List of publications

List of Publications

I. Peer-Reviewed Journals

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69. Candia J, mutSigMapper: an R package to map spectra to mutational signatures based on shot-noise modeling, bioRxiv 2020.10.12.336404 (under review).

68. Wang L, Candia J, Ma L, Zhao Y, Imberti L, Sottini A, Dobbs K, Delmonte O, Forgues M, Liu H, Matthews H, Shaw E, Stack M, Weber S, Zhang Y, Lisco A, Sereti I, Su H, Notarangelo L, Wang XW, Serological Responses to Human Virome Define Clinical Outcomes of Italian Patients Infected with SARS-CoV-2, medRxiv 2020.09.04.20187088 (under review).

67. Tanaka T, Landino K, Fantoni G, Candia J, Bandinelli S, Ferrucci L, Plasma proteomic signature of frailty syndrome (under review).

66. Ma L, Wang L, Chang C-W, Heinrich S, Dominguez D, Forgues M, Candia J, Hernandez MO, Kelly M, Zhao Y, Tran B, Hernandez JM, Davis JL, Kleiner DE, Wood BJ, Greten TF, Wang XW, Single-Cell Atlas of Tumor Clonal Evolution in Liver Cancer, bioRxiv 2020.08.18.254748 (under review).

65. Roberts JA, Varma VR, An Y, Varma S, Candia J, Fantoni G, Moaddel R, Khadeer M, Lovett J, Tanaka T, Pletnikova O, Troncoso JC, Bennett DA, Albert MS, Resnick SM, Ferrucci L, Thambisetty M, A Brain Proteomic Signature of Incipient Alzheimer's Disease in Young APOE ε4 Carriers (under review).

64. Han K, Singh K, Rodman MJ, Hassanzadeh S, Baumer Y, Huffstutler RD, Chen J, Candia J, Cheung F, Stagliano KER, Pirooznia M, Powell-Wiley TM, Sack MN, Identification and Validation of Nutrient State-Dependent Serum Protein Mediators of Human CD4+ T Cell Responsiveness, Nutrients 13:1492 (2021).

63. Matsuda K, Migueles SA, Huang J, Bolkhovitinov L, Stuccio S, Griesman T, Pullano AA, Kang BH, Ishida E, Zimmerman M, Kashyap N, Martins KM, Stadlbauer D, Pederson J, Patamawenu A, Wright N, Shofner T, Evans S, Liang CJ, Candia J, Biancotto A, Fantoni G, Poole A, Smith J, Alexander J, Gurwith M, Krammer F, Connors M, A Replication Competent Adenovirus-Vectored Influenza Vaccine Induces Durable Systemic and Mucosal Immunity, Journal of Clinical Investigation 131:e140794 (2021).

62. Zampino M, Tanaka T, Ubaida-Mohien C, Fantoni G, Candia J, Semba R, Ferrucci L, A plasma proteomic signature of skeletal muscle mitochondrial function, International Journal of Molecular Sciences 21:9540 (2020).

61. Tanaka T, Basisty N, Fantoni G, Candia J, Moore AZ, Biancotto A, Schilling B, Bandinelli S, Ferrucci L, Plasma proteomic biomarker signature of age predicts health and life span, eLife 9:e61073 (2020).

60. Candia J, Bayarsaikhan E, Tandon M, Budhu A, Forgues M, Tovuu L-O, Tudev U, Lack J, Chao A, Chinburen J, Wang XW, The genomic landscape of Mongolian hepatocellular carcinoma, Nature Communications 11:4383 (2020).

59. Liu J, Tang W, Budhu A, Forgues M, Hernandez MO, Candia J, Kim Y, Bowman ED, Ambs S, Zhao Y, Tran B, Wu X, Koh C, Surana P, Liang TJ, Guarnera M, Mann D, Rajaure M, Greten TF, Wang Z, Yu H, Wang XW, A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma, Cell 182:1-12 (2020).

58. Tanaka T, Lavery R, Varma V, Fantoni G, Colpo M, Thambisetty M, Candia J, Resnick SM, Bennett DA, Biancotto A, Bandinelli S, Ferrucci L, Plasma proteomic signatures predict dementia and cognitive impairment, Alzheimer's & Dementia: Translational Research & Clinical Interventions e12018 (2020).

57. Osawa Y, Semba RD, Fantoni G, Candia J, Biancotto A, Tanaka T, Bandinelli S, Ferrucci L, Plasma proteomic signature of the risk of developing mobility disability: A 9-year follow-up, Aging Cell e13132 (2020).

56. Celik H, Lindblad K, Popescu B, Gui G, Goswami M, Valdez J, DeStefano C, Lai C, Thompson J, Ghannam J, Fantoni G, Biancotto A, Candia J, Cheung F, Sukumar G, Dalgard C, Smith R, Larochelle A, Dillon L, Hourigan C, Highly multiplexed proteomic assessment of human bone marrow in acute myeloid leukemia, Blood Advances 4:367 (2020).

55. Semba RD, Gonzalez-Freire M, Tanaka T, Biancotto A, Zhang P, Shardell M, Moaddel R, CHI Consortium, Ferrucci L, Elevated Plasma Growth and Differentiation Factor 15 Is Associated With Slower Gait Speed and Lower Physical Performance in Healthy Community-Dwelling Adults, J Gerontol A Biol Sci Med Sci 75:175-180 (2020).

54. Karmaus PWF, Shi M, Perl S, Biancotto A, Candia J, Cheung F, Kotliarov Y, Young NS, Fessler MB, CHI Consortium, Effects of rosuvastatin on the immune system in healthy volunteers with normal serum cholesterol, JCI Insight 4:e131530 (2019).

53. Lee BH, Kelly G, Bradford S, Davila M, Guo XV, Amir EAD, Thrash EM, Solga MD, Lannigan J, Sellers B, Candia J, Tsang J, Montgomery RR, Tamaki SJ, Sigdel TK, Sarwal MM, Lanier LL, Tian Y, Kim C, Hinz D, Peters B, Sette A, Rahman AH, A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer, Cytometry Part A 95A:1019-1030 (2019).

52. Candia J, Tsang JS, eNetXplorer: an R package for the quantitative exploration of elastic net families for generalized linear models, BMC Bioinformatics 20:189 (2019).

51. Ciucci T, Vacchio MS, Gao Y, Tomassoni Ardori F, Candia J, Mehta M, Zhao Y, Tran B, Pepper M, Tessarollo L, McGavern DB, Bosselut R, The emergence and functional fitness of memory CD4+ T cells require the transcription factor Thpok, Immunity 50:91-105 (2019).

50. Brown D, Zingone A, Yu Y, Zhu B, Candia J, Cao L, Ryan BM, Relationship between circulating inflammation proteins and lung cancer diagnosis in the National Lung Screening Trial, Cancer Epidemiology, Biomarkers & Prevention 28(1):110-118 (2019).

49. Shen Y, Kubben N, Candia J, Morozov AV, Misteli T, Losert W, RefCell: Multi-dimensional analysis of image-based high-throughput screens based on 'typical cells' , BMC Bioinformatics 19:427 (2018).

48. Giudice V, Biancotto A, Wu Z, Cheung F, Candia J, Fantoni G, Kajigaya S, Rios O, Townsley D, Feng X, Young NS, Aptamer-based proteomics of serum and plasma in acquired aplastic anemia, Experimental Hematology 68:38-50 (2018).

47. Khurana S, Coyle EM, Manischewitz J, King LR, Gao J, Germain RN, Schwartzberg PL, Tsang JS, Golding H, CHI Consortium, AS03-adjuvanted H5N1 vaccine promotes antibody diversity and affinity maturation, NAI titers, cross-clade H5N1 neutralization, but not H1N1 cross-subtype neutralization, npj Vaccines 3:40 (2018).

46. Chen J, Cheung F, Shi R, Zhou H, Lu W, CHI Consortium, PBMC Fixation and Processing for Chromium Single-Cell RNA Sequencing, Journal of Translational Medicine 16:198 (2018).

45. Tanaka T, Biancotto A, Moaddel R, Moore Z, Gonzalez-Freire M, Aon MA, Candia J, Zhang P, Cheung F, Fantoni G, CHI consortium, Semba RD, Ferrucci L, Plasma proteomic signature of age in healthy humans, Aging Cell e12799 (2018).

44. Candia J, Cheung F, Kotliarov Y, Fantoni G, Sellers B, Griesman T, Huang J, Stuccio S, Zingone A, Ryan BM, Tsang JS, Biancotto A, Assessment of Variability in the SOMAscan Assay, Scientific Reports 7:14248 (2017).

43. Cheung F, Fantoni G, Conner M, Sellers BA, Kotliarov Y, Candia J, Stagliano K, Biancotto A, Web Tool for Navigating and Plotting SomaLogic ADAT Files, Journal of Open Research Software 5:20 (2017).

42. Dolatabadi S, Candia J, Akrap N, Vannas C, Tomic TT, Losert W, Landberg G, Aman P, Stahlberg A, Cell cycle and cell size dependent gene expression reveals distinct subpopulations at single-cell level, Frontiers in Genetics 8:1 (2017) [Reprinted in: Pan, X., Wu, S., Weissman, S. M. (Eds) Introduction to Single Cell Omics. Lausanne: Frontiers Media. doi: 10.3389/978-2-88945-920-9, Chapter 3, p.108-118 (2019).]

41. Lau WW, Sparks R, OMiCC Jamboree Working Group, Tsang JS, Meta-analysis of crowdsourced data compendia suggests pan-disease transcriptional signatures of autoimmunity. F1000Research 5:2884 (2016).

40. Chen D, Sarkar S, Candia J, Florczyk SJ, Bodhak S, Driscoll MK, Simon Jr CG, Dunkers JP, Losert W, Machine Learning Based Methodology to Identify Cell Shape Phenotypes Associated with Microenvironmental Cues, Biomaterials 104, 104-118 (2016).

39. Candia J, Cherukuri S, Guo Y, Doshi KA, Banavar JR, Civin CI, Losert W, Uncovering low-dimensional, miR-based signatures of acute myeloid and lymphoblastic leukemias with a machine-learning-driven network approach, Convergent Science Physical Oncology 1, 025002 (2015).

38. Goswami M, McGowan KS, Lu K, Jain N, Candia J, Hensel NF, Tang J, Calvo KR, Battiwalla M, Barrett AJ, Hourigan CS, A multigene array for measurable residual disease detection in AML patients undergoing SCT, Bone Marrow Transplantation 1-10 (2015).

37. Candia J, Banavar JR, Losert W, Understanding Health and Disease with Multidimensional Single-Cell Methods, Journal of Physics: Condensed Matter 26, 073102 (2014).

36. Candia J, Maunu R, Driscoll M, Biancotto A, Dagur P, McCoy Jr JP, Sen HN, Wei L, Maritan A, Cao K, Nussenblatt RB, Banavar JR, Losert W, From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells, PLoS Computational Biology 9(9): e1003215 (2013).

35. Mazzitello KI, Candia J, Albano EV, Far-from-equilibrium growth of magnetic thin films with Blume-Capel impurities, Physical Review E 91, 042118 (2015).

34. Baglietto G, Albano EV, Candia J, Complex Network Structure of Flocks in the Vicsek Model with Vectorial Noise , International Journal of Modern Physics C 25, 1350095 (2014).

33. Loscar ES, Candia J, Stochastic Resonance and Dynamic First-Order Pseudo-Phase Transitions in the Irreversible Growth of Thin Films under Spatially Periodic Magnetic Fields, Physical Review E 88, 042412 (2013).

32. Baglietto G, Albano EV, Candia J, Complex Network Structure of Flocks in the Standard Vicsek Model , Journal of Statistical Physics 153, 270 (2013).

31. Baglietto G, Albano EV, and Candia J, Gregarious vs Individualistic Behavior in Vicsek Swarms and the Onset of First-Order Phase Transitions, Physica A 392, 3240 (2013)

30. Candia J, Albano EV, Nonequilibrium critical behavior of magnetic thin films grown in a temperature gradient, Journal of Statistical Mechanics: Theory and Experiment P08006 (2012)

29. Baglietto G, Albano EV, Candia J, Criticality and the Onset of Ordering in the Standard Vicsek Model, Interface Focus 2, 708 (2012)

28. Mazzitello K, Candia J, Diffusion-Based Density-Equalizing Maps: an Interdisciplinary Approach to Visualizing Homicide Rates and Other Georeferenced Statistical Data, Brazilian Journal of Physics 42, 365 (2012)

27. Candia J, Albano EV, Far-from-equilibrium growth of thin films in a temperature gradient, Physical Review E 84, 050601 (Rapid Communication) (2011)

26. Candia J, Advertising and irreversible opinion spreading in complex social networks, International Journal of Modern Physics C 20, 799 (2009)

25. Candia J, Albano EV, The Magnetic Eden Model, International Journal of Modern Physics C 19, 1617 (2008)

24. Candia J, Mazzitello K, Mass media influence spreading in social networks with community structure, Journal of Statistical Mechanics: Theory and Experiment P07007 (2008)

23. Candia J, González MC, Wang P, Schoenharl T, Madey G, Barabási A-L, Uncovering individual and collective human dynamics from mobile phone records, Journal of Physics A: Mathematical and Theoretical 41, 224015 (2008)

22. Parris PE, Candia J, Kenkre VM, Random walk access times on partially-disordered complex networks: an effective medium theory, Physical Review E 77, 061113 (2008)

21. Candia J, Nonequilibrium opinion spreading on 2D small-world networks, Journal of Statistical Mechanics: Theory and Experiment P09001 (2007)

20. Candia J, Parris PE, and Kenkre VM, Transport properties of random walks on scale-free/regular-lattice hybrid networks, Journal of Statistical Physics 129, 323 (2007)

19. K. Mazzitello, J. Candia, and V. Dossetti, Effects of mass media and cultural drift in a model for social influence , International Journal of Modern Physics C 18, 1475 (2007)

18. J. Candia, Irreversible opinion spreading on scale-free networks, Physical Review E 75, 026110 (2007)

17. J. Candia, Irreversible growth of binary mixtures on small-world networks, Physical Review E 74, 031101 (2006)

16. V. Manías, J. Candia and E.V. Albano, Corner wetting in a far-from-equilibrium magnetic growth model, European Physical Journal B 47, 563 (2005)

15. J. Candia, Detectable neutrino fluxes due to enhanced cosmic ray densities in the Galactic Center region, Journal of Cosmology and Astroparticle Physics 11, 002 (2005)

14. J.F. Beacom and J. Candia, Shower power: Isolating the prompt atmospheric neutrino flux using electron neutrinos, Journal of Cosmology and Astroparticle Physics 11, 009 (2004)

13. J. Candia and E. Roulet, Diffusion and drift of cosmic rays in highly turbulent magnetic fields, Journal of Cosmology and Astroparticle Physics 10, 007 (2004)

12. J. Candia and E.V. Albano, Order-disorder criticality, wetting, and morphological phase transitions in the irreversible growth of far-from-equilibrium magnetic films, Journal of Magnetism and Magnetic Materials 260, 338 (2003)

11. J. Candia and E. Roulet, Rigidity dependent knee and cosmic ray induced high energy neutrino fluxes, Journal of Cosmology and Astroparticle Physics 09, 005 (2003)

10. J. Candia, S. Mollerach, and E. Roulet, Cosmic ray spectrum and anisotropies from the knee to the second knee, Journal of Cosmology and Astroparticle Physics 05, 003 (2003)

9. J. Candia and E.V. Albano, Quasi-wetting and morphological phase transitions in confined far-from-equilibrium magnetic thin films , Journal of Chemical Physics 117, 6699 (2002)

8. J. Candia, S. Mollerach, and E. Roulet, Cosmic ray drift, the second knee and galactic anisotropies , Journal of High Energy Physics 12, 32 (2002)

7. J. Candia, E. Roulet, and L.N. Epele, Turbulent diffusion and drift in galactic magnetic fields and the explanation of the knee in the cosmic ray spectrum , Journal of High Energy Physics 12, 33 (2002)

6. J. Candia and E.V. Albano, Interfacial phase transitions in a far-from-equilibrium magnetic growth model , Journal of Physics: Condensed Matter 14, 4927 (2002)

5. J. Candia and E.V. Albano, Irreversible growth of a binary mixture confined in a thin film geometry with competing walls , Physical Review Letters 88, 016103 (2002)

4. J. Candia, L.N. Epele and E. Roulet, Cosmic ray photodisintegration and the knee of the spectrum , Astroparticle Physics 17, 23 (2002)

3. J. Candia and E.V. Albano, Monte Carlo simulation of the irreversible growth of magnetic thin films , Journal of Applied Physics 90, 5395 (2001)

2. J. Candia and E.V. Albano, Comparative study of an Eden model for the irreversible growth of spins and the equilibrium Ising model , Physical Review E 63, 066127 (2001)

1. J. Candia and E.V. Albano, Non-equilibrium wetting transition in a magnetic Eden model , European Physical Journal B 16, 531 (2000)

II. Book Chapters

2. Candia J, Banavar JR, Losert W, Uncovering Phenotypes with Supercells: Applications to Single-Cell Sequencing. In: X. Wang (Ed.), Single Cell Sequencing and Systems Immunology, Translational Bioinformatics (Vol. 5), ISBN 978-94-017-9752-8, ISBN 978-94-017-9753-5 (eBook), Springer (2015), Chapter 2.

1. Pawling A, Yan P, Candia J, Schoenharl T, Madey G, Anomaly detection in streaming sensor data. Chapter in "Intelligent Techniques for Warehousing and Mining Sensor Network Data", A. Cuzzocrea (Editor), ISBN13: 9781605663289 IGI Global, Hershey PA (2010)

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