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1. Full Text Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures
by Zaitsev, K and Bambouskova, M and Swain, A and Artyomov, MN
NATURE COMMUNICATIONS, ISSN 2041-1723, 05/2019, Volume 10, Issue 1, pp. 2209 - 16
Changes in bulk transcriptional profiles of heterogeneous samples often reflect changes in proportions of individual cell types. Several robust techniques have... 
HEAD | EXPRESSION | MULTIDISCIPLINARY SCIENCES | Deconvolution | Composition | Transcription | Experimental design | Bias | Linearity | Cell size | Ribonucleic acid--RNA | Signatures | Design of experiments
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2. Full Text Itaconate: the poster child of metabolic reprogramming in macrophage function
by O’Neill, Luke A. J and Artyomov, Maxim N
Nature Reviews Immunology, ISSN 1474-1733, 05/2019, Volume 19, Issue 5, pp. 273 - 281
Itaconate is one of the best examples of the consequences of metabolic reprogramming during immunity. It is made by diverting aconitate away from the... 
SUCCINATE-DEHYDROGENASE | ACID | NRF2 | PATHWAY | IMPLANTATION | DENDRITIC CELL | MITOCHONDRIA | RECEPTOR | IMMUNE-RESPONSIVE GENE-1 | ISOCITRATE LYASE | IMMUNOLOGY | Physiological aspects | Nuclear reprogramming | Metabolites | Macrophages | Immunological research | Tricarboxylic acid cycle | Cell activation | Immune response | Oxidative metabolism | Tumorigenesis | Interferon | Inflammation | Metabolism | Immunity | Tumors
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3. Full Text Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity
by Jarjour, NN and Schwarzkopf, EA and Bradstreet, TR and Shchukina, I and Lin, CC and Huang, SCC and Lai, CW and Cook, ME and Taneja, R and Stappenbeck, TS and Randolph, GJ and Artyomov, MN and Urban, JF and Edelson, BT
NATURE IMMUNOLOGY, ISSN 1529-2908, 06/2019, Volume 20, Issue 6, pp. 687 - 687
Most tissue-resident macrophage populations develop during embryogenesis, self-renew in the steady state and expand during type 2 immunity. Whether shared... 
REGULATOR | CELLS | TRANSCRIPTION | PERITONEAL | SIGNALS | TUMOR-ASSOCIATED MACROPHAGES | SELF-RENEWAL | STRA13 | IMMUNOLOGY | EXPRESSION | RESIDENT MACROPHAGES | Helicobacter pylori - immunology | Cell Cycle - genetics | Cell Proliferation | Homeodomain Proteins - metabolism | Transcriptome | Monocytes - metabolism | Gene Expression Profiling | Monocytes - immunology | Organ Specificity - immunology | Organ Specificity - genetics | Basic Helix-Loop-Helix Transcription Factors - metabolism | Cell Cycle - immunology | Macrophages - immunology | Basic Helix-Loop-Helix Transcription Factors - genetics | Gene Expression Regulation | Homeostasis - immunology | Macrophages, Peritoneal - immunology | Immunophenotyping | Mice, Transgenic | Helicobacter Infections - immunology | Gene Knockout Techniques | Helicobacter Infections - genetics | Homeodomain Proteins - genetics | Macrophages - metabolism | Animals | Biomarkers | Mice | Macrophages, Peritoneal - metabolism | Immunity - genetics | Homeostasis - genetics | Cell proliferation | Transcription factors | Analysis | Physiological aspects | Homeostasis | Influence | Macrophages | Immunity | c-Maf protein | Gene expression | Tissues | Proteins | Embryonic growth stage | Embryogenesis | PU.1 protein | Interleukin 4 | Cell cycle | Peritoneum
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4. Full Text Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization
by Jha, Abhishek K and Huang, Stanley Ching-Cheng and Sergushichev, Alexey and Lampropoulou, Vicky and Ivanova, Yulia and Loginicheva, Ekaterina and Chmielewski, Karina and Stewart, Kelly M and Ashall, Juliet and Everts, Bart and Pearce, Edward J and Driggers, Edward M and Artyomov, Maxim N
Immunity, ISSN 1074-7613, 03/2015, Volume 42, Issue 3, pp. 419 - 430
Macrophage polarization involves a coordinated metabolic and transcriptional rewiring that is only partially understood. By using an integrated high-throughput... 
IMMUNITY | CELLS | ACTIVATION | INFLAMMATION | NITRIC-OXIDE | INNATE | GLYCOSYLATION | IMMUNOLOGY | Glutamine - deficiency | Aspartic Acid - immunology | Argininosuccinic Acid - immunology | Mitochondria - immunology | Chemokine CCL22 - immunology | Metabolic Networks and Pathways - immunology | Mitochondria - genetics | Argininosuccinic Acid - metabolism | Gene Regulatory Networks - immunology | Isocitrate Dehydrogenase - immunology | Macrophages - immunology | Uridine Diphosphate N-Acetylglucosamine - metabolism | Nitric Oxide - immunology | Macrophages - classification | Aspartate Aminotransferase, Mitochondrial - immunology | Interleukin-6 - genetics | Signal Transduction | Gene Expression Regulation | Isocitrate Dehydrogenase - genetics | Glycosylation | Mitochondria - metabolism | Macrophages - cytology | Immunity, Innate | Citric Acid Cycle | Uridine Diphosphate N-Acetylglucosamine - immunology | Chemokine CCL22 - genetics | Macrophages - metabolism | Metabolic Networks and Pathways - genetics | Animals | Interleukin-6 - immunology | Transcription, Genetic - immunology | Aspartic Acid - metabolism | Mice | Aspartate Aminotransferase, Mitochondrial - genetics | Nitric Oxide - metabolism | Enzymes | Tracers (Biology) | Analysis | Nitric oxide | Physiological aspects | Aspartate | Genetic aspects | Genetic transcription | Macrophages | Glutamine | Metabolites | Rodents | Scientific imaging | Metabolism | Labeling | Mass spectrometry
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5. Full Text Tumor neoantigens: Building a framework for personalized cancer immunotherapy
by Gubin, Matthew M and Artyomov, Maxim N and Mardis, Elaine R and Schreiber, Robert D
Journal of Clinical Investigation, ISSN 0021-9738, 09/2015, Volume 125, Issue 9, pp. 3413 - 3421
It is now well established that the immune system can recognize developing cancers and that therapeutic manipulation of immunity can induce tumor regression.... 
MEDICINE, RESEARCH & EXPERIMENTAL | CELLS | IN-VITRO | MELANOMA | PEPTIDE BINDING PREDICTION | CANCER/TESTIS ANTIGENS | IMMUNE-RESPONSES | GENERATION | BLOCKADE | T-LYMPHOCYTE | EPITOPES | Antigens, Neoplasm - genetics | Immunotherapy - methods | Immunity, Cellular - genetics | Antigens, Neoplasm - immunology | Humans | Epitopes - genetics | Epitopes - immunology | Neoplasms - therapy | Immunity, Cellular - drug effects | Neoplasms - genetics | Antigens, Neoplasm - therapeutic use | Epigenesis, Genetic - immunology | Neoplasms - immunology | T-Lymphocytes - immunology | Epigenesis, Genetic - drug effects | High-Throughput Nucleotide Sequencing | Mutation | Neoplasms - pathology | Epitopes - therapeutic use | Precision Medicine - methods | Antigens | T cell receptors | Immunotherapy | Review Series
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6. Full Text Tumor neoantigens: building a framework for personalized cancer immunotherapy
by Gubin, Matthew M and Artyomov, Maxim N and Mardis, Elaine R and Schreiber, Robert D
Journal of Clinical Investigation, ISSN 0021-9738, 09/2015, Volume 125, Issue 9, p. 3413
Research | Health aspects | Tumor antigens | Immunotherapy
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7. Tumor neoantigens: building a framework for personalized cancer immunotherapy
by Gubin, Matthew M and Artyomov, Maxim N and Mardis, Elaine R and Schreiber, Robert D
Journal of Clinical Investigation, ISSN 0021-9738, 09/2015, Volume 125, Issue 9, pp. 3413 - 3413
It is now well established that the immune system can recognize developing cancers and that therapeutic manipulation of immunity can induce tumor regression.... 
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8. Full Text Leveraging existing data sets to generate new insights into Alzheimer's disease biology in specific patient subsets
by Fowler, Kevin D and Funt, Jason M and Artyomov, Maxim N and Zeskind, Benjamin and Kolitz, Sarah E and Towfic, Fadi
Scientific Reports, ISSN 2045-2322, 09/2015, Volume 5, p. 14324
To generate new insights into the biology of Alzheimer's Disease (AD), we developed methods to combine and reuse a wide variety of existing data sets in new... 
OXIDATIVE STRESS | MICE MODEL | PROTEIN | PROBE LEVEL | MULTIDISCIPLINARY SCIENCES | CONNECTIVITY MAP | CANDIDATE GENES | RNA-BINDING-SITES | EXPRESSION | BRAIN | BETA | Synaptosomal-Associated Protein 25 - genetics | Genetic Predisposition to Disease | Apolipoprotein E4 - metabolism | Basic Helix-Loop-Helix Transcription Factors - genetics | Gene Expression Regulation - genetics | Humans | Alzheimer Disease - drug therapy | Male | Algorithms | Databases, Protein | Sex Factors | Polymorphism, Single Nucleotide - genetics | Female | Alzheimer Disease - genetics | Datasets | Apolipoprotein E4 | Neurodegenerative diseases | Neural networks | Data processing | SNAP-25 protein | Single-nucleotide polymorphism | Gene expression | Alzheimers disease | Alzheimer's disease
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9. Full Text Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
by Campbell, Joshua D and Alexandrov, Anton and Kim, Jaegil and Wala, Jeremiah and Berger, Alice H and Pedamallu, Chandra Sekhar and Shukla, Sachet A and Guo, Guangwu and Brooks, Angela N and Murray, Bradley A and Imielinski, Marcin and Hu, Xin and Ling, Shiyun and Akbani, Rehan and Rosenberg, Mara and Cibulskis, Carrie and Ramachandran, Aruna and Collisson, Eric A and Kwiatkowski, David J and Lawrence, Michael S and Weinstein, John N and Verhaak, Roel G.W and Wu, Catherine J and Hammerman, Peter S and Cherniack, Andrew D and Getz, Gad and Artyomov, Maxim N and Schreiber, Robert and Govindan, Ramaswamy and Meyerson, Matthew and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Nature Genetics, ISSN 1061-4036, 06/2016, Volume 48, Issue 6, pp. 607 - 616
To compare lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) and to identify new drivers of lung carcinogenesis, we examined the exome... 
HETEROGENEITY | MUTATIONAL PROCESSES | LANDSCAPE | QUANTIFICATION | KINASE | GENETICS & HEREDITY | IDENTIFICATION | CANCER | EXPRESSION | DRIVER MUTATIONS | PREDICTION | Lung Neoplasms - genetics | Recurrence | Antigens, Neoplasm | Carcinoma, Squamous Cell - genetics | Humans | Adenocarcinoma - genetics | Genome, Human | DNA Copy Number Variations | Adenocarcinoma | Usage | Squamous cell carcinoma | Nucleotide sequencing | Risk factors | DNA sequencing | Genomics | Lung cancer | Colleges & universities | Quality control | Defense contracts | Genomes | Mutation | Grants | Signatures | Tumors | Smoking | Index Medicus
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10. Full Text Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens
by Gubin, Matthew M and Zhang, Xiuli and Schuster, Heiko and Caron, Etienne and Ward, Jeffrey P and Noguchi, Takuro and Ivanova, Yulia and Hundal, Jasreet and Arthur, Cora D and Krebber, Willem-Jan and Mulder, Gwenn E and Toebes, Mireille and Vesely, Matthew D and Lam, Samuel S.K and Korman, Alan J and Allison, James P and Freeman, Gordon J and Sharpe, Arlene H and Pearce, Erika L and Schumacher, Ton N and Aebersold, Ruedi and Rammensee, Hans-Georg and Melief, Cornelis J.M and Mardis, Elaine R and Gillanders, William E and Artyomov, Maxim N and Schreiber, Robert D
Nature, ISSN 0028-0836, 11/2014, Volume 515, Issue 7528, pp. 577 - 581
The immune system influences the fate of developing cancers by not only functioning as a tumour promoter that facilitates cellular transformation, promotes... 
IMMUNITY | RESPONSES | IMMUNOGENICITY | MELANOMA | QUANTITATIVE PROTEOMICS | INFLAMMATION | MULTIDISCIPLINARY SCIENCES | EQUILIBRIUM | PD-1 | EXOME ANALYSIS REVEALS | T-CELLS | Antigens, Neoplasm - genetics | Sarcoma - immunology | Antigens, Neoplasm - immunology | Antibodies, Monoclonal - therapeutic use | Male | Vaccines, Synthetic - therapeutic use | Epitopes - genetics | Sarcoma - therapy | Cancer Vaccines - therapeutic use | Animals | Immunotherapy | Mice | CD8-Positive T-Lymphocytes - immunology | Cell Cycle Checkpoints - immunology | Care and treatment | Sarcoma | Analysis | Development and progression | Drug therapy | Health aspects | Antigenic determinants | Cancer | Antigens | Peptides | Lymphocytes | Mutation | Tumors
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11. Full Text Cell-intrinsic lysosomal lipolysis is essential for alternative activation of macrophages
by Huang, Stanley Ching-Cheng and Everts, Bart and Ivanova, Yulia and O'Sullivan, David and Nascimento, Marcia and Smith, Amber M and Beatty, Wandy and Love-Gregory, Latisha and Lam, Wing Y and O'Neill, Christina M and Yan, Cong and Du, Hong and Abumrad, Nada A and Urban, Joseph F and Artyomov, Maxim N and Pearce, Erika L and Pearce, Edward J
Nature Immunology, ISSN 1529-2908, 2014, Volume 15, Issue 9, pp. 846 - 855
Alternative (M2) activation of macrophages driven via the a-chain of the receptor for interleukin 4 (IL-4R alpha) is important for immunity to parasites, wound... 
REGULATES LIPID-METABOLISM | INFLAMMATION | IN-VIVO | DISEASE | GENE-EXPRESSION | ATHEROSCLEROSIS | MICE | DIFFERENTIATION | IMMUNOLOGY | ACID LIPASE | FOAM CELLS | Macrophage Activation - immunology | Humans | Oxidative Phosphorylation | Oxygen Consumption | Transcriptome | CD36 Antigens - immunology | Lipolysis - immunology | Receptors, Interleukin-4 - immunology | Sterol Esterase - immunology | Interleukin-4 - immunology | Signal Transduction - immunology | Animals | Cell Respiration | Helminthiasis, Animal - immunology | Mice | Fatty Acids - metabolism | Lysosomes - immunology | Macrophages - immunology | Lysosomes | Research | Macrophages | Cell transformation | Lipolysis
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12. Full Text Exact Identification of Topologically Essential Interactions in the Networks Derived from Perturbation Experiments
by Artyomov, Maxim N and Leite, Ana Paula and Regev, Aviv
Biophysical Journal, ISSN 0006-3495, 2011, Volume 100, Issue 3, pp. 32a - 32a
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13. Full Text Itaconate Links Inhibition of Succinate Dehydrogenase with Macrophage Metabolic Remodeling and Regulation of Inflammation
by Lampropoulou, Vicky and Sergushichev, Alexey and Bambouskova, Monika and Nair, Sharmila and Vincent, Emma E and Loginicheva, Ekaterina and Cervantes-Barragan, Luisa and Ma, Xiucui and Huang, Stanley Ching-Cheng and Griss, Takla and Weinheimer, Carla J and Khader, Shabaana and Randolph, Gwendalyn J and Pearce, Edward J and Jones, Russell G and Diwan, Abhinav and Diamond, Michael S and Artyomov, Maxim N
Cell Metabolism, ISSN 1550-4131, 07/2016, Volume 24, Issue 1, pp. 158 - 166
Remodeling of the tricarboxylic acid (TCA) cycle is a metabolic adaptation accompanying inflammatory macrophage activation. During this process, endogenous... 
IMMUNITY | CELLS | ACTIVATION | ACID | INTEGRATION | ENDOCRINOLOGY & METABOLISM | INJURY | NLRP3 INFLAMMASOME | EXPRESSION | CELL BIOLOGY | Inflammation - pathology | Reactive Oxygen Species - metabolism | Macrophages - pathology | Reperfusion Injury - pathology | Reperfusion Injury - enzymology | Succinate Dehydrogenase - antagonists & inhibitors | Mice, Inbred C57BL | Mitochondria - metabolism | Mitochondria - drug effects | Macrophages - enzymology | Macrophages - metabolism | Animals | Succinic Acid - metabolism | Cell Respiration - drug effects | Lipopolysaccharides - pharmacology | Female | Macrophages - drug effects | Succinate Dehydrogenase - metabolism | Macrophage Activation - drug effects | Inflammation - enzymology | Succinates - pharmacology | Medical colleges | Inflammation | Metabolites | Macrophages
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14. Full Text TLR-driven early glycolytic reprogramming via the kinases TBK1-IKK[epsilon] supports the anabolic demands of dendritic cell activation
by Everts, Bart and Amiel, Eyal and Huang, Stanley Ching-Cheng and Smith, Amber M and Chang, Chih-Hao and Lam, Wing Y and Redmann, Veronika and Freitas, Tori C and Blagih, Julianna and van der Windt, Gerritje J.W and Artyomov, Maxim N and Jones, Russell G and Pearce, Erika L and Pearce, Edward J
Nature Immunology, ISSN 1529-2908, 04/2014, Volume 15, Issue 4, pp. 323 - 332
  The ligation of Toll-like receptors (TLRs) leads to rapid activation of dendritic cells (DCs). However, the metabolic requirements that support this process... 
Dendritic cells | Cellular control mechanisms | Toll-like receptors | Physiological aspects | Physiological research | Research | Properties
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15. Full Text Comment on "reciprocal relations for nonlinear coupled transport"
by Artyomov, Maxim N
Physical Review Letters, ISSN 0031-9007, 04/2009, Volume 102, Issue 14, p. 149701; discussion 149702
A Comment on the Letter by R. Dean Astumian, [Phys. Rev. Lett. 101, 046802 (2008)]. The author of the Letter offers a Reply. 
PHYSICS, MULTIDISCIPLINARY
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