Medical College of Wisconsin
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Publications indexed to the term Metabolic Networks and Pathways

1Global mapping of glycosylation pathways in human-derived cells. (Huang YF, Aoki K, Akase S, Ishihara M, Liu YS, Yang G, Kizuka Y, Mizumoto S, Tiemeyer M, Gao XD, Aoki-Kinoshita KF, Fujita M) Dev Cell 2021 Apr 19;56(8):1195-1209.e7       37 Citations
1Novel targeted therapies for the management of liver fibrosis. (Trivella JP, Martin P, Carrion AF) Expert Opin Emerg Drugs 2020 Mar;25(1):59-70       13 Citations
2Pathway and network analysis of more than 2500 whole cancer genomes. (Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ, PCAWG Consortium) Nat Commun 2020 Feb 05;11(1):729       62 Citations
2Integrative pathway enrichment analysis of multivariate omics data. (Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group, Reimand J, PCAWG Consortium) Nat Commun 2020 Feb 05;11(1):735       93 Citations
1Chewing the Fat: The Conserved Ability of DNA Viruses to Hijack Cellular Lipid Metabolism. (Lange PT, Lagunoff M, Tarakanova VL) Viruses 2019 Jan 29;11(2)       28 Citations
2Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. (Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C) Cell Rep 2018 Apr 03;23(1):194-212.e6       213 Citations
1Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. (Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H, Cancer Genome Atlas Research Network, Piwnica-Worms H, Ma L, Liang H) Cell Rep 2018 Apr 03;23(1):213-226.e3       72 Citations
1Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. (Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, Cancer Genome Atlas Research Network, Bathe OF, Liang H) Cell Rep 2018 Apr 03;23(1):255-269.e4       171 Citations
3Transcriptomic analysis reveals inflammatory and metabolic pathways that are regulated by renal perfusion pressure in the outer medulla of Dahl-S rats. (Evans LC, Dayton A, Yang C, Liu P, Kurth T, Ahn KW, Komas S, Stingo FC, Laud PW, Vannucci M, Liang M, Cowley AW Jr) Physiol Genomics 2018 Jun 01;50(6):440-447       10 Citations
1T-Cell Metabolism in Hematopoietic Cell Transplantation. (Nguyen HD, Kuril S, Bastian D, Yu XZ) Front Immunol 2018;9:176       26 Citations
1Conceptual and Experimental Tools to Understand Spatial Effects and Transport Phenomena in Nonlinear Biochemical Networks Illustrated with Patchy Switching. (Pompano RR, Chiang AH, Kastrup CJ, Ismagilov RF) Annu Rev Biochem 2017 Jun 20;86:333-356       8 Citations
1Teaching the basics of cancer metabolism: Developing antitumor strategies by exploiting the differences between normal and cancer cell metabolism. (Kalyanaraman B) Redox Biol 2017 Aug;12:833-842       145 Citations
2Abnormalities in Functional Connectivity in Collegiate Football Athletes with and without a Concussion History: Implications and Role of Neuroactive Kynurenine Pathway Metabolites. (Meier TB, Lancaster MA, Mayer AR, Teague TK, Savitz J) J Neurotrauma 2017 Feb 15;34(4):824-837       18 Citations
1Sequence and expression variations in 23 genes involved in mitochondrial and non-mitochondrial apoptotic pathways and risk of oral leukoplakia and cancer. (Datta S, Ray A, Singh R, Mondal P, Basu A, De Sarkar N, Majumder M, Maiti G, Baral A, Jha GN, Mukhopadhyay I, Panda C, Chowdhury S, Ghosh S, Roychoudhury S, Roy B) Mitochondrion 2015 Nov;25:28-33       11 Citations
4Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease. (Petri V, Hayman GT, Tutaj M, Smith JR, Laulederkind SJ, Wang SJ, Nigam R, De Pons J, Shimoyama M, Dwinell MR, Worthey EA, Jacob HJ) Hum Genomics 2014 Sep 30;8(1):17       7 Citations
1A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies. (Chang LC, Jamain S, Lin CW, Rujescu D, Tseng GC, Sibille E) PLoS One 2014;9(3):e90980       77 Citations
1The NADPH metabolic network regulates human αB-crystallin cardiomyopathy and reductive stress in Drosophila melanogaster. (Xie HB, Cammarato A, Rajasekaran NS, Zhang H, Suggs JA, Lin HC, Bernstein SI, Benjamin IJ, Golic KG) PLoS Genet 2013 Jun;9(6):e1003544       23 Citations
2The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information. (Hayman GT, Jayaraman P, Petri V, Tutaj M, Liu W, De Pons J, Dwinell MR, Shimoyama M) Hum Genomics 2013 Feb 05;7(1):4       7 Citations
1Xenocin export by the flagellar type III pathway in Xenorhabdus nematophila. (Singh P, Park D, Forst S, Banerjee N) J Bacteriol 2013 Apr;195(7):1400-10       9 Citations
1PathCase-SB: integrating data sources and providing tools for systems biology research. (Coskun SA, Qi X, Cakmak A, Cheng E, Cicek AE, Yang L, Jadeja R, Dash RK, Lai N, Ozsoyoglu G, Ozsoyoglu ZM) BMC Syst Biol 2012 Jun 14;6(1):67       6 Citations
1The retinoblastoma tumor suppressor regulates a xenobiotic detoxification pathway. (Sáenz Robles MT, Case A, Chong JL, Leone G, Pipas JM) PLoS One 2011;6(10):e26019       5 Citations
1Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation. (Schlüter A, Ruiz-Trillo I, Pujol A) PLoS One 2011;6(7):e21989       6 Citations
1Primers on molecular pathways--caspase pathway. (Lomberk G, Urrutia R) Pancreatology 2009;9(1-2):6-8       6 Citations
1Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multi-scale, top-down integrated model. (Dash RK, Li Y, Kim J, Beard DA, Saidel GM, Cabrera ME) PLoS One 2008 Sep 09;3(9):e3168       24 Citations
1Modeling of cellular metabolism and microcirculatory transport. (Beard DA, Wu F, Cabrera ME, Dash RK) Microcirculation 2008 Nov;15(8):777-93       15 Citations
1High perfusion pressure accelerates renal injury in salt-sensitive hypertension. (Mori T, Polichnowski A, Glocka P, Kaldunski M, Ohsaki Y, Liang M, Cowley AW Jr) J Am Soc Nephrol 2008 Aug;19(8):1472-82       89 Citations
1Primers on molecular pathways--notch. (Lomberk G, Urrutia R) Pancreatology 2008;8(2):103-4       6 Citations