Neema Jamshidi - Publications

Affiliations: 
2009 Bioengineering University of California, San Diego, La Jolla, CA 

52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 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. 14: e1005895. PMID 29300748 DOI: 10.1371/journal.pcbi.1005895  1
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. 8: 279. PMID 29109698 DOI: 10.3389/fendo.2017.00279  0.8
2017 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. 7: 41241. PMID 28120890 DOI: 10.1038/srep41241  1
2016 Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SY, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO, Nigam SK. Construction and Evaluation of an Organic Anion Transporter 1 (OAT1)-Centered Metabolic Network. The Journal of Biological Chemistry. PMID 27440044 DOI: 10.1074/jbc.M116.745216  1
2016 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. 160259. PMID 27082783 DOI: 10.1148/radiol.2016160259  1
2015 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. 1: 283-292. PMID 27136057 DOI: 10.1016/j.cels.2015.10.003  1
2015 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. PMID 26560727 DOI: 10.1007/s00330-015-4082-8  1
2015 Jamshidi N, Raghunathan A. Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods. Frontiers in Microbiology. 6: 1032. PMID 26500611 DOI: 10.3389/fmicb.2015.01032  1
2015 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, ... ... Jamshidi N, et al. Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology. 11: 831. PMID 26467284  1
2015 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. 277: 114-123. PMID 26402495 DOI: 10.1148/radiol.2015150800  1
2015 Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. PMID 26306749 DOI: 10.1002/wsbm.1311  1
2015 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. 3: 51-61. PMID 26251846 DOI: 10.1016/j.bbrep.2015.07.012  1
2015 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. 275: 384-92. PMID 25734557 DOI: 10.1148/radiol.15142698  1
2015 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. 1: 283-292. DOI: 10.1016/j.cels.2015.10.003  1
2014 Thomas A, Rahmanian S, Bordbar A, Palsson BØ, Jamshidi N. Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance. Scientific Reports. 4: 3925. PMID 24473230 DOI: 10.1038/srep03925  1
2014 Kuo MD, Jamshidi N. Behind the numbers: Decoding molecular phenotypes with radiogenomics--guiding principles and technical considerations. Radiology. 270: 320-5. PMID 24471381 DOI: 10.1148/radiol.13132195  1
2014 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. 270: 1-2. PMID 24056404 DOI: 10.1148/radiol.13130078  1
2013 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. 41: 1825-34. PMID 23920220 DOI: 10.1124/dmd.113.052647  1
2013 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, ... ... Jamshidi N, et al. A community-driven global reconstruction of human metabolism. Nature Biotechnology. 31: 419-25. PMID 23455439 DOI: 10.1038/nbt.2488  1
2013 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, et al. Updating and curating metabolic pathways of TB. Tuberculosis (Edinburgh, Scotland). 93: 47-59. PMID 23375378 DOI: 10.1016/j.tube.2012.11.001  1
2013 Jamshidi N, Bordbar A, Palsson B. Modeling Mycobacterium tuberculosis H37Rv in silico Systems Biology of Tuberculosis. 1-19. DOI: 10.1007/978-1-4614-4966-9_1  1
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. 5: 200. PMID 22185482 DOI: 10.1186/1752-0509-5-200  1
2011 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. 286: 31522-31. PMID 21757732 DOI: 10.1074/jbc.M111.272534  1
2011 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. 5: 110. PMID 21749716 DOI: 10.1186/1752-0509-5-110  1
2011 Jamshidi N, Palsson BO. Metabolic network dynamics: Properties and principles Understanding the Dynamics of Biological Systems: Lessons Learned From Integrative Systems Biology. 19-37. DOI: 10.1007/978-1-4419-7964-3_2  1
2010 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. 6: 422. PMID 20959820 DOI: 10.1038/msb.2010.68  1
2010 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. 4: 140. PMID 20959003 DOI: 10.1186/1752-0509-4-140  1
2010 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. 3: 643-51. PMID 20842468 DOI: 10.1007/s12265-010-9223-5  1
2010 Obrzut S, Jamshidi N, Karimi A, Birgersdotter-Green U, Hoh C. Imaging and modeling of myocardial metabolism. Journal of Cardiovascular Translational Research. 3: 384-96. PMID 20559785 DOI: 10.1007/s12265-010-9170-1  1
2010 Jamshidi N, Palsson BØ. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophysical Journal. 98: 175-85. PMID 20338839 DOI: 10.1016/j.bpj.2009.09.064  1
2009 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. 5: e1000554. PMID 19956660 DOI: 10.1371/journal.pcbi.1000554  1
2009 Jamshidi N, Palsson BØ. Flux-concentration duality in dynamic nonequilibrium biological networks. Biophysical Journal. 97: L11-3. PMID 19720010 DOI: 10.1016/j.bpj.2009.06.049  1
2009 Jamshidi N, Palsson BO. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. Bmc Systems Biology. 3: 44. PMID 19405968 DOI: 10.1186/1752-0509-3-44  1
2009 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. 5: e1000312. PMID 19282977 DOI: 10.1371/journal.pcbi.1000312  1
2009 Li F, Thiele I, Jamshidi N, Palsson BØ. Identification of potential pathway mediation targets in Toll-like receptor signaling. Plos Computational Biology. 5: e1000292. PMID 19229310 DOI: 10.1371/journal.pcbi.1000292  1
2009 Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BO. Genome-scale network analysis of imprinted human metabolic genes. Epigenetics. 4: 43-6. PMID 19218833 DOI: 10.4161/epi.4.1.7603  1
2009 Ganji DD, Jamshidi N, Ganji ZZ. Hpm and vim methods for finding the exact solutions of the nonlinear dispersive equations and seventh-order sawadakotera equation International Journal of Modern Physics B. 23: 39-52. DOI: 10.1142/S0217979209049607  0.01
2008 Jamshidi N, Palsson BØ. Top-down analysis of temporal hierarchy in biochemical reaction networks. Plos Computational Biology. 4: e1000177. PMID 18787685 DOI: 10.1371/journal.pcbi.1000177  1
2008 Jamshidi N, Palsson BØ. Formulating genome-scale kinetic models in the post-genome era. Molecular Systems Biology. 4: 171. PMID 18319723 DOI: 10.1038/msb.2008.8  1
2007 Mo ML, Jamshidi N, Palsson BØ. A genome-scale, constraint-based approach to systems biology of human metabolism. Molecular Biosystems. 3: 598-603. PMID 17700859 DOI: 10.1039/b705597h  1
2007 Jamshidi N, Vo TD, Palsson BO. In silico analysis of SNPs and other high-throughput data. Methods in Molecular Biology (Clifton, N.J.). 366: 267-85. PMID 17568130 DOI: 10.1007/978-1-59745-030-0_15  0.92
2007 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. 1: 26. PMID 17555602 DOI: 10.1186/1752-0509-1-26  1
2007 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. 104: 1777-82. PMID 17267599 DOI: 10.1073/pnas.0610772104  1
2006 Jamshidi N, Palsson BØ. Systems biology of SNPs. Molecular Systems Biology. 2: 38. PMID 16820779 DOI: 10.1038/msb4100077  1
2006 Jamshidi N, Palsson BØ. Systems biology of the human red blood cell. Blood Cells, Molecules & Diseases. 36: 239-47. PMID 16533612 DOI: 10.1016/j.bcmd.2006.01.006  1
2005 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, ... ... Jamshidi N, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research. 33: 5691-702. PMID 16214803 DOI: 10.1093/nar/gki866  1
2002 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. 12: 1687-92. PMID 12421755 DOI: 10.1101/gr.329302  1
2002 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. 83: 646-62. PMID 12124254 DOI: 10.1016/S0006-3495(02)75198-9  1
2002 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. 23: 1543-50. PMID 12116167 DOI: 10.1002/1522-2683(200205)23:10<1543::AID-ELPS1543>3.0.CO;2-#  0.92
2001 Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BO. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics (Oxford, England). 17: 286-7. PMID 11294796  1
1999 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. 276: H2135-40. PMID 10362697  0.92
1998 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. 95: 4754-9. PMID 9539811 DOI: 10.1073/pnas.95.8.4754  0.92
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