Publications

2026

  • Aryl hydrocarbon receptor in the kidney regulates metabolic cross-talk with the liver and gut microbiome. Jamshidi N, Nigam SK. Nature Scientific Reports. 2026 Mar 24. PMID: 41876749
  • The loss of peroxiredoxin 2 in mice disrupts the biochemical aging phenotype in erythrocytes. Jamshidi N, von Löhneysen K, Soldau K, Friedman JS. iScience. 2026 Jan 2;29(2):114608. PMID: 41623488

2024

  • Dysfunctional β-cell longevity in diabetes relies on energy conservation and positive epistasis. Raval K, Jamshidi N, Seyran B, Salwinski L, Pillai R, Yang L, Ma F, Pellegrini M, Shin J, Yang X, Tudzarova S.  Life Sci Alliance. 2024 Sep 23;7(12):e202402743. PMID: 39313296
  • A Computer Vision Algorithm to Predict Superior Mesenteric Artery Margin Status for Patients with Pancreatic Ductal Adenocarcinoma. 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. Ann Surg. 2024 Aug 23. PMID: 39176476

2023

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

2022

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

2021

  • Mechanical thrombectomy of COVID-19 DVT with congenital heart disease leading to phlegmasia cerulea dolens: a case report. Jamshidi N, Tan W, Foote D, Reardon L, Lluri G, Aboulhosn J, Moriarty J, Lin J. BMC Cardiovasc Disord. 2021 Dec 9;21(1):592. PMID: 34886795
  • A key role for the transporter OAT1 in systemic lipid metabolism. Granados JC, Nigam AK, Bush KT, Jamshidi N, Nigam SK. Journal of Biological Chemistry. 2021:100603. PMID: 33785360
  • Tissue clearing techniques for three-dimensional optical imaging of intact human prostate and correlations with multi-parametric MRI. Cipollari S, Jamshidi N, Du L, Sung K, Huang D, Margolis DJ, Huang J, Reiter RE, Kuo MD. Prostate. 2021;81(9):521-9. PMID: 33876838
  • Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration. Ranganayaki S, Jamshidi N, Aiyaz M, Rashmi SK, Gayathri N, Harsha PK, Padmanabhan B, Bharath MMMS. Nature Scientific Reports. 2021 Jan 15;11(1):1483. PMID: 33452321

2020

  • Metabolome Changes during In Vivo Red Cell Aging Reveal Disruption of Key Metabolic Pathways. Jamshidi N, Xu X, von L ̈ohneysen K, Soldau K, Mohney RP, Karoly ED, Scott M, Friedman JS. iScience. 2020 Sep 29;23(10):101630. PMID: 33103072
  • Inline balloon-assisted vascular sheath fragment removal. Jamshidi N, Chiang J. CVIR Endovascular. 2020 Oct; 3(1):53. PMID: 32886241
  • Transcatheter Embolization of Renal-Splenic Shunt to Treat Hematemesis. Jamshidi N, Kee ST. CardioVascular and Interventional Radiology. 2020 Jul 24. PMID: 32710128
  • PK Papyrus Coronary Stent for the Treatment of Diminutive and Tortuous Visceral Artery Pseudoaneurysms. Jamshidi N. CardioVascular and Interventional Radiology. 2020 Mar; 43:1097–1098. PMID: 32133552
  • Evaluation of the predictive ability of ultrasound-based assessment of breast cancer using BI-RADS natural language reporting against commercial transcriptome-based tests. Jamshidi N, Chang J, Mock K, Nguyen B, Dauphine C, Kuo MD. PLoS One. 2020 Jan 10;15(1):e0226634. PMID: 31923222

2019

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

2018

  • Receptor-based Surrogate Subtypes and Discrepancies with Breast Cancer Intrinsic Subtypes: Implications for Image Biomarker Development. Jamshidi N, Yamamoto S, Gornbein J, Kuo MD. Radiology. 2018 Jul 24:171118. PMID: 30040052
  • Integrated Host-Pathogen Metabolic Reconstructions. Raghunathan A, Jamshidi N. Methods Mol Biol. 2018 1716:197-217. PMID: 29222755
  • Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BØ, Lewis NE, *Jamshidi N. PLoS Computational Biology. 2018 Jan 4;14(1):e1005895. PMID: 29300748

2017

  • The Emerging Facets of Non-Cancerous Warburg Effect. Abdel-Haleem AM, Lewis NE, Jamshidi N, Mineta K, Gao X, Gojobori T. Frontiers in Endocrinology. 2017 Oct 23;8:279. PMID: 29109698
  • Multiregional Radiogenomic Assessment of Prostate Microenvironments with Multiparametric MR Imaging and DNA Whole-Exome Sequencing of Prostate Glands with Adenocarcinoma. Jamshidi N, Margolis DJ, Raman S, Huang J, Reiter RE, Kuo MD. Radiology. 2017 Apr 28:162827. PMID: 28453432
  • Quality of Radiomic Features in Glioblastoma Multiforme: Impact of Semi-Automated Tumor Segmentation Software. Lee M, Woo B, Kuo MD, Jamshidi N, Kim JH. Korean J Radiol. 2017 May- Jun;18(3):498-509. PMID: 28458602
  • Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BØ.  Nature Scientific Reports. 2017 Jan 25;7:41241. PMID: 28120890
  • Genomic Adequacy from Solid Tumor Core Needle Biopsies of ex Vivo Tissue and in Vivo Lung Masses: Prospective Study. Jamshidi N, Huang D, Abtin FG, Loh CT, Kee ST, Suh RD, Yamamoto S, Das K, Dry S, Binder S, Enzmann DR, Kuo MD. Radiology. 2017 Mar;282(3):903-912. PMID: 27755912

2016

  • An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network. Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SY, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO, Nigam SK. Journal of Biological Chemistry. 2016 Sep 9;291(37):19474-86. PMID: 27440044
  • Transcriptome profiling reveals novel gene expression signatures and regulating transcription factors of TGFβ-induced epithelial-to-mesenchymal transition. Du L, Yamamoto S, Burnette BL, Huang D, Gao K, Jamshidi N, Kuo MD. Cancer Medicine. 2016 Aug;5(8):1962-72. PMID: 27318801
  • Radiogenomic Analysis Demonstrates Associations between 18F-Fluoro-2-Deoxyglucose PET, Prognosis, and Epithelial- Mesenchymal Transition in Non-Small Cell Lung Cancer. Yamamoto S, Huang D, Du L, Korn RL, Jamshidi N, Burnette BL, Kuo MD. Radiology. 2016 Apr 15:160259. PMID: 27082783

2015

  • Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Bordbar A, McCloskey D, Zielinski DC, Sonnenschein N, *Jamshidi N, Palsson BØ. Cell Systems. 2015 Oct 28;1(4):283-92. PMID: 27136057
  • The radiogenomic risk score stratifies outcomes in a renal cell cancer phase 2 clinical trial. Jamshidi N, Jonasch E, Zapala M, Korn RL, Brooks JD, Ljungberg B, Kuo MD. European Radiology. 2015 Nov 11. PMID: 26560727
  • Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Jamshidi N, Raghunathan A. Frontiers in Microbiology 2015; 6:1032. 2015. PMID: 26500611
  • Do genome-scale models need exact solvers or clearer standards? 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. Molecular Systems Biology. 201511(10):831. PMID: 26467284
  • The Radiogenomic Risk Score: Construction of a Prognostic Quantitative, Noninvasive Image-based Molecular Assay for Renal Cell Carcinoma. 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. Radiology. 2015 Oct;277(1):114-23. 2015 Aug 19. PMID: 26402495
  • Systems analysis of host-parasite interactions. Swann J, Jamshidi N, Lewis NE, Winzeler EA. Wiley Interdiscip Rev Syst Biol Med. 2015 Nov;7(6):381-400. 2015 Aug 26. PMID: 26306749
  • Transcriptome-based reconstructions from the murine knockout suggest involvement of the urate transporter, URAT1 (slc22a12), in novel metabolic pathways. Eraly SA, Liu HC, Jamshidi N, Nigam SK. Biochem Biophys Rep. 2015 Sep 1;3:51-61. PMID: 26251846
  • A Spatiotemporal Image Phenotyping Pipeline for Radiogenomic Profiling of Breast Cancer with DCE MRI. Kim J, Kim Y, Yang Z, Hong B, Kuo MD, Han W, Yamamoto S, Jamshidi N. Med Phys. 2015 Jun;42(6):3605.
  • Breast Cancer: Radiogenomic Biomarker Reveals Associations among Dynamic Contrast-enhanced MR Imaging, Long Noncoding RNA, and Metastasis. Yamamoto S, Han W, Kim Y, Du L, Jamshidi N, Huang D, Kim JH, Kuo MD. Radiology. 2015:142698. PMID: 25734557.

2014

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

2013

  • Illuminating Radiogenomic Characteristics of Glioblastoma Multiforme through Integration of MR Imaging, Messenger RNA Expression, and DNA Copy Number Variation. Jamshidi N, Diehn M, Bredel M, Kuo MD. Radiology 2013 Sep 20. PMID: 24056404.
  • Multispecific Drug Transporter Oat3 (Slc22a8) Regulates Multiple Metabolic Pathways.Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson BØ, Nigam SK.  Drug Metab Dispos. 2013 Aug 6. PMID: 23920220
  • Updating and curating metabolic pathways of TB. 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. Tuberculosis (Edinb). 2013 Jan;93(1):47-59. PMID:: 23375378
  • A community-driven global reconstruction of human metabolism. 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. Nature Biotechnology. 2013 Mar 3. PMID: 23455439

2012

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

2011

  • Individualized Therapy of HHT Driven by Network Analysis of Metabolomic Profiles. Jamshidi N, Miller FJ, Mandel J, Evans T, Kuo MD. BMC Systems Biology. 2011; 5(1):200. PMID: 22185482
  • Linkage of organic anion transporter-1 to metabolic pathways through integrated ”omics”-driven network and functional analysis. Ahn SY, Jamshidi N, Mo ML, Wu W, Eraly SA, Dnyanmote A, Bush KT, Gallegos TF, Sweet DH, Palsson BØ, and Nigam SK. Journal of Biological Chemistry. 2011; 286(36):31522-31. PMID: 21757732

2010

  •  Imaging and modeling of myocardial metabolism. Obrzut S, Jamshidi N, Karimi A, Birgersdotter-Green U, Hoh C. Journal of Cardiovascular Translational Research. 2010 Aug; 3(4):384-96. PMID: 20559785
  • Assessment of metabolic phenotypes in patients with non-ischemic dilated cardiomyopathy undergoing cardiac resynchronization therapy. Obrzut S, Tiongson J, Jamshidi N, Phan HM, Hoh C, Birgersdotter-Green U. Journal of Cardiovascular Translational Research. 2010 Dec;3 (6):643-51. PMID: 20842468
  • Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, *Jamshidi N. Molecular Systems Biology. 2010 Oct 19; 6:422. PMID: 20959820
  • A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ.  BMC Systems Biology. 2010; 4:140. PMID: 20959003
  • Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models. Jamshidi N, Palsson BØ. Biophysical Journal. 2010 Jan 2; 98(2):175-185. PMID: 20338839

2009

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

2008

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

2007

  • A genome-scale, constraint-based approach to system biology of human metabolism. Mo ML, Jamshidi N, Palsson BØ. Molecular BioSystems, 2007 3, 598-603. PMID: 17700859
  • Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. Jamshidi N, and Palsson BØ. BMC Systems Biology 2007. 1, 26. PMID: 17555602
  • Global reconstruction of the human metabolic network based on genomic and bibliomic data. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ. Proceedings of the National Academy of Sciences of the United States of America, 2007 104, 1777-1782. PMID: 17267599

2006

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

2005

  • Systems biology of SNPs. Jamshidi N and Palsson BØ. Molecular Systems Biology, 2006. 2:38. PMID: 16820779
  • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. 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. Nucleic Acids Research, 2005. 33(17): p. 5691-702. PMID: 16214803

Pre-2004

  • In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism. Jamshidi N, Wiback SJ, Palsson BØ. Genome Research, 2002. 12(11):1687-92. PMID: 12421755
  • Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Kauffman KJ, Pajerowski JD, Jamshidi N, Palsson BØ, Edwards JS. Biophysical Journal, 2002. 83(2):646- 62. PMID: 12124254
  • Microelectronic array devices and techniques for electric field enhanced DNA hybridization in low- conductance buffers. Gurtner C, Tu E, Jamshidi N, Haigis RW, Onofrey TJ, Edman CF, Sosnowski R, Wallace B, Heller MJ. Electrophoresis. 2002. 23(10):1543-50. PMID: 12116167
  • Dynamic simulation of the human red blood cell metabolic network. Jamshidi N, Fahland T, Edwards JS, Church GM, Palsson BØ. Bioinformatics. 2001. 17: 286-7. PMID: 11294796
  • Enhanced DNA Fragmentation in the Thymus of Spontaneously Hypertensive Rats. Suzuki H, DeLano FA, Jamshidi N, Katz D, Mori M, Kosaki K, Gottlieb RA, Ishii H, Schimd- Schonbein GW. American Journal of Physiology. 1999. H2135-H2140. PMID: 10362697
  • Xanthine Oxidase Activity Associated with Arterial Blood Pressure in Spontaneously Hypertensive Rats. Suzuki H, DeLano FA, Parks DA, Jamshidi N, Granger DN, Ishii H, Suematsu M, Zweifach. BW, Schmid-Schonbein GW. Proceedings of the National Academy of Sciences of the United States of America, 1998. 95(8):4754-9. PMID: 9539811