Publications:

1.     Ren R, Hutcheon AE, Guo XQ, Saeidi N, Melotti SA, Ruberti JW, Zieske JD, Trinkaus-Randall V. Human primary corneal fibroblasts synthesize and deposit proteoglycans in long-term 3-D cultures. Dev Dyn. 2008 Oct;237(10):2705-2715. doi: 10.1002/dvdy.21606.

2.     Zareian R, Saeidi N, Ruberti JW. Strain-Influenced Degradation of Native Collagenous Tissue in a Very-Low Volume, Environmentally-Controlled Bioreactor. ASME. 2009; 2:113-118.

3.     Saeidi N, Sander EA, Ruberti JW. Dynamic shear-influenced collagen self-assembly. Biomaterials. 2009 Dec;30(34):6581-6592. doi: 10.1016/j.biomaterials.2009.07.070.

4.     Bueno EM, Saeidi N, Melotti S, Ruberti JW. Effect of serum and insulin modulation on the organization and morphology of matrix synthesized by bovine corneal stromal cells. Tissue Eng Part A. 2009 Nov;15(11):3559-3573. doi: 10.1089/ten.TEA.2008.0404.

5.     Bhole AP, Flynn BP, Liles M, Saeidi N, Dimarzio CA, Ruberti JW. Mechanical strain enhances survivability of collagen micronetworks in the presence of collagenase: implications for load-bearing matrix growth and stability. Philos Trans A Math Phys Eng Sci. 2009 Sep 13;367(1902):3339-3362. doi: 10.1098/rsta.2009.0093.

6.     Zareian R, Church KP, Saeidi N, Flynn BP, Beale JW, Ruberti JW. Probing collagen/enzyme mechanochemistry in native tissue with dynamic, enzyme-induced creep. Langmuir. 2010 Jun 15;26(12):9917-9926. doi: 10.1021/la100384e.

7.     Flynn BP, Bhole AP, Saeidi N, Liles M, Dimarzio CA, Ruberti JW. Mechanical strain stabilizes reconstituted collagen fibrils against enzymatic degradation by mammalian collagenase matrix metalloproteinase 8 (MMP-8). PLoS One. 2010 Aug 23;5(8):e12337. doi: 10.1371/journal.pone.0012337.

8.     Uygun BE, Price G, Saeidi N, Izamis ML, Berendsen T, Yarmush M, Uygun K. Decellularization and recellularization of whole livers. J Vis Exp. 2011 Feb 4;(48). pii: 2394. doi: 10.3791/2394.

9.     Saeidi N, Sander EA, Zareian R, Ruberti JW. Production of highly aligned collagen lamellae by combining shear force and thin film confinement. Acta Biomater. 2011 Jun;7(6):2437-2447. doi: 10.1016/j.actbio.2011.02.038.

10.  Paten JA, Zareian R, Saeidi N, Melotti SA, Ruberti JW. Design and performance of an optically accessible, low-volume, mechanobioreactor for long-term study of living constructs. Tissue Eng Part C Methods. 2011 Jul;17(7):775-788. doi: 10.1089/ten.TEC.2010.0642.

11.  Izamis ML, Sharma NS, Uygun B, Bieganski R, Saeidi N, Nahmias Y, Uygun K, Yarmush ML, Berthiaume F. In situ metabolic flux analysis to quantify the liver metabolic response to experimental burn injury. Biotechnol Bioeng. 2011 Apr;108(4):839-852. doi: 10.1002/bit.22998.

12.  Camp RJ, Liles M, Beale J, Saeidi N, Flynn BP, Moore E, Murthy SK, Ruberti JW. Molecular mechanochemistry: low force switch slows enzymatic cleavage of human type I collagen monomer. J Am Chem Soc. 2011 Mar 23;133(11):4073-4078. doi: 10.1021/ja110098b.

13.  Saeidi N, Nestoridi E, Kucharczyk J, Uygun MK, Yarmush ML, Stylopoulos N. Sleeve gastrectomy and Roux-en-Y gastric bypass exhibit differential effects on food preferences, nutrient absorption and energy expenditure in obese rats. Int J Obes (Lond). 2012 Nov;36(11):1396-1402. doi: 10.1038/ijo.2012.167.

14.  Saeidi N, Karmelek KP, Paten JA, Zareian R, DiMasi E, Ruberti JW. Molecular crowding of collagen: a pathway to produce highly-organized collagenous structures. Biomaterials. 2012 Oct;33(30):7366-7374. doi: 10.1016/j.biomaterials.2012.06.041.

15.  Saeidi N, Guo X, Hutcheon AE, Sander EA, Bale SS, Melotti SA, Zieske JD, Trinkaus-Randall V, Ruberti JW. Disorganized collagen scaffold interferes with fibroblast mediated deposition of organized extracellular matrix in vitro. Biotechnol Bioeng. 2012 Oct;109(10):2683-2698. doi: 10.1002/bit.24533.

16.  Saeidi N, Meoli L, Nestoridi E, Gupta NK, Kvas S, Kucharczyk J, Bonab AA, Fischman AJ, Yarmush ML, Stylopoulos N. Reprogramming of intestinal glucose metabolism and glycemic control in rats after gastric bypass. Science. 2013 Jul 26;341(6144):406-410. doi: 10.1126/science.1235103.

17.  Izamis ML, Calhoun C, Uygun BE, Guzzardi MA, Price G, Luitje M, Saeidi N, Yarmush ML, Uygun K. Simple Machine Perfusion Significantly Enhances Hepatocyte Yields of Ischemic and Fresh Rat Livers. Cell Med. 2013;4(3):109-123. doi: 10.3727/215517912X658927.

18.  Fletcher AL, Elman JS, Astarita J, Murray R, Saeidi N, D'Rozario J, Knoblich K, Brown FD, Schildberg FA, Nieves JM, Heng TS, Boyd RL, Turley SJ, Parekkadan B. Lymph node fibroblastic reticular cell transplants show robust therapeutic efficacy in high-mortality murine sepsis. Sci Transl Med. 2014 Aug 13;6(249):249ra109. doi: 10.1126/scitranslmed.3009377.

19.  Bruinsma BG, Yeh H, Ozer S, Martins PN, Farmer A, Wu W, Saeidi N, Op den Dries S, Berendsen TA, Smith RN, Markmann JF, Porte RJ, Yarmush ML, Uygun K, Izamis ML. Subnormothermic machine perfusion for ex vivo preservation and recovery of the human liver for transplantation. Am J Transplant. 2014 Jun;14(6):1400-1409. doi: 10.1111/ajt.12727.

20.  Berendsen TA, Bruinsma BG, Puts CF, Saeidi N, Usta OB, Uygun BE, Izamis ML, Toner M, Yarmush ML, Uygun K. Supercooling enables long-term transplantation survival following 4 days of liver preservation. Nat Med. 2014 Jul;20(7):790-793. doi: 10.1038/nm.3588.

21.  Bale SS, Price G, Casali M, Saeidi N, Bhushan A, Yarmush ML. A highly sensitive microsphere- based assay for early detection of Type I diabetes. TECHNOLOGY. 2014;2:200-205.

22.  Bruinsma BG, Uygun K, Yarmush ML, Saeidi N. Surgical models of Roux-en-Y gastric bypass surgery and sleeve gastrectomy in rats and mice. Nat Protoc. 2015 Mar;10(3):495-507. doi: 10.1038/nprot.2015.027.

23.  Bale SS, Saeidi N, Kidambi S, Yarmush ML, Casali M. FMR1 Deficiency Alters Self-Renewal and Proliferation of Mouse Embryonic Cells. Nano LIFE. 2015;05:1550003.

24.  Zareian R, Susilo ME, Paten J, McLean JP, Hollmann J, Karamichos D, Messer CS, Tambe DT Saeidi N, Zieske JD, Ruberti JW. Human corneal fibroblast pattern evolution and matrix synthesis on mechanically-biased substrates. Tissue Eng Part A. 2016 Oct;22(19-20):1204-1217. doi: 10.1089/ten.TEA.2016.0164

25.  Bruinsma BG, Sridharan GV, Weeder PD, Avruch JH, Saeidi N, Ozer S, Geerts S, Porte RJ, Heger M, van Gulik TM, Martins PN, Markmann JF, Yeh H, Uygun K. Metabolic profiling during ex vivo machine perfusion of the human liver. Sci Rep. 2016 Mar 3;6:22415. doi: 10.1038/srep22415.

26.  Yarmush ML, D'Alessandro M, Saeidi N. (2017). Regulation of Energy Homeostasis After Gastric Bypass Surgery. Annual Review of Biomedical Engineering, 19:459-484.

27.  Shridharan GV, D'Alessandro M, Bale SS, Gagnon H, Asara JM, Uygun K, Yarmush ML, Saeidi N. (2017). Multi-omic Network-based Interrogation of Rat Liver Metabolism Following Gastric Bypass Surgery featuring SWATH Proteomics Technology. Technology, 5:139-184.

28.  Sridharan GV, Bruinsma BG, Bale SS, Swaminathan A, Saeidi N, Yarmush ML, Uygun K. (2018). Metabolomic Modularity Analysis (MMA) to Quantify Human Liver Perfusion Dynamics. Metabolites. 7:E58

29.  Li X, Saeidi N, Villiger M, Albadawi H, Jones JD, Quinn KP, Austin WG Jr, Golberg A, Yarmush ML. (2018). Rejuvenation of aged rat skin with pulsed electric fields. J Tissue Eng Regen Med, 12:2309- 2318.

30.  Meoli L, Gupta NK, Saeidi N, Panciotti CA, Biddinger SB, Corey KE, Stylopoulos N. (2018). Nonalcoholic fatty liver disease and gastric bypass surgery regulate serum and hepatic levels of pyruvate kinase isoenzyme M2. Am J Physiol Endocrinol Metab, 315:E613-E62.

31.  Krishnan S, Ding Y, Saeidi N, Choi M, Sridharan GV, Sherr DH, Yarmush ML, Alaniz RC, Jayaraman A, Lee K. (2018). Gut Microbiota-Derived Tryptophan Metabolites Modulate Inflammatory Response in Hepatocytes and Macrophages. Cell Rep, 23(4):1099-1111.

32.  Spencer RKW, Saeidi N, Ha BY. (2019). Nematic ordering of worm-like polymers near an interface. J Chem Phys, 52(20):204907.

33. He S, Green Y, Saeidi N, Li X, Fredberg JJ, Ji B, Pismen LM. A theoretical model of collective cell polarization and alignment. (2020). J Mech Phys Solids. 137:103860.

34. Saeidi N, Stefater M, Stylopoulos N. Effect of Diet versus Gastric Bypass on Metabolic Function in Diabetes. (2020). N Engl J Med. 383(24):2391-2392.

35. Spencer RKW, Ha BY, Saeidi N. Self-consistent field theory of chiral nematic worm-like chains. (2022). J Chem Phys. 156(11):114902.

36. Spencer RKW, Ha BY, Saeidi N. Interplay between nematic and cholesteric interactions in self-consistent field theory. (2022). Phys Rev E. 105(5-1):054501.

37. He S, Azar DA, Esfahani FN, Azar GA, Shazly T, Saeidi N. Mechanoscopy: A Novel Device and Procedure for in vivo Detection of Chronic Colitis in Mice. (2022). Inflamm Bowel Dis. 28(8):1143-1150.

38. Lei P, Chukwudi C, Pannu PR, He S, Saeidi N. Rewiring of the Liver Transcriptome across Multiple Time-Scales Is Associated with the Weight Loss-Independent Resolution of NAFLD Following RYGB. (2022). Metabolites. doi: 10.3390/metabo12040318.

39. He S, Lei P, Kang W, Cheung P, Xu T, Mana M, Park CY, Wang H, Imada S, Russell JO, Wang J, Wang R, Zhou Z, Chetal K, Stas E, Mohad V, Bruun-Rasmussen P, Sadreyev RI, Hodin RA, Zhang Y, Breault DT, Camargo FD, Yilmaz ÖH, Fredberg JJ, Saeidi N. Stiffness Restricts the Stemness of the Intestinal Stem Cells and Skews Their Differentiation Towards Goblet Cells. (2023). Gastroenterology. S0016-5085(23)00215-9.

Patents:

Invention coversheet filed - A biopolymer-based therapy for type II diabetes

Patent US No. 9018355 - Collagen fibrillar construction

Patent US No. 9187329 - Microparticle organization