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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. Design principles of dose-response alignment in coupled GTPase switches. Lingxia Qiao, Pradipta Ghosh, Padmini Rangamani. bioRxiv 2022.06.14.496184; doi: https://doi.org/10.1101/2022.06.14.496184 - ConCISE. 

  2. Formation of protein-mediated bilayer tubes is governed by a snapthrough transition
    A. Mahapatra, P. Rangamani
    bioRxiv 2022.06.07.494774; doi: https://doi.org/10.1101/2022.06.07.494774.- ConCISE

  3. Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling
    A. Leung, P. Rangamani
    bioRxiv 2022.08.17.504291; doi: https://doi.org/10.1101/2022.08.17.504291. - ConCISE

  4. Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling
    A. Khalilimeybodi, S.I. Fraley, P. Rangamani
    bioRxiv 2022.10.06.511161; doi: https://doi.org/10.1101/2022.10.06.511161. - ConCISE

  5. The ins and outs of membrane bending by intrinsically disordered proteins
    Feng Yuan, Justin Houser, Arjun Sangani, Liping Wang, Eileen Lafer, Padmini Rangamani, Jeanne Stachowiak
    bioRxiv 2022.12.17.520884; doi: https://doi.org/10.1101/2022.12.17.520884. - ConCISE

  6. Modeling membrane curvature generation using mechanics and machine learning
    S. A. Malingen, P. Rangamani
    bioRxiv 2022.06.06.495017; doi: https://doi.org/10.1101/2022.06.06.495017- ConCISE

  7. Machine Learning Identifies Signatures of Macrophage Reactivity and Tolerance that Predict Disease Outcomes. Pradipta Ghosh, Saptarshi Sinha, Gajanan D. Katkar, Daniella Vo, Sahar Taheri, Dharanidhar Dang, Soumita Das, Debashis Sahoo. bioRxiv 2022.06.27.497783; doi: https://doi.org/10.1101/2022.06.27.497783. - PreCSN. 

  8. Morphological principles of neuronal mitochondriaRachel MendelsohnGuadalupe C. GarciaThomas M. BartolChristopher T. LeeP. KhandelwalEmily LiuDonald J. SpencerAdam HusarEric A. BushongSebastien PhanGuy PerkinsMark H. EllismanAlexander SkupinTerrence J. SejnowskiPadmini Rangamani. bioRxiv 2021.03.15.435547; doi: https://doi.org/10.1101/2021.03.15.435547. - ConCISE

  9. Phosphorylation of Gαi shapes canonical Gα(i)βγ/GPCR signaling. Suchismita Roy, Ananta James Silas, Majid Ghassemian, Irina Kufareva, Pradipta Ghosh. bioRxiv 2022.09.11.507491; doi: https://doi.org/10.1101/2022.09.11.507491. - ConCISE. 

  10. Growth Signaling Autonomy in Circulating Tumor Cells Aids Metastatic Seeding. Saptarshi Sinha, Alex Farfel, Kathryn E. Luker, Debashis Sahoo, Barbara A. Parker, Kay Yeung, Gary D. Luker, Pradipta Ghosh
    bioRxiv 2022.12.02.518910; doi: https://doi.org/10.1101/2022.12.02.518910. - PreCSN.

  11. A Circuit for Secretion-coupled Cellular Autonomy in Multicellular Eukaryotes. Lingxia Qiao, Saptarshi Sinha, Amer Ali Abd El-Hafeez, I-Chung Lo, Krishna K. Midde, Tony Ngo, Nicolas Aznar, Inmaculada Lopez-Sanchez, Vijay Gupta, Marilyn G. Farquhar, Padmini Rangamani, Pradipta Ghosh. bioRxiv 2021.03.18.436048; doi: https://doi.org/10.1101/2021.03.18.436048. - ConCISE.
  12. Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayersArijit MahapatraDavid SaintillanPadmini Rangamani. bioRxiv 2021.04.02.438263; doi: https://doi.org/10.1101/2021.04.02.438263. ConCISE. 

  13. Coupling of NOD2 to GIV is Required for Bacterial Sensing
    Gajanan D. Katkar, Mahitha Shree Anandachar, Saptarshi Sinha, Stella-Rita Ibeawuchi, Celia R. Espinoza, Jane Coates, Yashaswat S. Malhotra, Madhubanti Mullick, Vanessa Castillo, Daniella T. Vo, Debashis Sahoo, Pradipta Ghosh
    bioRxiv 2022.04.26.489574; doi: https://doi.org/10.1101/2022.04.26.489574. - iNetMed


  14. 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 


PUBLISHED: Peer-Reviewed Original Articles

  1. Artificial Intelligence Guided Discovery of Gastric Cancer Continuum. Daniella Vo, Pradipta Ghosh*, Debashis Sahoo*. * Equal Contribution. Accepted in Press, Gastric Cancers (Impact Factor: 7.37): bioRxiv 2022.10.05.510975; doi: https://doi.org/10.1101/2022.10.05.510975. - PreCSN. 


  2. GIV/Girdin binds BRCA1 and links trimeric G-proteins to DNA damage response. Amer Ali Abd El-Hafeez, Nina Sun, Anirban Chakraborty, Jason Ear, Suchismita Roy, Pranavi Chamarthi, Navin Rajapakse, Soumita Das, Kathryn E. Luker, Tapas K. Hazra, Gary D. Luker, Pradipta Ghosh. Accepted, in Press, iScience, Dec 2022. bioRxiv 2021.07.21.452842; doi: https://doi.org/10.1101/2021.07.21.452842.
  3. Bayesian parameter estimation for dynamical models in systems biology. Linden NJ, Kramer B, Rangamani P. PLoS Comput Biol. 2022 Oct 21;18(10):e1010651. doi: 10.1371/journal.pcbi.1010651. eCollection 2022 Oct. PMID: 36269772. - ConCISE. 

  4. Boolean implication analysis of single-cell data predicts retinal cell type markers. Subramanian R, Sahoo D. BMC Bioinformatics. 2022 Sep 16;23(1):378. doi: 10.1186/s12859-022-04915-4.
    PMID: 36114457 - PreCSN. 


  5. A Boolean approach for novel hypoxia-related gene discovery. Stobdan T, Sahoo D, Haddad GG.
    PLoS One. 2022 Aug 25;17(8):e0273524. doi: 10.1371/journal.pone.0273524. eCollection 2022.
    PMID: 36006949 - PreCSN


  6. AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas. Ghosh P, Campos VJ, Vo DT, Guccione C, Goheen-Holland V, Tindle C, Mazzini GS, He Y, Alexandrov LB, Lippman SM, Gurski RR, Das S, Yadlapati R, Curtius K, Sahoo D. JCI Insight. 2022 Sep 22;7(18):e161334. doi: 10.1172/jci.insight.161334.
    PMID: 36134663 - PreCSN and HUMANOID


  7. COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis. 
    Sinha S, Castillo V, Espinoza CR, Tindle C, Fonseca AG, Dan JM, Katkar GD, Das S, Sahoo D, Ghosh P.
    EBioMedicine. 2022 Aug;82:104185. doi: 10.1016/j.ebiom.2022.104185. Epub 2022 Jul 20.
    PMID: 35870428 - PreCSN and HUMANOID

  8. Effects of iron modulation on mesenchymal stem cell-induced drug resistance in estrogen receptor-positive breast cancer. Buschhaus JM, Rajendran S, Humphries BA, Cutter AC, Muñiz AJ, Ciavattone NG, Buschhaus AM, Cañeque T, Nwosu ZC, Sahoo D, Bevoor AS, Shah YM, Lyssiotis CA, Ghosh P, Wicha MS, Rodriguez R, Luker GD. Oncogene. 2022 Jul;41(29):3705-3718. doi: 10.1038/s41388-022-02385-9. Epub 2022 Jun 22. PMID: 35732800. - PreCSN



  9. Hepatocyte Deletion of IGF2 Prevents DNA Damage and Tumor Formation in Hepatocellular Carcinoma. Kumar D, Das M, Oberg A, Sahoo D, Wu P, Sauceda C, Jih L, Ellies LG, Langiewicz MT, Sen S, Webster NJG. Adv Sci (Weinh). 2022 Jul;9(21):e2105120. doi: 10.1002/advs.202105120. Epub 2022 May 26.
    PMID: 35615981 - PreCSN


  10. A Microsatellite in the Coding Sequence of HLA-A/B Is a Mutation Hotspot in Colon Cancer With Microsatellite Instability. Raab WJ, Mazzocchi A, Radice P, Sahoo D, Castelli C, Dalerba P; Colon Cancer Immunology and Immunotherapy (CCII) study group. Gastroenterology. 2022 Mar;162(3):960-963.e3. doi: 10.1053/j.gastro.2021.10.006. Epub 2021 Oct 12. PMID: 34653421. - PreCSN 


  11. Upregulation of BMI1-suppressor miRNAs (miR-200c, miR-203) during terminal differentiation of colon epithelial cells. Hisamori S, Mukohyama J, Koul S, Hayashi T, Rothenberg ME, Maeda M, Isobe T, Valencia Salazar LE, Qian X, Johnston DM, Qian D, Lao K, Asai N, Kakeji Y, Gennarino VA, Sahoo D, Dalerba P, Shimono Y. J Gastroenterol. 2022 Jun;57(6):407-422. doi: 10.1007/s00535-022-01865-9. Epub 2022 Mar 4. PMID: 35244768. - PreCSN.


  12. Mechanistic insights into actin force generation during vesicle formation from cryo-electron tomography. Serwas D, Akamatsu M, Moayed A, Vegesna K, Vasan R, Hill JM, Schöneberg J, Davies KM, Rangamani P, Drubin DG. Dev Cell. 2022 May 9;57(9):1132-1145.e5. doi: 10.1016/j.devcel.2022.04.012. Epub 2022 May 2. PMID: 35504288. - ConCISE. 


  13. Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks. Hernández Mesa M, van den Brink J, Louch WE, McCabe KJ, Rangamani P. PLoS Comput Biol. 2022 Jun 6;18(6):e1010126. doi: 10.1371/journal.pcbi.1010126. eCollection 2022 Jun. PMID: 35666763. - ConCISE. 

  14. Nanoscale dynamics of actin filaments in the red blood cell membrane skeleton. Nowak RB, Alimohamadi H, Pestonjamasp K, Rangamani P, Fowler VM. Mol Biol Cell. 2022 Mar 1;33(3):ar28. doi: 10.1091/mbc.E21-03-0107. Epub 2022 Jan 12. PMID: 35020457. - ConCISE. 

  15. The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection.
    Hazra T, Tapryal N, Chakraborty A, Rayavara K, Wakamiya M, Islam A, Pan L, Hsu J, Tat V, Maruyama J, Hosoki K, Sayed I, Alcantara J, Castillo V, Tindle C, Sarker A, Cardenas V, Sharma G, Alexander LC, Sur S, Ghosh G, Paessler S, Sahoo D, Ghosh P, Das S, Boldogh I, Tseng CT.
    Nature Communications. Dec. 2022 May 27:rs.3.rs-1690354. doi: 10.21203/rs.3.rs-1690354/v1. Preprint.
    PMID: 35665009. - PreCSN and HUMANOID.

  16. An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. Ghosh P, Katkar GD, Shimizu C, Kim J, Khandelwal S, Tremoulet AH, Kanegaye JT; Pediatric Emergency Medicine Kawasaki Disease Research Group, Bocchini J, Das S, Burns JC, Sahoo D.
    Nat Commun. 2022 May 16;13(1):2687. doi: 10.1038/s41467-022-30357-w.
    PMID: 35577777 - PreCSN and HUMANOID. 

  17. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients.
    Gonzalez CG, Mills RH, Kordahi MC, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey JC Jr, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS. Cell Mol Gastroenterol Hepatol. 2022;14(1):35-53. doi: 10.1016/j.jcmgh.2022.03.008. Epub 2022 Apr 1. PMID: 35378331 - PreCSN.


  18. Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. Katkar GD, Sayed IM, Anandachar MS, Castillo V, Vidales E, Toobian D, Usmani F, Sawires JR, Leriche G, Yang J, Sandborn WJ, Das S, Sahoo D, Ghosh P.
    Commun Biol. 2022 Mar 14;5(1):231. doi: 10.1038/s42003-022-03168-4. PMID: 35288651. - PreCSN and HUMANOID. 


  19. RNA binding protein DDX5 directs tuft cell specification and function to regulate microbial repertoire and disease susceptibility in the intestine. Long T, Abbasi N, Hernandez JE, Li Y, Sayed IM, Ma S, Iemolo A, Yee BA, Yeo GW, Telese F, Ghosh P, Das S, Huang WJM. Gut. 2022 Sep;71(9):1790-1802. doi: 10.1136/gutjnl-2021-324984. Epub 2021 Dec 1. PMID: 34853057. - HUMANOID.


  20. SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia. Vo DT, Fuller MR, Tindle C, Anandachar MS, Das S, Sahoo D, Ghosh P.
    iScience. 2021 Sep 11;24(10):103121. doi: 10.1016/j.isci.2021.103121. eCollection 2021 Oct 22.
    PMID: 34622168. - PreCSN and HUMANOID.

  21. Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematics and revealed by a three dimensional computational framework.
    Auddya D, Zhang X, Gulati R, Vasan R, Garikipati K, Rangamani P, Rudraraju S.
    Proc Math Phys Eng Sci. 2021 Nov;477(2255):20210246. doi: 10.1098/rspa.2021.0246. Epub 2021 Nov 10.
    PMID: 35153593 - ConCISE. 
  22. Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. Tindle C, Fuller M, Fonseca A, Taheri S, Ibeawuchi SR, Beutler N, Katkar GD, Claire A, Castillo V, Hernandez M, Russo H, Duran J, Crotty Alexander LE, Tipps A, Lin G, Thistlethwaite PA, Chattopadhyay R, Rogers TF, Sahoo D, Ghosh P, Das S. Elife. 2021 Aug 13;10:e66417. doi: 10.7554/eLife.66417. PMID: 34463615. - HUMANOID and PreCSN. 


  23. Bladder Cancer Invasion Is Mediated by Mammalian Target of Rapamycin Complex 2-Driven Regulation of Nitric Oxide and Invadopodia Formation. Sahu D, Huan J, Wang H, Sahoo D, Casteel DE, Klemke RL, Boss GR, Hansel DE. Am J Pathol. 2021 Dec;191(12):2203-2218. doi: 10.1016/j.ajpath.2021.08.002. Epub 2021 Aug 21. PMID: 34428425. - PreCSN


  24. GIV/Girdin, a Non-receptor Modulator for Gαi/s, Regulates Spatiotemporal Signaling during Sperm Capacitation and is Required for Male Fertility. Sequoyah Reynoso, Vanessa Castillo, Gajanan Dattatray Katkar, Inmaculada Lopez-Sanchez, Sahar Taheri, Celia R. Espinoza, Cristina Rohena, Debashis Sahoo, Pascal Gagneux, and Pradipta Ghosh. bioRxiv 2021. Accepted, eLife - ConCISE and PreCSN
  25. Modeling membrane nanotube morphology: the role of heterogeneity in composition and material propertiesHaleh AlimohamadiBen OvrynPadmini Rangamani. Sci Rep. 2020 Feb 13;10(1):2527. doi: 10.1038/s41598-020-59221-x. PMID: 32054874; PMCID: PMC7018976. - ConCISE.
  26. AI-guided Discovery of a Barrier-Protective Therapy in Inflammatory Bowel Disease. Sahoo, D*, Swanson L, Sayed, I, Katkar G.D., Ibeawuchi S., Mittal Y., Pranadinata RF, Tindle C, Fuller MR, Stec DL, Chang JT, Sandborn WJ, Das S*, Ghosh*, P. Nat Commun. 2021 Jul 12;12(1):4246. doi: 10.1038/s41467-021-24470-5. PMID: 34253728 - PreCSN and HUMANOID.
  27. AI-guided discovery of the invariant host response to viral pandemics. Sahoo D, Katkar GD, Khandelwal S, Behroozikhah M, Claire A, Castillo V, Tindle C, Fuller M, Taheri S, Rogers TF, Beutler N, Ramirez SI, Rawlings SA, Pretorius V, Smith DM, Burton DR, Crotty Alexander LE, Duran J, Crotty S, Dan JM, Das S, Ghosh P. EBioMedicine. 2021 Jun;68:103390. doi: 10.1016/j.ebiom.2021.103390. Epub 2021 Jun 11. PMID: 34127431 - PreCSN and HUMANOID  
  28. Transfer function for YAP/TAZ nuclear translocation revealed through spatial systems modelingKiersten E. ScottStephanie I. FraleyPadmini Rangamani. Proc Natl Acad Sci U S A. 2021 May 18;118(20):e2021571118. doi: 10.1073/pnas.2021571118. Epub 2021 May 14. PMID: 33990464.
  29. Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. Malina Bakowski, Nathan Beutler , Dr Karen Wolff , Melanie Kirkpatrick , Emily Chen , Tu-Trinh Nguyen , Dr Laura Riva , Dr Namir Shaabani , Mara Parren , James Ricketts , Dr Anil Gupta , Kastin Pan , Peiting Kuo , Mackenzie Fuller , Elijah Garcia , Dr John Teijaro , Linlin Yang , Dr Debashis Sahoo , Victor Chi , Edward Huang , Natalia Vargas , Dr Amanda Roberts , Dr Soumita Das , Professor Pradipta Ghosh , Dr Ashley Woods , Dr Sean Joseph , Dr Peter Schultz , Dr Dennis Burton , Dr Arnab Chatterjee , Dr Case McNamara , Dr Thomas Rogers , Mr Mitchell Hull. Nat Commun. 2021 Jun 3;12(1):3309. doi: 10.1038/s41467-021-23328-0. PMID: 34083527 - PreCSN and HUMANOID.
  30. Building Unconventional G-protein Coupled Receptors: One block at a time. Ghosh, Pradipta and Mullick, Madhubanti. Trends Pharmacol Sci. 2021 Jul;42(7):514-517. doi: 10.1016/j.tips.2021.04.005. Epub 2021 May 10. PMID: 33985816. -ConCISE.
  31. Immunosuppression of Macrophages Underlies the Cardioprotective Effects of CST (Catestatin). Ying W, Tang K, Avolio E, Schilling JM, Pasqua T, Liu MA, Cheng H, Gao H, Zhang J, Mahata S, Ko MS, Bandyopadhyay G, Das S, Roth DM, Sahoo D, Webster NJG, Sheikh F, Ghosh G, Patel HH, Ghosh P, van den Bogaart G, Mahata SK.Hypertension. 2021 May 5;77(5):1670-1682. doi: 10.1161/HYPERTENSIONAHA.120.16809. Epub 2021 Apr 7.PMID: 33826401 - PreCSN.

  32. Chromogranin A regulates gut permeability via the antagonistic actions of its proteolytic peptides. Muntjewerff EM, Tang K, Lutter L, Christoffersson G, Nicolasen MJT, Gao H, Katkar GD, Das S, Ter Beest M, Ying W, Ghosh P, Aidy SE, Oldenburg B, van den Bogaart G, Mahata SK.Acta Physiol (Oxf). 2021 Mar 30:e13655. doi: 10.1111/apha.13655. Online ahead of print.PMID: 33783968. 

  33. Discovery of antiproliferative and anti-FAK inhibitory activity of 1,2,4-triazole derivatives containing acetamido carboxylic acid skeleton. Mustafa M, Abuo-Rahma GEA, Abd El-Hafeez AA, Ahmed ER, Abdelhamid D, Ghosh P, Hayallah AM.Bioorg Med Chem Lett. 2021 May 15;40:127965. doi: 10.1016/j.bmcl.2021.127965. Epub 2021 Mar 17.PMID: 33744442. - Drug Discovery Program

  34. Deletion of intestinal epithelial AMP-activated protein kinase alters distal colon permeability but not glucose homeostasis. Olivier S, Pochard C, Diounou H, Castillo V, Divoux J, Alcantara J, Leclerc J, Guilmeau S, Huet C, Charifi W, Varin TV, Daniel N, Foretz M, Neunlist M, Salomon BL, Ghosh P, Marette A, Rolli-Derkinderen M, Viollet B.Mol Metab. 2021 May;47:101183. doi: 10.1016/j.molmet.2021.101183. Epub 2021 Feb 4.PMID: 33548500.  

  35. Value of models for membrane budding. Lee CT, Akamatsu M, Rangamani P. Curr Opin Cell Biol. 2021 Mar 8;71:38-45. doi: 10.1016/j.ceb.2021.01.011. Online ahead of print.PMID: 33706232- ConCISE 

  36. Isolation and characterization of hESC-derived heart field-specific cardiomyocytes unravels new insights into their transcriptional and electrophysiological profiles. Pezhouman A, Engel JL, Nguyen NB, Skelton RJP, Gilmore WB, Qiao R, Sahoo D, Zhao P, Elliott DA, Ardehali R.Cardiovasc Res. 2021 Mar 21:cvab102. doi: 10.1093/cvr/cvab102. Online ahead of print.PMID: 33744937. - PreCSN


  37. Membrane bending by protein phase separation. Yuan F, Alimohamadi H, Bakka B, Trementozzi AN, Day KJ, Fawzi NL, Rangamani P, Stachowiak JC. Proc Natl Acad Sci U S A. 2021 Mar 16;118(11):e2017435118. doi: 10.1073/pnas.2017435118. PMID: 33688043- ConCISE.

  38. SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation. Li J, Xu X, Tiwari M, Chen Y, Fuller M, Bansal V, Tamayo P, Das S, Ghosh P, Sen GL.Nat Commun. 2021 Feb 4;12(1):784. doi: 10.1038/s41467-021-21067-w.PMID: 33542242. - HUMANOID 

  39. Apurinic/Apyrimidinic Endonuclease 1 Restricts the Internalization of Bacteria Into Human Intestinal Epithelial Cells Through the Inhibition of Rac1. den Hartog G, Butcher LD, Ablack AL, Pace LA, Ablack JNG, Xiong R, Das S, Stappenbeck TS, Eckmann L, Ernst PB, Crowe SE.Front Immunol. 2021 Feb 2;11:553994. doi: 10.3389/fimmu.2020.553994. eCollection 2020. PMID: 33603730. - HUMANOID

  40. A zebrafish model of granulin deficiency reveals essential roles in myeloid cell differentiation. Campbell CA, Fursova O, Cheng X, Snella E, McCune A, Li L, Solchenberger B, Schmid B, Sahoo D, Morton M, Traver D, Espín-Palazón R.Blood Adv. 2021 Feb 9;5(3):796-811. doi: 10.1182/bloodadvances.2020003096.PMID: 33560393. -PreCSN

  41. Stability Analysis of a Signaling Circuit with Dual Species of GTPase Switches. Stolerman LM, Ghosh P, Rangamani P. Bull Math Biol. 2021 Feb 20;83(4):34. doi: 10.1007/s11538-021-00864-w. PMID: 33609194 - ConCISE.

  42. Boolean implication analysis unveils candidate universal relationships in microbiome data. Vo D, Singh SC, Safa S, Sahoo D.BMC Bioinformatics. 2021 Feb 5;22(1):49. doi: 10.1186/s12859-020-03941-4.PMID: 33546590. PreCSN. 

  43. Computational modeling approaches to cAMP/PKA signaling in cardiomyocytes. McCabe KJ, Rangamani P.J Mol Cell Cardiol. 2021 May;154:32-40. doi: 10.1016/j.yjmcc.2021.01.008. Epub 2021 Feb 4.PMID: 33548239 -ConCISE. 

  44. E-cigarettes compromise the gut barrier and trigger inflammation. Sharma A, Lee J, Fonseca AG, Moshensky A, Kothari T, Sayed IM, Ibeawuchi SR, Pranadinata RF, Ear J, Sahoo D, Crotty-Alexander LE, Ghosh P, Das S.iScience. 2021 Jan 6;24(2):102035. doi: 10.1016/j.isci.2021.102035. eCollection 2021 Feb 19.PMID: 33537654. - HUMANOID

  45. The Mechanics and Thermodynamics of Tubule Formation in Biological Membranes. Mahapatra A, Uysalel C, Rangamani P. J Membr Biol. 2021 Jan 19. doi: 10.1007/s00232-020-00164-9. Online ahead of print. PMID: 33462667 -ConCISE.
  46. Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit. Tenner B, Getz M, Ross B, Ohadi D, Bohrer CH, Greenwald E, Mehta S, Xiao J, Rangamani P, Zhang J.Elife. 2020 Nov 17;9:e55013. doi: 10.7554/eLife.55013.PMID: 33201801 -ConCISE

  47. Receptor tyrosine kinases activate heterotrimeric G proteins via phosphorylation within the interdomain cleft of Gαi. Kalogriopoulos NA, Lopez-Sanchez I, Lin C, Ngo T, Midde KK, Roy S, Aznar N, Murray F, Garcia-Marcos M, Kufareva I, Ghassemian M, Ghosh P.Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):28763-28774. doi: 10.1073/pnas.2004699117. Epub 2020 Nov 2.PMID: 33139573 - ConCISE

  48. TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin. Swanson L, Katkar GD, Tam J, Pranadinata RF, Chareddy Y, Coates J, Anandachar MS, Castillo V, Olson J, Nizet V, Kufareva I, Das S, Ghosh P.Proc Natl Acad Sci U S A. 2020 Oct 27;117(43):26895-26906. doi: 10.1073/pnas.2011667117. Epub 2020 Oct 14.PMID: 33055214. - ConCISE.

  49. ATP synthase: Evolution, energetics, and membrane interactions. Nirody JA, Budin I, Rangamani P.J Gen Physiol. 2020 Nov 2;152(11):e201912475. doi: 10.1085/jgp.201912475. PMID: 32966553. - ConCISE

  50. Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h. Espanola SG, Song H, Ryu E, Saxena A, Kim ES, Manegold JE, Nasamran CA, Sahoo D, Oh CK, Bickers C, Shin U, Grainger S, Park YH, Pandolfo L, Kang MS, Kang S, Myung K, Cooper KL, Yelon D, Traver D, Lee Y. Nat Cell Biol. 2020 Dec;22(12):1411-1422. doi: 10.1038/s41556-020-00604-7. Epub 2020 Nov 23. PMID: 33230303 - PreCSN.

  51. Diffuso-kinetic membrane budding dynamics. Rojas Molina R , Liese S , Alimohamadi H , Rangamani P , Carlson A . Soft Matter. 2020 Dec 28;16(48):10889-10899. doi: 10.1039/d0sm01028f. Epub 2020 Oct 30. PMID: 33125025. - ConCISE.

  52. The DNA Glycosylase NEIL2 Suppresses Fusobacterium-Infection-Induced Inflammation and DNA Damage in Colonic Epithelial Cells. Sayed IM, Chakraborty A, Abd El-Hafeez AA, Sharma A, Sahan AZ, Huang WJM, Sahoo D, Ghosh P, Hazra TK, Das S.Cells. 2020 Aug 28;9(9):1980. doi: 10.3390/cells9091980.PMID: 32872214 - HUMANOID

  53. DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. Abbasi 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 

  54. 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
  55. 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
  56. 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  

  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants. 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. Commun Biol. 2020 May 22;3(1):259. doi: 10.1038/s42003-020-0985-2.PMID: 32444859 - PreCSN
  63. 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
  64. 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
  65. 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 
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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 
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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