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Publications

Publications are annotated with the name of the Institute's Center that led the efforts in each case.

  • PreCSN = The Center for Precision Computational Systems Network
  • ConCISE = The Consortium for Cell-Inspired Systems Engineering
  • HUMANOID = Human Organoid Center of Research Excellence (CoRE)

DEPOSITED IN PRE-PRINT SERVER:

  1. Stability analysis of a signaling circuit with dual species of GTPase switches. Lucas Stollerman, Pradipta Ghosh, Padmini Rangamani. [Co-Corresponding author] doi: https://doi.org/10.1101/2020.08.31.276311. https://www.biorxiv.org/content/10.1101/2020.08.31.276311v1 - ConCISE
  2. Catestatin (CST) is a key mediator of the immunoendocrine regulation of cardiovascular function. Wei Ying, Kechun Tang, Ennio Avolio, Jan M. Schilling, Teresa Pasqua, Matthew A. Liu, Hongqiang Cheng, Jing Zhang, Sumana Mahata, Gautam Bandyopadhyay, Soumita Das, David M. Roth, Debashis Sahoo, Nicholas J.G. Webster, Farah Sheikh, Hemal H. Patel, Pradipta Ghosh, Sushil K. Mahata. bioRxiv 2020.05.12.092254; doi: https://doi.org/10.1101/2020.05.12.092254 - PreCSN
  3.  E-cigarettes compromise the gut barrier and trigger gut inflammation Aditi Sharma, Jasper Lee, Ayden G. Fonseca, Alex Moshensky, Taha Kothari, Ibrahim M. Sayed, Stella-Rita Ibeawuchi, Rama F. Pranadinata, Jason Ear, Debashis Sahoo, Laura E. Crotty-Alexander, Pradipta Ghosh, Soumita Das. [Co-Corresponding author] bioRxiv 2020.07.29.227348; doi: https://doi.org/10.1101/2020.07.29.227348 - HUMANOID
  4. Rapid community-driven development of a SARS-CoV-2 tissue simulator. Wang Y, An G, Becker A, Cockrell C, Collier N, Craig M, Davis CL, Faeder J, Versypt ANF, Gianlupi JF, Glazier JA, Heiland R, Hillen T, Islam MA, Jenner A, Liu B, Morel PA, Narayanan A, Ozik J, Rangamani P, Shoemaker JE, Smith AM, Macklin P bioRxiv. 2020 Apr 5:2020.04.02.019075. doi: 10.1101/2020.04.02.019075. Preprint.PMID: 32511322. - ConCISE
  5. TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin. Swanson L, Katkar GD, Tam, J., Pranadinata R, Chreddy, Y, Coates, J., Castillo V., Olson J., Nizet V., Kufareva I., Das S and Ghosh P. doi: https://doi.org/10.1101/2020.08.29.273516 - ConCISE


ACCEPTED, IN PRESS:

  1. Receptor tyrosine kinases activate heterotrimeric G proteins via phosphorylation within the interdomain cleft of Gαi. Kalogriopoulos NA, Lopez-Sanchez I, Lin C, Ngo T , Aznar N, Murray F, Garcia-Marcos M, Kufareva I, Majid Ghassemian, M, and Ghosh, P. Accepted, In press. Proc Natl Acad Sci U S A 2020. https://doi.org/10.1101/2020.08.09.229716 - ConCISE
  2. DNA glycosylase NEIL2 prevents Fusobacterium-mediated inflammation and DNA damage in colonic epithelial cells. Ibrahim M Sayed, Anirban Chakraborty, Amer Ali, Aditi Sharma, Ayse Z. Sahan, Debashis Sahoo, Pradipta Ghosh, Tapas K Hazra, Soumita Das. bioRxiv 2020.06.11.147454; doi: https://doi.org/10.1101/2020.06.11.147454. Accepted, In Press, Cells, 2020. - HUMANOID


PUBLISHED: Peer-Reviewed Original Articles

  1. Potentiation of calcium-activated chloride secretion and barrier dysfunction may underlie EGF receptor tyrosine kinase inhibitor-induced diarrhea. Kim Y, Quach A, Das S, Barrett KE. Physiol Rep. 2020 Jul;8(13):e14490. doi: 10.14814/phy2.14490.PMID: 32652816 - HUMANOID
  2. Primary Female Urethral Carcinoma: Proposed Staging Modifications Based on Assessment of Female Urethral Histology and Analysis of a Large Series of Female Urethral Carcinomas. Aron M, Park S, Lowenthal BM, Gupta S, Sahoo D, Cheville JC, Hansel DE. Am J Surg Pathol. 2020 Aug 28. doi: 10.1097/PAS.0000000000001569. Online ahead of print.PMID: 32868524 - PreCSN
  3. Upregulation of CD47 Is a Host Checkpoint Response to Pathogen Recognition. Tal MC, Torrez Dulgeroff LB, Myers L, Cham LB, Mayer-Barber KD, Bohrer AC, Castro E, Yiu YY, Lopez Angel C, Pham E, Carmody AB, Messer RJ, Gars E, Kortmann J, Markovic M, Hasenkrug M, Peterson KE, Winkler CW, Woods TA, Hansen P, Galloway S, Wagh D, Fram BJ, Nguyen T, Corey D, Kalluru RS, Banaei N, Rajadas J, Monack DM, Ahmed A, Sahoo D, Davis MM, Glenn JS, Adomati T, Lang KS, Weissman IL, Hasenkrug KJ. mBio. 2020 Jun 23;11(3):e01293-20. doi: 10.1128/mBio.01293-20.PMID: 32576678. - PreCSN  

  4. Non-uniform distribution of myosin-mediated forces governs red blood cell membrane curvature through tension modulation. Alimohamadi H, Smith AS, Nowak RB, Fowler VM, Rangamani P. PLoS Comput Biol. 2020 May 26;16(5):e1007890. doi: 10.1371/journal.pcbi.1007890. eCollection 2020 May.PMID: 32453720. - ConCISE
  5. Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling. Zhang JZ, Lu TW, Stolerman LM, Tenner B, Yang JR, Zhang JF, Falcke M, Rangamani P, Taylor SS, Mehta S, Zhang J. Cell. 2020 Aug 20:S0092-8674(20)30991-0. doi: 10.1016/j.cell.2020.07.043. Online ahead of print.PMID: 32846158. - ConCISE
  6. Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. Ordyan M, Bartol T, Kennedy M, Rangamani P, Sejnowski T. PLoS Comput Biol. 2020 Jul 17;16(7):e1008015. doi: 10.1371/journal.pcbi.1008015. eCollection 2020 Jul.PMID: 32678848  - ConCISE
  7. DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesisAbbasi N, Long T, Li Y, Yee BA, Cho BS, Hernandez JE, Ma E, Patel PR, Sahoo D, Sayed IM, Varki N, Das S, Ghosh P, Yeo GW, Huang WJM. Life Sci Alliance. 2020 Aug 18;3(10):e202000772. doi: 10.26508/lsa.202000772. Print 2020 Oct. PMID: 32817263 - HUMANOID and PreCSN
  8. GIV/Girdin and Exo70 Collaboratively Regulate the Mammalian Polarized Exocytic Machinery. Rohena C, Rajapakse N, Lo IC, Novick P, Sahoo D, Ghosh P. iScience. 2020 Jul 24;23(7):101246. doi: 10.1016/j.isci.2020.101246. Epub 2020 Jun 7. PMID: 32590327 - ConCISE
  9. GIV•Kindlin Interaction Is Required for Kindlin-Mediated Integrin Recognition and Activation. Rohena C, Kalogriopoulos N, Rajapakse N, Roy S, Lopez-Sanchez I, Ablack J, Sahoo D, Ghosh P. iScience. 2020 Jun 26;23(6):101209. doi: 10.1016/j.isci.2020.101209. Epub 2020 May 28. PMID: 32535026 - ConCISE
  10. Sahoo D, Zaramela LS, Hernandez GE, Mai U, Taheri S, Dang D, Stouch AN, Medal RM, McCoy AM, Aschner JL, Blackwell TS, Zengler K, Prince LS. Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants. Commun Biol. 2020 May 22;3(1):259. doi: 10.1038/s42003-020-0985-2.PMID: 32444859 - PreCSN
  11. Helicobacter pylori infection downregulates the DNA glycosylase NEIL2, resulting in increased genome damage and inflammation in gastric epithelial cells. Sayed IM, Sahan AZ, Venkova T, Chakraborty A, Mukhopadhyay D, Bimczok D, Beswick EJ, Reyes VE, Pinchuk I, Sahoo D, Ghosh P, Hazra TK, Das S. J Biol Chem. 2020 Aug 7;295(32):11082-11098. doi: 10.1074/jbc.RA119.009981. Epub 2020 Jun 9. PMID: 32518160 - HUMANOID
  12. Enhanced mitochondrial fission suppresses signaling and metastasis in triple-negative breast cancer. Humphries BA, Cutter AC, Buschhaus JM, Chen YC, Qyli T, Palagama DSW, Eckley S, Robison TH, Bevoor A, Chiang B, Haley HR, Sahoo S, Spinosa PC, Neale DB, Boppisetti J, Sahoo D, Ghosh P, Lahann J, Ross BD, Yoon E, Luker KE, Luker GD. Breast Cancer Res. 2020 Jun 5;22(1):60. doi: 10.1186/s13058-020-01301-x. PMID: 32503622 - PreCSN
  13. Regulating cellular cyclic adenosine monophosphate: "Sources," "sinks," and now, "tunable valves". Getz M, Rangamani P, Ghosh P. Wiley Interdiscip Rev Syst Biol Med. 2020 Apr 23:e1490. doi: 10.1002/wsbm.1490. Online ahead of print.PMID: 32323924 - ConCISE 
  14. Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput Biol. 2020 Apr 6;16(4):e1007756. doi: 10.1371/journal.pcbi.1007756. eCollection 2020 Apr.PMID: 32251448 - ConCISE
  15. Das B, Okamoto K, Rabalais J, Marchelletta RR, Barrett KE, Das S, Niwa M, Sivagnanam M. Congenital Tufting Enteropathy-Associated Mutant of Epithelial Cell Adhesion Molecule Activates the Unfolded Protein Response in a Murine Model of the Disease. Cells. 2020 Apr 11;9(4):946. doi: 10.3390/cells9040946.PMID: 32290509 - HUMANOID
  16. Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophys J. 2020 Mar 10;118(5):1003-1008. doi: 10.1016/j.bpj.2019.11.3400. Epub 2020 Jan 22.PMID: 32032503 - ConCISE
  17. Stolerman LM, Getz M, Smith SGL, Holst M, Rangamani P. Stability Analysis of a Bulk-Surface Reaction Model for Membrane Protein Clustering. Bull Math Biol. 2020 Feb 6;82(2):30. doi: 10.1007/s11538-020-00703-4.PMID: 32025918 - ConCISE
  18. Computational Approach to Identifying Universal Macrophage Biomarkers. Dang D, Taheri S, Das S, Ghosh P, Prince LS, Sahoo D. Front Physiol. 2020 Apr 8;11:275. doi: 10.3389/fphys.2020.00275. eCollection 2020.PMID: 32322218 - PreCSN 
  19. Pearce KM, Bell M, Linthicum WH, Wen Q, Srinivasan J, Rangamani P, Scarlata S. Gαq-mediated calcium dynamics and membrane tension modulate neurite plasticity. Mol Biol Cell. 2020 Mar 19;31(7):683-694. doi: 10.1091/mbc.E19-09-0536. Epub 2019 Dec 11.PMID: 31825720 - ConCISE
  20. The stress polarity signaling (SPS) pathway serves as a marker and a target in the leaky gut barrier: implications in aging and cancer. Ghosh P, Swanson L, Sayed IM, Mittal Y, Lim BB, Ibeawuchi SR, Foretz M, Viollet B, Sahoo D, Das S. Life Sci Alliance. 2020 Feb 10;3(3):e201900481. doi: 10.26508/lsa.201900481. Print 2020 Mar. PMID: 32041849 - HUMANOID
  21. Alimohamadi H, Ovryn B, Rangamani P. Modeling membrane nanotube morphology: the role of heterogeneity in composition and material properties. Sci Rep. 2020 Feb 13;10(1):2527. doi: 10.1038/s41598-020-59221-x.PMID: 32054874. - ConCISE
  22. Host engulfment pathway controls inflammation in inflammatory bowel disease. Sayed IM, Suarez K, Lim E, Singh S, Pereira M, Ibeawuchi SR, Katkar G, Dunkel Y, Mittal Y, Chattopadhyay R, Guma M, Boland BS, Dulai PS, Sandborn WJ, Ghosh P, Das S. FEBS J. 2020 Jan 30:10.1111/febs.15236. doi: 10.1111/febs.15236. Online ahead of print. PMID: 32003126 - HUMANOID
  23. Akamatsu M, Vasan R, Serwas D, Ferrin MA, Rangamani P, Drubin DG. Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis. Elife. 2020 Jan 17;9:e49840. doi: 10.7554/eLife.49840.PMID: 31951196. - ConCISE
  24. Lowenthal BM, Sahoo D, Amin MB, Hansel DE. Urothelial Proliferation of Unknown Malignant Potential Involving the Bladder: Histopathologic Features and Risk of Progression in De Novo Cases and Cases With Prior Neoplasia. Arch Pathol Lab Med. 2019 Dec 11. doi: 10.5858/arpa.2019-0005-OA. Online ahead of print. PMID: 31825667 - PreCSN
  25. Ohadi D, Schmitt DL, Calabrese B, Halpain S, Zhang J, Rangamani P. Computational Modeling Reveals Frequency Modulation of Calcium-cAMP/PKA Pathway in Dendritic Spines. Biophys J. 2019 Nov 19;117(10):1963-1980. doi: 10.1016/j.bpj.2019.10.003. Epub 2019 Oct 9.PMID: 31668749. - ConCISE
  26. Wong J, Garcia-Carbonell R, Zelic M, Ho SB, Boland BS, Yao SJ, Desai SA, Das S, Planell N, Harris PA, Font-Burgada J, Taniguchi K, Bertin J, Salas A, Pasparakis M, Gough PJ, Kelliher M, Karin M, Guma M. RIPK1 Mediates TNF-Induced Intestinal Crypt Apoptosis During Chronic NF-κB Activation. Cell Mol Gastroenterol Hepatol. 2020;9(2):295-312. doi: 10.1016/j.jcmgh.2019.10.002. Epub 2019 Oct 10.PMID: 31606566 - HUMANOID
  27. Mukohyama J, Isobe T, Hu Q, Hayashi T, Watanabe T, Maeda M, Yanagi H, Qian X, Yamashita K, Minami H, Mimori K, Sahoo D, Kakeji Y, Suzuki A, Dalerba P, Shimono Y. miR-221 Targets QKI to Enhance the Tumorigenic Capacity of Human Colorectal Cancer Stem Cells. Cancer Res. 2019 Oct 15;79(20):5151-5158. doi: 10.1158/0008-5472.CAN-18-3544. Epub 2019 Aug 15.PMID: 31416845. - PreCSN
  28. Das B, Okamoto K, Rabalais J, Kozan PA, Marchelletta RR, McGeough MD, Durali N, Go M, Barrett KE, Das S, Sivagnanam M. Enteroids expressing a disease-associated mutant of EpCAM are a model for congenital tufting enteropathy. Am J Physiol Gastrointest Liver Physiol. 2019 Nov 1;317(5):G580-G591. doi: 10.1152/ajpgi.00098.2019. Epub 2019 Aug 21.PMID: 31433211 - HUMANOID
  29. Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, Komives EA, Chang G, Ghosh P, Kufareva I. Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16394-16403. doi: 10.1073/pnas.1906658116. Epub 2019 Jul 30. PMID: 31363053 - ConCISE
  30. Dabydeen SA, Desai A, Sahoo D. Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. Mol Biol Cell. 2019 Jul 1;30(14):1770-1779. doi: 10.1091/mbc.E19-01-0013. Epub 2019 May 15.PMID: 31091168. - PreCSN
  31. Garcia-Carbonell R, Yao SJ, Das S, Guma M. Dysregulation of Intestinal Epithelial Cell RIPK Pathways Promotes Chronic Inflammation in the IBD Gut. Front Immunol. 2019 May 20;10:1094. doi: 10.3389/fimmu.2019.01094. eCollection 2019.PMID: 31164887 - HUMANOID
  32. Rajasekaran S, Nagarajha Selvan LD, Dotts K, Kumar R, Rishi P, Khetan V, Bisht M, Sivaraman K, Krishnakumar S, Sahoo D, Campbell MJ, Elchuri SV, Miles WO. Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors. Front Oncol. 2019 Apr 16;9:221. doi: 10.3389/fonc.2019.00221. eCollection 2019.PMID: 31058073. - PreCSN
  33. Stobdan T, Sahoo D, Azad P, Hartley I, Heinrichsen E, Zhou D, Haddad GG. High fat diet induces sex-specific differential gene expression in Drosophila melanogaster. PLoS One. 2019 Mar 12;14(3):e0213474. doi: 10.1371/journal.pone.0213474. eCollection 2019.PMID: 30861021 - PreCSN
  34. Rubinstein MR, Baik JE, Lagana SM, Han RP, Raab WJ, Sahoo D, Dalerba P, Wang TC, Han YW. Fusobacterium nucleatum promotes colorectal cancer by inducing Wnt/β-catenin modulator Annexin A1. EMBO Rep. 2019 Apr;20(4):e47638. doi: 10.15252/embr.201847638. Epub 2019 Mar 4.PMID: 30833345. - PreCSN
  35. A predictive computational model reveals that GIV/girdin serves as a tunable valve for EGFR-stimulated cyclic AMP signals. Getz M, Swanson L, Sahoo D, Ghosh P, Rangamani P. Mol Biol Cell. 2019 Jun 15;30(13):1621-1633. doi: 10.1091/mbc.E18-10-0630. Epub 2019 Apr 24. PMID: 31017840 - ConCISE
  36. Near-Infrared Light-Activated DNA-Agonist Nanodevice for Nongenetically and Remotely Controlled Cellular Signaling and Behaviors in Live Animals. Wang M, He F, Li H, Yang S, Zhang J, Ghosh P, Wang HH, Nie Z. Nano Lett. 2019 Apr 10;19(4):2603-2613. doi: 10.1021/acs.nanolett.9b00421. Epub 2019 Mar 28. PMID: 30907088 - ConCISE
  37. Kahn SA, Wang X, Nitta RT, Gholamin S, Theruvath J, Hutter G, Azad TD, Wadi L, Bolin S, Ramaswamy V, Esparza R, Liu KW, Edwards M, Swartling FJ, Sahoo D, Li G, Wechsler-Reya RJ, Reimand J, Cho YJ, Taylor MD, Weissman IL, Mitra SS, Cheshier SH. Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma. Nat Commun. 2018 Oct 8;9(1):4121. doi: 10.1038/s41467-018-06564-9.PMID: 30297829. - PreCSN
  38. Chan CKF, Gulati GS, Sinha R, Tompkins JV, Lopez M, Carter AC, Ransom RC, Reinisch A, Wearda T, Murphy M, Brewer RE, Koepke LS, Marecic O, Manjunath A, Seo EY, Leavitt T, Lu WJ, Nguyen A, Conley SD, Salhotra A, Ambrosi TH, Borrelli MR, Siebel T, Chan K, Schallmoser K, Seita J, Sahoo D, Goodnough H, Bishop J, Gardner M, Majeti R, Wan DC, Goodman S, Weissman IL, Chang HY, Longaker MT. Identification of the Human Skeletal Stem Cell. Cell. 2018 Sep 20;175(1):43-56.e21. doi: 10.1016/j.cell.2018.07.029.PMID: 30241615. - PreCSN
  39. Garcia-Carbonell R, Wong J, Kim JY, Close LA, Boland BS, Wong TL, Harris PA, Ho SB, Das S, Ernst PB, Sasik R, Sandborn WJ, Bertin J, Gough PJ, Chang JT, Kelliher M, Boone D, Guma M, Karin M. Elevated A20 promotes TNF-induced and RIPK1-dependent intestinal epithelial cell death. Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):E9192-E9200. doi: 10.1073/pnas.1810584115. Epub 2018 Sep 12.PMID: 30209212. - HUMANOID
  40. Das S, Jayaratne R, Barrett KE. The Role of Ion Transporters in the Pathophysiology of Infectious Diarrhea. Cell Mol Gastroenterol Hepatol. 2018 Mar 5;6(1):33-45. doi: 10.1016/j.jcmgh.2018.02.009. eCollection 2018.PMID: 29928670. - HUMANOID