Bold fonts indicate lab members
* denotes co-first authorship
† denotes corresponding authorship
^ denotes co-senior authorship
Halu A†, Decano JL, Matamalas J, Whelan M, Asano T, Kalicharran N, Singh SA, Loscalzo J, Aikawa M†. Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery. BioRxiv preprint doi: 10.1101/2022.12.21.521456
Matamalas JT, Chelvanambi S, Decano JL, França RF, Halu A, Santinelli-Pestana DV, Aikawa E, Malhotra R, Aikawa M. Obesity and age are transmission risk factors for SARS-CoV-2 infection among exposed individuals. PNAS Nexus (in press).
Kılıç A*, Halu A*† , De Marzio M, Maiorino E, Duvall MG, Brüggemann TR, Quintero JJ, Chase R, Mirzakhani H, Sungur AÖ, Koepke J, Nakano T, Peh HY, Krishnamoorthy N, Abdulnour R-E, Georgopoulos K, Litonjua AA, Demay MB, Renz H, Levy BD, Weiss, ST† . Vitamin D constrains inflammation by modulating the expression of key genes on Chr17q12-21.1. eLife. 2024 Apr 3;12:RP89270. PMID: 38567749.
Martini L*, Baek SH*, Lo I, Raby B, Silverman EK, Weiss ST, Glass K^, Halu A^†. Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions. Nucleic Acids Res. 2024 Jan 11;52(1):e5. PMID: 37953325. PMC10783515.
Blaser MC, Buffolo F, Halu A, Turner ME, Schlotter F, Higashi H, Pantano L, Clift CL, Saddic LA, Atkins SK, Rogers MA, Tan Pham, Vromman A, Shvartz E, Sukhova GK, Monticone S, Camussi G, Robson SC, Body SC, Muehlschlegel JD, Singh SA, Aikawa M, Aikawa E. Multiomics of Tissue Extracellular Vesicles Identifies Unique Modulators of Atherosclerosis and Calcific Aortic Valve Stenosis. Circulation. 2023 Aug 22;148(8):661-78. PMID: 37427430. PMC10527599.
Iqbal F, Schlotter F, Becker-Greene D, Lupieri A, Goettsch C, Hutcheson JD, Rogers MA, Itoh S, Halu A, Lee LH and Blaser MC, Mlynarchik AK, Hagita S, Kuraoka S, Chen HY, Engert JC, Passos LSA, Jha PK, Osborn EA, Jaffer FA, Body SC, Robson SC, Thanassoulis G, Aikawa M, Singh SA, Sonawane AR, Aikawa E. Sortilin enhances fibrosis and calcification in aortic valve disease by inducing interstitial cell heterogeneity. European Heart Journal. 2023 Mar 7;44(10):885-98. PMID: 36660854. PMC9991042.
Katsuki S, K. Jha P, Lupieri A, Nakano T, Passos LS, Rogers MA, Becker-Greene D, Le TD, Decano JL, Ho Lee L, Guimaraes GC. Abdelhamid I, Halu A, Muscoloni A, Cannistraci CV, Higashi H, Zhang H, Vromman A, Libby P, Ozaki CK, Sharma A, Singh SA, Aikawa E, Aikawa M. Proprotein convertase subtilisin/kexin 9 (PCSK9) promotes macrophage activation via LDL receptor-independent mechanisms. Circulation Research. 2022 Nov 11;131(11):873-89. PMID: 36263780. PMC9973449.
Decano JL, Iwamoto Y, Goto S, Lee JY, Matamalas JT, Halu A, Blaser M, Lee LH, Pieper B, Chelvanambi S, Silva-Nicolau J, Bartoli-Leonard F, Higashi H, Shibata H, Vyas P, Wang J, Gostjeva E, Body SC, Singh SA, Aikawa M, Aikawa E. A disease-driver population within interstitial cells of human calcific aortic valves identified via single-cell and proteomic profiling. Cell Reports. 2022 Apr 12;39(2):110685. PMID: 35417712.
Morgan S, Lee LH, Halu A, Nicolau JS, Higashi H, Ha AH, Wen JR, Daugherty A, Libby P, Cameron SJ, Mix D, Aikawa E, Owens AP, Singh SA, Aikawa M. Identifying novel mechanisms of abdominal aortic aneurysm via unbiased proteomics and systems biology. Frontiers in Cardiovascular Medicine. 2022 Aug 3:9:889994. PMID: 35990960. PMCID: PMC9382335.
Decano JL, Singh SA, Bueno CG, Lee LH, Halu A, Chelvanambi S, Matamalas JT, Zhang H, Mlynarchik AK, Qiao J, Sharma A, Mukai S, Wang J, Anderson DG, Ozaki CK, Libby P, Aikawa E, Aikawa M. Systems approach to discovery of therapeutic targets for vein graft disease: PPARα pivotally regulates metabolism, activation, and heterogeneity of macrophages and lesion development. Circulation 2021;143(25):2454-70. PMID: 33821665. PMCID: PMC8212880
Rogers MA, Hutcheson JD, Okui T, Goettsch C, Singh SA, Halu A, Schlotter F, Higashi H, Wang L, Whelan MC, Mlynarchik AK, Daugherty A, Nomura M, Aikawa M, Aikawa E. Dynamin-related protein 1 inhibition reduces hepatic PCSK9 secretion. Cardiovascular Research. 2021 Sep 18;117(11):2340-53. PMID: 33523181. PMC8479802
Schlotter F, de Freitas RC, Rogers MA, Blaser MC, Wu PJ, Higashi H, Halu A, Iqbal F, Andraski AB, Rodia CN, Kuraoka S, Wen JR, Creager M, Pham T, Hutcheson JD, Body SC, Kohan AB, Sacks FM, Aikawa M, Singh SA, Aikawa E. ApoC-III is a novel inducer of calcification in human aortic valves. Journal of Biological Chemistry. 2021 Jan 1;296:100193. PMID: 33334888. PMC7948477.
Okui T, Iwashita M, Rogers MA, Halu A, Atkins SK, Kuraoka S, Abdelhamid I, Higashi H, Ramsaroop A, Aikawa M, Singh SA, Aikawa E. CROT (Carnitine O-Octanoyltransferase) Is a Novel Contributing Factor in Vascular Calcification via Promoting Fatty Acid Metabolism and Mitochondrial Dysfunction. Arteriosclerosis, Thrombosis, and Vascular Biology. 2021 Feb;41(2):755-68. PMID: 33356393. PMC8105275
Liu X*, Maiorino E*, Halu A*, Glass K, Prasad RB, Loscalzo J, Gao J, Sharma A. Robustness and lethality in multilayer biological molecular networks. Nature Communications. 2020 Nov 27;11(1):1-2. PMID: 33247151. PMC7699651.
Rogers MA, Buffolo F, Schlotter F, Atkins SK, Lee LH, Halu A, Blaser MC, Tsolaki E, Higashi H, Luther K, Daaboul G, Bouten CVC, Body SC, Singh SA, Bertazzo S, Libby P, Aikawa M, Aikawa E. Annexin A1–dependent tethering promotes extracellular vesicle aggregation revealed with single–extracellular vesicle analysis. Science advances. 2020 Sep 1;6(38):eabb1244. PMID: 32938681. PMC7494353.
Jha PK, Vijay A, Halu A, Uchida S, Aikawa M. Gene Expression Profiling Reveals the Shared and Distinct Transcriptional Signatures in Human Lung Epithelial Cells Infected With SARS-CoV-2, MERS-CoV, or SARS-CoV: Potential Implications in Cardiovascular Complications of COVID-19. Frontiers in cardiovascular medicine. 2020;7:623012. PMID: 33521069. PMC7844200.
Arima N, Sasaki Y, Lee LH, Zhang H, Figueiredo JL, Mlynarchik AK, Qiao J, Yamada I, Higashi H, Ha AH, Halu A, Mizuno K, Singh SA, Yamazaki Y, Aikawa M. Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery. J Proteome Res. 2020 Jan 3;19(1):129-43. PMID: 31661273. PMC7844200.
Halu A, Liu S, Baek SH, Hobbs BD, Hunninghake GM, Cho MH, Silverman EK, Sharma A. Exploring the cross-phenotype network region of disease modules reveals concordant and discordant pathways between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Hum Mol Genet. 2019 Jul 15;28(14):2352-64. PMID: 30997486. PMC6606854.
Halu A, De Domenico M, Arenas A, Sharma A. The multiplex network of human diseases. NPJ Syst Biol Appl. 2019;5:15. doi: 10.1038/s41540-019-0092-5. PMID: 31044086. PMC6478736.
Lee LH, Halu A, Morgan S, Iwata H, Aikawa M, Singh SA. XINA: A Workflow for the Integration of Multiplexed Proteomics Kinetics Data with Network Analysis. J Proteome Res. 2019 Feb 1;18(2):775-81. PMID: 30370770.
Nakano T, Katsuki S, Chen M, Decano JL, Halu A, Lee LH, Pestana DVS, Kum AST, Kuromoto RK, Golden WS, Boff MS, Guimaraes GC, Higashi H, Kauffman KJ, Maejima T, Suzuki T, Iwata H, Barabási AL, Aster JC, Anderson DG, Sharma A, Singh SA, Aikawa E, Aikawa M. Uremic Toxin Indoxyl Sulfate Promotes Proinflammatory Macrophage Activation Via the Interplay of OATP2B1 and Dll4-Notch Signaling. Circulation. 2019 Jan 2;139(1):78-96. PMID: 30586693. PMC6311723.
Gottlieb Sen D, Halu A, Razzaque A, Gorham JM, Hartnett J, Seidman JG, Aikawa E, Seidman CE. The Transcriptional Signature of Growth in Human Fetal Aortic Valve Development. Ann Thorac Surg. 2018 Dec;106(6):1834-40. PMID: 30071238.
Halu A, Wang JG, Iwata H, Mojcher A, Abib AL, Singh SA, Aikawa M, Sharma A. Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. Elife. 2018 Oct 10;7:e37059. PMID: 30303482. PMC6179386.
Schlotter F*, Halu A*, Goto S, Blaser MC, Body SC, Lee LH, Higashi H, DeLaughter DM, Hutcheson JD, Vyas P, Pham T, Rogers MA, Sharma A, Seidman CE, Loscalzo J, Seidman JG, Aikawa M, Singh SA, Aikawa E. Spatiotemporal Multi-Omics Mapping Generates a Molecular Atlas of the Aortic Valve and Reveals Networks Driving Disease. Circulation. 2018 Jul 24;138(4):377-93. PMID: 29588317. PMC6160370.
Sharma A*, Halu A*, Decano JL, Padi M, Liu YY, Prasad RB, Fadista J, Santolini M, Menche J, Weiss ST, Vidal M, Silverman EK, Aikawa M, Barabási AL, Groop L, Loscalzo J. Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. NPJ Syst Biol Appl. 2018;4:25. PMID: 29977601. PMC6028434.
Zhou X*, Lei L*, Liu J*, Halu A*, Zhang Y, Li B, Guo Z, Liu G, Sun C, Loscalzo J, Sharma A, Wang Z. A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks. EBioMedicine. 2018 May;31:79-91. PMID: 29669699. PMC6013753.
De Marinis Y, Sun J, Bompada P, Domènech Omella J, Luan C, Halu A, Renström E, Sharma A, Ridderstråle M. Regulation of Nuclear Receptor Interacting Protein 1 (NRIP1) Gene Expression in Response to Weight Loss and Exercise in Humans. Obesity (Silver Spring). 2017 Aug;25(8):1400-09. PMID: 28656645.
Iwata H, Goettsch C, Sharma A, Ricchiuto P, Goh WW, Halu A, Yamada I, Yoshida H, Hara T, Wei M, Inoue N, Fukuda D, Mojcher A, Mattson PC, Barabási AL, Boothby M, Aikawa E, Singh SA, Aikawa M. PARP9 and PARP14 cross-regulate macrophage activation via STAT1 ADP-ribosylation. Nature Communications. 2016 Oct 31;7:12849. PMID: 27796300. PMC5095532.
Halu A, Scala A, Khiyami A, González MC. Data-driven modeling of solar-powered urban microgrids. Science Advances. 2016 Jan;2(1):e1500700. PMID: 26824071. PMC4730862.
Halu A, Mukherjee S, Bianconi G. Emergence of overlap in ensembles of spatial multiplexes and statistical mechanics of spatial interacting network ensembles. Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jan;89(1):012806. PMID: 24580280.
Halu A, Mondragón RJ, Panzarasa P, Bianconi G. Multiplex PageRank. PLoS One. 2013;8(10):e78293. PMID: 24205186. PMC3813491.
Halu A, Garnerone S, Vezzani A, Bianconi G. Phase transition of light on complex quantum networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb;87(2):022104. PMID: 23496457.
Halu A, Zhao K, Baronchelli A, Bianconi G. Connect and win: The role of social networks in political elections. Europhysics letters. 2013; 102(1):16001. doi: 10.1209/0295-5075/102/16002.
Halu A, Bianconi G. Monochromaticity in neutral evolutionary network models. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Dec;86(6 Pt 2):066101. PMID: 23367998.
Halu A, Ferretti L, Vezzani A, Bianconi G. Phase diagram of the Bose-Hubbard Model on Complex Networks. Europhysics letters. 2012; 99(1):18001. doi: 10.1209/0295-5075/99/18001.
Zhao K, Halu A, Severini S, Bianconi G. Entropy rate of nonequilibrium growing networks. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Dec;84(6 Pt 2):066113. PMID: 22304161.