical model. PLoS Computational Biology, 2009 Mar;5(3):e1000312. PMID: 19282977
  • Sigurdsson M, Jamshidi N, Jonsson J, Palsson BØ. Genome-scale network analysis of imprinted human metabolic genes. Epigenetics, 2009 Jan; 4(1):43-6. PMID: 19218833
  • Li F, Thiele I, Jamshidi N, Palsson BØ. Identification of Potential Pathway Mediation Targets in Toll- Like Receptor Signaling. PLoS Computational Biology, 2009 Feb; 5(2):e1000292. PMID: 19229310

2008

  • Jamshidi N, Palsson BØ. Top-down analysis of temporal hierarchy in biochemical reaction networks. PLoS Computational Biology, 2008, 4(9): e1000177. PMID: 18787685
  • Jamshidi N, Palsson BØ. Formulating genome-scale kinetic models in the post-genome era. Molecular Systems Biology, 2008;4:171. PMID: 18319723

2007

  • Mo ML, Jamshidi N, Palsson BØ. A genome-scale, constraint-based approach to system biology of human metabolism. Molecular BioSystems, 2007 3, 598-603. PMID: 17700859
  • Jamshidi N, and 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. 1, 26. PMID: 17555602
  • 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 104, 1777-1782. PMID: 17267599

2006

  • Jamshidi N and Palsson BØ. Systems biology of the human red blood cell. Blood Cells Molecules and Disease, 2006. 36(2): p. 239-47. PMID: 16533612

2005

  • Jamshidi N and Palsson BØ. Systems biology of SNPs. Molecular Systems Biology, 2006. 2:38. PMID: 16820779
  • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Cr ́ecy-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, Ru ̈ckert 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. 33(17): p. 5691-702. PMID: 16214803

Pre-2004

  • Jamshidi N, Wiback SJ, Palsson BØ. In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism. Genome Research, 2002. 12(11):1687-92. PMID: 12421755
  • Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BØ, Edwards JS. Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophysical Journal, 2002. 83(2):646- 62. PMID: 12124254
  • 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. 23(10):1543-50. PMID: 12116167
  • Jamshidi N, Fahland T, Edwards JS, Church GM, Palsson BØ. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics. 2001. 17: 286-7. PMID: 11294796
  • Suzuki H, DeLano FA, Jamshidi N, Katz D, Mori M, Kosaki K, Gottlieb RA, Ishii H, Schimd- Schonbein GW. Enhanced DNA Fragmentation in the Thymus of Spontaneously Hypertensive Rats. American Journal of Physiology. 1999. H2135-H2140. PMID: 10362697
  • Suzuki H, DeLano FA, Parks DA, Jamshidi N, Granger DN, Ishii H, Suematsu M, Zweifach. BW, Schmid-Schonbein 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. 95(8):4754-9. PMID: 9539811