Full Text Journal Articles by
Author Neema Jamshidi

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Inline balloon-assisted vascular sheath fragment removal.

Neema Jamshidi, Jason Chiang,

BACKGROUND:Unretrievable foreign bodies are associated with high morbidity and mortality. While the majority of reported cases involve the venous circulation, intra-arterial foreign body displacement have the potential to migrate more distally with a higher risk for dissection and hemorrhagic complications during retrieval. As the number of intravascular procedures continues to ... Read more >>

CVIR Endovasc (CVIR endovascular)
[2020, 3(1):53]

Cited: 0 times

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Metabolome Changes during In Vivo Red Cell Aging Reveal Disruption of Key Metabolic Pathways.

Neema Jamshidi, Xiuling Xu, Katharina von Löhneysen, Katrin Soldau, Rob P Mohney, Edward D Karoly, Mike Scott, Jeffrey S Friedman,

Understanding the mechanisms for cellular aging is a fundamental question in biology. Normal red blood cells (RBCs) survive for approximately 100 days, and their survival is likely limited by functional decline secondary to cumulative damage to cell constituents, which may be reflected in altered metabolic capabilities. To investigate metabolic changes during ... Read more >>

iScience (iScience)
[2020, 23(10):101630]

Cited: 0 times

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Transcatheter Embolization of Renal-Splenic Shunt to Treat Hematemesis.

Neema Jamshidi, Stephen T Kee,

Although sequelae of chronic liver disease are the most common causes of altered pressure dynamics in the portal and splanchnic circulations, there are other mechanisms resulting in increased venous pressures with subsequent development of splenic and gastric varices. We report a case of a patient without portal hypertension, but with ... Read more >>

Cardiovasc Intervent Radiol (Cardiovascular and interventional radiology)
[2020, 43(11):1708-1711]

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PK Papyrus Coronary Stent for the Treatment of Diminutive and Tortuous Visceral Artery Pseudoaneurysms.

Neema Jamshidi,

Cardiovasc Intervent Radiol (Cardiovascular and interventional radiology)
[2020, 43(7):1097-1098]

Cited: 0 times

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Correction: Evaluation of the predictive ability of ultrasound-based assessment of breast cancer using BI-RADS natural language reporting against commercial transcriptome-based tests.

Neema Jamshidi, Jason Chang, Kyle Mock, Brian Nguyen, Christine Dauphine, Michael D Kuo,

[This corrects the article DOI: 10.1371/journal.pone.0226634.]. ... Read more >>

PLoS One (PloS one)
[2020, 15(2):e0229584]

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Insights into Dynamic Network States Using Metabolomic Data.

Reihaneh Mostolizadeh, Andreas Dräger, Neema Jamshidi,

Metabolomic data is the youngest of the high-throughput data types; however, it is potentially one of the most informative, as it provides a direct, quantitative biochemical phenotype. There are a number of ways in which metabolomic data can be analyzed in systems biology; however, the thermodynamic and kinetic relevance of ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2019, 1978:243-258]

Cited: 0 times

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Radiomics and radiogenomics of primary liver cancers.

Woo Kyoung Jeong, Neema Jamshidi, Ely Richard Felker, Steven Satish Raman, David Shinkuo Lu,

Concurrent advancements in imaging and genomic biomarkers have created opportunities to identify non-invasive imaging surrogates of molecular phenotypes. In order to develop such imaging surrogates radiomics and radiogenomics/imaging genomics will be necessary; there has been consistent progress in these fields for primary liver cancers. In this article we evaluate the ... Read more >>

Clin Mol Hepatol (Clinical and molecular hepatology)
[2019, 25(1):21-29]

Cited: 5 times

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Receptor-based Surrogate Subtypes and Discrepancies with Breast Cancer Intrinsic Subtypes: Implications for Image Biomarker Development.

Neema Jamshidi, Shota Yamamoto, Jeffrey Gornbein, Michael D Kuo,

Purpose To determine the concordance and accuracy of imaging surrogates of immunohistochemical (IHC) markers and the molecular classification of breast cancer. Materials and Methods A total of 3050 patients from 17 public breast cancer data sets containing IHC marker receptor status (estrogen receptor/progesterone receptor/human epidermal growth factor receptor 2 [HER2]) ... Read more >>

Radiology (Radiology)
[2018, 289(1):210-217]

Cited: 0 times

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Integrated Host-Pathogen Metabolic Reconstructions.

Anu Raghunathan, Neema Jamshidi,

The science and art of Genome scale metabolic network reconstructions have been explicitly documented in the literature for organisms across all the three kingdoms of life. Constraints-based models derived from such reconstructions have been used to assess metabolic phenotypes of their complex connections to genotype accurately. The problem of infectious ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2018, 1716:197-217]

Cited: 1 time

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Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

Alyaa M Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O Palsson, Nathan E Lewis, Neema Jamshidi,

Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale metabolic models (GeMMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, ... Read more >>

PLoS Comput. Biol. (PLoS computational biology)
[2018, 14(1):e1005895]

Cited: 4 times

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The Emerging Facets of Non-Cancerous Warburg Effect.

Alyaa M Abdel-Haleem, Nathan E Lewis, Neema Jamshidi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori,

The Warburg effect (WE), or aerobic glycolysis, is commonly recognized as a hallmark of cancer and has been extensively studied for potential anti-cancer therapeutics development. Beyond cancer, the WE plays an important role in many other cell types involved in immunity, angiogenesis, pluripotency, and infection by pathogens (e.g., malaria). Here, ... Read more >>

Front Endocrinol (Lausanne) (Frontiers in endocrinology)
[2017, 8:279]

Cited: 10 times

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Multiregional Radiogenomic Assessment of Prostate Microenvironments with Multiparametric MR Imaging and DNA Whole-Exome Sequencing of Prostate Glands with Adenocarcinoma.

Neema Jamshidi, Daniel J Margolis, Steven Raman, Jiaoti Huang, Robert E Reiter, Michael D Kuo,

Purpose To assess the underlying genomic variation of prostate gland microenvironments of patients with prostate adenocarcinoma in the context of colocalized multiparametric magnetic resonance (MR) imaging and histopathologic assessment of normal and abnormal regions by using whole-exome sequencing. Materials and Methods Six patients with prostate adenocarcinoma who underwent robotic prostatectomy ... Read more >>

Radiology (Radiology)
[2017, 284(1):109-119]

Cited: 7 times

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Quality of Radiomic Features in Glioblastoma Multiforme: Impact of Semi-Automated Tumor Segmentation Software.

Myungeun Lee, Boyeong Woo, Michael D Kuo, Neema Jamshidi, Jong Hyo Kim,

The purpose of this study was to evaluate the reliability and quality of radiomic features in glioblastoma multiforme (GBM) derived from tumor volumes obtained with semi-automated tumor segmentation software.MR images of 45 GBM patients (29 males, 16 females) were downloaded from The Cancer Imaging Archive, in which post-contrast T1-weighted imaging ... Read more >>

Korean J Radiol (Korean journal of radiology)
[2017, 18(3):498-509]

Cited: 5 times

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Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.

Daniel C Zielinski, Neema Jamshidi, Austin J Corbett, Aarash Bordbar, Alex Thomas, Bernhard O Palsson,

Malignant transformation is often accompanied by significant metabolic changes. To identify drivers underlying these changes, we calculated metabolic flux states for the NCI60 cell line collection and correlated the variance between metabolic states of these lines with their other properties. The analysis revealed a remarkably consistent structure underlying high flux ... Read more >>

Sci Rep (Scientific reports)
[2017, 7:41241]

Cited: 22 times

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Genomic Adequacy from Solid Tumor Core Needle Biopsies of ex Vivo Tissue and in Vivo Lung Masses: Prospective Study.

Neema Jamshidi, Danshan Huang, Fereidoun G Abtin, Christopher T Loh, Stephen T Kee, Robert D Suh, Shota Yamamoto, Kingshuk Das, Sarah Dry, Scott Binder, Dieter R Enzmann, Michael D Kuo,

Purpose To identify the variables and factors that affect the quantity and quality of nucleic acid yields from imaging-guided core needle biopsy. Materials and Methods This study was approved by the institutional review board and compliant with HIPAA. The authors prospectively obtained 232 biopsy specimens from 74 patients (177 ex ... Read more >>

Radiology (Radiology)
[2017, 282(3):903-912]

Cited: 5 times

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An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network.

Henry C Liu, Neema Jamshidi, Yuchen Chen, Satish A Eraly, Sai Yee Cho, Vibha Bhatnagar, Wei Wu, Kevin T Bush, Ruben Abagyan, Bernhard O Palsson, Sanjay K Nigam,

There has been a recent interest in the broader physiological importance of multispecific "drug" transporters of the SLC and ABC transporter families. Here, a novel multi-tiered systems biology approach was used to predict metabolites and signaling molecules potentially affected by the in vivo deletion of organic anion transporter 1 (Oat1, ... Read more >>

J Biol Chem (The Journal of biological chemistry)
[2016, 291(37):19474-19486]

Cited: 10 times

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Transcriptome profiling reveals novel gene expression signatures and regulating transcription factors of TGFβ-induced epithelial-to-mesenchymal transition.

Liutao Du, Shota Yamamoto, Barry L Burnette, Danshang Huang, Kun Gao, Neema Jamshidi, Michael D Kuo,

Dysregulated epithelial to mesenchymal transition (EMT) in cancer cells endows invasive and metastatic properties upon cancer cells that favor successful colonization of distal target organs and therefore play a critical role in transforming early-stage carcinomas into invasive malignancies. EMT has also been associated with tumor recurrence and drug resistance and ... Read more >>

Cancer Med (Cancer medicine)
[2016, 5(8):1962-1972]

Cited: 10 times

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Radiogenomic Analysis Demonstrates Associations between (18)F-Fluoro-2-Deoxyglucose PET, Prognosis, and Epithelial-Mesenchymal Transition in Non-Small Cell Lung Cancer.

Shota Yamamoto, Danshan Huang, Liutao Du, Ronald L Korn, Neema Jamshidi, Barry L Burnette, Michael D Kuo,

Purpose To investigate whether non-small cell lung cancer (NSCLC) tumors that express high normalized maximum standardized uptake value (SUVmax) are associated with a more epithelial-mesenchymal transition (EMT)-like phenotype. Materials and Methods In this institutional review board-approved study, a public NSCLC data set that contained fluorine 18 ((18)F) fluoro-2-deoxyglucose positron emission ... Read more >>

Radiology (Radiology)
[2016, 280(1):261-270]

Cited: 11 times

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Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics.

Aarash Bordbar, Douglas McCloskey, Daniel C Zielinski, Nikolaus Sonnenschein, Neema Jamshidi, Bernhard O Palsson,

Understanding individual variation is fundamental to personalized medicine. Yet interpreting complex phenotype data, such as multi-compartment metabolomic profiles, in the context of genotype data for an individual is complicated by interactions within and between cells and remains an unresolved challenge. Here, we constructed multi-omic, data-driven, personalized whole-cell kinetic models of erythrocyte ... Read more >>

Cell Syst (Cell systems)
[2015, 1(4):283-292]

Cited: 31 times

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The radiogenomic risk score stratifies outcomes in a renal cell cancer phase 2 clinical trial.

Neema Jamshidi, Eric Jonasch, Matthew Zapala, Ronald L Korn, James D Brooks, Borje Ljungberg, Michael D Kuo,

OBJECTIVES:To characterize a radiogenomic risk score (RRS), a previously defined biomarker, and to evaluate its potential for stratifying radiological progression-free survival (rPFS) in patients with metastatic renal cell carcinoma (mRCC) undergoing pre-surgical treatment with bevacizumab. METHODOLOGY:In this IRB-approved study, prospective imaging analysis of the RRS was performed on phase II ... Read more >>

Eur Radiol (European radiology)
[2016, 26(8):2798-2807]

Cited: 15 times

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Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods.

Neema Jamshidi, Anu Raghunathan,

Constraint-based models have become popular methods for systems biology as they enable the integration of complex, disparate datasets in a biologically cohesive framework that also supports the description of biological processes in terms of basic physicochemical constraints and relationships. The scope, scale, and application of genome scale models have grown ... Read more >>

(Frontiers in microbiology)
[2015, 6:1032]

Cited: 4 times

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Do genome-scale models need exact solvers or clearer standards?

Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P Burgard, Roger L Chang, Andreas Dräger, Iman Famili, Adam M Feist, Ronan Mt Fleming, Stephen S Fong, Vassily Hatzimanikatis, Markus J Herrgård, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A Lerman, Nathan E Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Nathan D Price, Jennifer L Reed, Michael Saunders, Ryan S Senger, Nikolaus Sonnenschein, Yuekai Sun, Ines Thiele,

Mol. Syst. Biol. (Molecular systems biology)
[2015, 11(10):831]

Cited: 19 times

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Transcriptome-based reconstructions from the murine knockout suggest involvement of the urate transporter, URAT1 (slc22a12), in novel metabolic pathways.

Satish A Eraly, Henry C Liu, Neema Jamshidi, Sanjay K Nigam,

URAT1 (slc22a12) was identified as the transporter responsible for renal reabsorption of the medically important compound, uric acid. However, subsequent studies have indicated that other transporters make contributions to this process, and that URAT1 transports other organic anions besides urate (including several in common with the closely related multi-specific renal ... Read more >>

Biochem Biophys Rep (Biochemistry and biophysics reports)
[2015, 3:51-61]

Cited: 3 times

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Systems analysis of host-parasite interactions.

Justine Swann, Neema Jamshidi, Nathan E Lewis, Elizabeth A Winzeler,

Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug-resistant parasites necessitates that the research community take an active role ... Read more >>

Wiley Interdiscip Rev Syst Biol Med (Wiley interdisciplinary reviews. Systems biology and medicine)
[2015, 7(6):381-400]

Cited: 9 times

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The Radiogenomic Risk Score: Construction of a Prognostic Quantitative, Noninvasive Image-based Molecular Assay for Renal Cell Carcinoma.

Neema Jamshidi, Eric Jonasch, Matthew Zapala, Ronald L Korn, Lejla Aganovic, Hongjuan Zhao, Raviprakash Tumkur Sitaram, Robert J Tibshirani, Sudeep Banerjee, James D Brooks, Borje Ljungberg, Michael D Kuo,

To evaluate the feasibility of constructing radiogenomic-based surrogates of molecular assays (SOMAs) in patients with clear-cell renal cell carcinoma (CCRCC) by using data extracted from a single computed tomographic (CT) image.In this institutional review board approved study, gene expression profile data and contrast material-enhanced CT images from 70 patients with ... Read more >>

Radiology (Radiology)
[2015, 277(1):114-123]

Cited: 27 times

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