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Publications

Publications are annotated with the name of the Institute's Center that led the efforts:

  • 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. FORWARD: A Learning Framework for Logical Network Perturbations to Prioritize Targets for Drug Development.
    Sinha S, McLaren E, Mullick M, Singh S, Boland BS, Ghosh P.bioRxiv [Preprint]. 2024 Jul 21:2024.07.16.602603. doi: 10.1101/2024.07.16.602603.PMID: 39071297
  2. Molecular Signatures for Microbe-Associated Colorectal Cancers.
    Sayed IM, Vo DT, Alcantara J, Inouye KM, Pranadinata RF, Luo L, Boland CR, Goyal NP, Kuo DJ, Huang SC, Sahoo D, Ghosh P, Das S.bioRxiv [Preprint]. 2024 May 27:2024.05.26.595902. doi: 10.1101/2024.05.26.595902.PMID: 38853996
  3. A Living Organoid Biobank of Crohn's Disease Patients Reveals Distinct Clinical Correlates of Molecular Disease Subtypes. Penrose HM, Sinha S, Tindle C, Zablan K, Le HN, Neill J, Ghosh P, Boland BS.medRxiv [Preprint]. 2025 Jul 9:2025.04.01.25325058. doi: 10.1101/2025.04.01.25325058.PMID: 40236416 
  4. A Foundational Model for Biological Logic and Disease. Sinha S. and Ghosh P. October 2025, Pre-Print: https://zenodo.org/records/17490789
  5. Obstacles Regulate Membrane Tension Propagation to Enable Localized Mechanotransduction. Català-Castro F, Bonilla-Quintana M, Sanfeliu-Cerdán N, Rangamani P, Krieg M. bioRxiv [Preprint]. 2025 Sep 23:2025.01.14.632796. doi: 10.1101/2025.01.14.632796.PMID: 41040213
  6. A balance between nucleating and elongating actin filaments controls deformation of protein condensates. Walker C, Mansour D, Effiong U, Jordan D, Wang L, Lafer EM, Alvarado J, Belardi B, Rangamani P, Stachowiak JC. bioRxiv [Preprint]. 2025 Jun 21:2025.06.18.660423. doi: 10.1101/2025.06.18.660423.PMID: 40667218. - ConCISE
  7. Formation of extracellular vesicles depends on mechanical feedback of the cortex and the glycocalyx. Xiao K, Rangamani P.bioRxiv [Preprint]. 2025 Jun 15:2025.06.14.659723. doi: 10.1101/2025.06.14.659723.PMID: 40661588. - ConCISE
  8. Mechanochemical feedback between confinement and actin crosslinking drives the shape dynamics of liquid-like droplets. Mansour D, Jordan D, Walker C, Chandrasekaran A, Lee CT, Graham K, Stachowiak J, Rangamani P. bioRxiv [Preprint]. 2025 Jun 15:2025.06.13.659650. doi: 10.1101/2025.06.13.659650.PMID: 40661572. - ConCISE 
  9. Dynamics of the formation of flat clathrin lattices in response to growth factor stimulus. Qiao L, Alfonzo-Méndez MA, Taraska JW, Rangamani P.bioRxiv [Preprint]. 2025 May 23:2025.05.22.655576. doi: 10.1101/2025.05.22.655576.PMID: 40475677 

PUBLISHED: Peer-Reviewed Original Articles

  1. CANDiT: A machine learning framework for differentiation therapy in colorectal cancer. Sinha S, Alcantara J, Perry K, Castillo V, Ondersma AK, Banerjee S, McLaren E, Espinoza CR, Taheri S, Vidales E, Tindle C, Adel A, Amirfakhri S, Sawires JR, Yang J, Bouvet M, Ghosh P. Cell Rep Med. 2025 Oct 20:102421. doi: 10.1016/j.xcrm.2025.102421.  PMID: 41118768 – iNetMed

  2. Systems modeling and uncertainty quantification of AMP-activated protein kinase signaling. Linden-Santangeli N, Zhang J, Kramer B, Rangamani P.NPJ Syst Biol Appl. 2025 Oct 14;11(1):113. doi: 10.1038/s41540-025-00588-w.PMID: 41087369. - ConCISE

  3. Calcium dynamics in small spaces: Lessons learned from modeling in dendritic spines. McCabe KJ, Hernández Mesa M, Rangamani P. Biophys J. 2025 Sep 29:S0006-3495(25)00618-6. doi: 10.1016/j.bpj.2025.09.038. Online ahead of print. PMID: 41029900 – ConCISE.

  4. Longitudinal Metabolic Trajectories in Diabetes Prevention Program Participants Reveal Subgroups With Varying Micro- and Macrovascular Complication Risks. Kobayashi E, Linden-Santangeli NJ, Chan N, Toomey CB, Mudaliar S, Temprosa M, Edelstein S, Goyal R, Rangamani P, Majithia AR; Diabetes Prevention Program Research Group.Diabetes Care. 2025 Oct 1;48(10):1704-1712. doi: 10.2337/dc25-0866.PMID: 40857122. – ConCISE

  5. Differential Efficacy of Advanced Therapies in Inducing Remission in Ulcerative Colitis Based on Prior Exposure to TNF Antagonists. Lee HH, Solitano V, Singh S, Ananthakrishnan AN, Jairath V, Syal G, Boland BS, Ghosh P, Chang JT, Singh S.Clin Gastroenterol Hepatol. 2025 Nov;23(12):2102-2114.e5. doi: 10.1016/j.cgh.2024.12.007. Epub 2024 Dec 26.PMID: 39732355. - iNetMed

  6. Increasing certainty in systems biology models using Bayesian multimodel inference. Linden-Santangeli N, Zhang J, Kramer B, Rangamani P. Nat Commun. 2025 Aug 11;16(1):7416. doi: 10.1038/s41467-025-62415-4.PMID: 40790297. ConCISE

  7. Local enrichment of cardiolipin to transient membrane undulations. Lee CT, Venkatraman K, Budin I, Rangamani P. Biophys J. 2025 Aug 5;124(15):2476-2487. doi: 10.1016/j.bpj.2025.06.025. Epub 2025 Jun 25.PMID: 40574331 - ConCISE

  8. Bright and Specific Targeting of Metastatic Lymph Nodes in Orthotopic Mouse Models of Gastric Cancer with a Fluorescent Anti-CEA Antibody. Cox KE, Amirfakhri S, Lwin TM, Hosseini M, Ghosh P, Obonyo M, Hoffman RM, Yazaki PJ, Bouvet M.Ann Surg Oncol. 2025 May;32(5):3796-3803. doi: 10.1245/s10434-025-16919-4. Epub 2025 Jan 29.PMID: 39878844. – iNetMed

  9. Nootropic benzothiazoles promote dendritic spine formation by targeting fascin-1. Shivkumar A, Berg KR, Sibucao KC, Leriche G, Dozier LE, Espinoza CA, Patrick GN, Gaieb Z, Seitz C, Amaro RE, Park HH, Hoe HS, Wozniak J, Gonzalez DJ, Sinha S, Ghosh P, Yang J.J Biol Chem. 2025 Sep;301(9):110572. doi: 10.1016/j.jbc.2025.110572. Epub 2025 Aug 8.PMID: 40784448. - PreCSN

  10. Breast cancers that disseminate to bone marrow acquire aggressive phenotypes through CX43-related tumor-stroma tunnels.
    Sinha S, Callow BW, Farfel AP, Roy S, Chen S, Masotti M, Rajendran S, Buschhaus JM, Espinoza CR, Luker KE, Ghosh P, Luker GD.J Clin Invest. 2024 Oct 31;134(24):e170953. doi: 10.1172/JCI170953.PMID: 39480488
  11. A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeutics.
    Tindle C, Fonseca AG, Taheri S, Katkar GD, Lee J, Maity P, Sayed IM, Ibeawuchi SR, Vidales E, Pranadinata RF, Fuller M, Stec DL, Anandachar MS, Perry K, Le HN, Ear J, Boland BS, Sandborn WJ, Sahoo D, Das S, Ghosh P.Cell Rep Med. 2024 Oct 15;5(10):101748. doi: 10.1016/j.xcrm.2024.101748. Epub 2024 Sep 26.PMID: 39332415
  12. Targeting Patient-Derived Orthotopic Gastric Cancers with a Fluorescent Humanized Anti-CEA Antibody.
    Cox KE, Turner MA, Lwin TM, Amirfakhri S, Kelly KJ, Hosseini M, Ghosh P, Obonyo M, Hoffman RM, Yazaki PJ, Bouvet M.Ann Surg Oncol. 2024 Sep;31(9):6291-6299. doi: 10.1245/s10434-024-15570-9. Epub 2024 Jun 18.PMID: 38888861
  13. Human-specific elimination of epithelial Siglec-XII suppresses the risk of inflammation-driven colorectal cancers.
    Cuello HA, Sinha S, Verhagen AL, Varki N, Varki A, Ghosh P.JCI Insight. 2024 Jul 11;9(16):e181539. doi: 10.1172/jci.insight.181539.PMID: 38990656
  14. Engineered bacterial therapeutics for detecting and treating CRC.
    Siguenza N, Brevi A, Zhang JT, Pabani A, Bhushan A, Das M, Ding Y, Hasty J, Ghosh P, Zarrinpar A.Trends Cancer. 2024 Jul;10(7):588-597. doi: 10.1016/j.trecan.2024.04.001. Epub 2024 Apr 30.PMID: 38693003
  15. Growth factor-dependent phosphorylation of Gαi shapes canonical signaling by G protein-coupled receptors.
    Roy S, Sinha S, Silas AJ, Ghassemian M, Kufareva I, Ghosh P.Sci Signal. 2024 Jun 4;17(839):eade8041. doi: 10.1126/scisignal.ade8041. Epub 2024 Jun 4.PMID: 38833528
  16. MDA5-autoimmunity and interstitial pneumonitis contemporaneous with the COVID-19 pandemic (MIP-C).
    David P, Sinha S, Iqbal K, De Marco G, Taheri S, McLaren E, Maisuria S, Arumugakani G, Ash Z, Buckley C, Coles L, Hettiarachchi C, Payne E, Savic S, Smithson G, Slade M, Shah R, Marzo-Ortega H, Keen M, Lawson C, Mclorinan J, Nizam S, Reddy H, Sharif O, Sultan S, Tran G, Wood M, Wood S, Ghosh P, McGonagle D.EBioMedicine. 2024 Jun;104:105136. doi: 10.1016/j.ebiom.2024.105136. Epub 2024 May 8.PMID: 38723554 
  17. Interlinked switch circuits of biological intelligence.
    Mukherjee R, Sinha S, Luker GD, Ghosh P.Trends Biochem Sci. 2024 Apr;49(4):286-289. doi: 10.1016/j.tibs.2024.01.006. Epub 2024 Feb 9.PMID: 38341333
  18. Growth signaling autonomy in circulating tumor cells aids metastatic seeding.
    Sinha S, Farfel A, Luker KE, Parker BA, Yeung KT, Luker GD, Ghosh P.PNAS Nexus. 2024 Jan 25;3(2):pgae014. doi: 10.1093/pnasnexus/pgae014. eCollection 2024 Feb.PMID: 38312224
  19. Humanized Anti-Carcinoembryonic Antigen Antibodies Brightly Target and Label Gastric Cancer in Orthotopic Mouse Models.
    Cox KE, Turner MA, Amirfakhri S, Lwin TM, Hosseini M, Ghosh P, Obonyo M, Murakami T, Hoffman RM, Yazaki PJ, Bouvet M.J Surg Res. 2024 Jan;293:701-708. doi: 10.1016/j.jss.2023.08.038. Epub 2023 Oct 14.PMID: 37839102
  20. The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection.
    Tapryal N, Chakraborty A, Saha K, Islam A, Pan L, Hosoki K, Sayed IM, Duran JM, Alcantara J, Castillo V, Tindle C, Sarker AH, Wakamiya M, Cardenas VJ, Sharma G, Crotty Alexander LE, Sur S, Sahoo D, Ghosh G, Das S, Ghosh P, Boldogh I, Hazra TK.Nat Commun. 2023 Dec 9;14(1):8169. doi: 10.1038/s41467-023-43938-0.PMID: 38071370
  21. Macrophage states: there's a method in the madness.
    Katkar G, Ghosh P.Trends Immunol. 2023 Dec;44(12):954-964. doi: 10.1016/j.it.2023.10.006. Epub 2023 Nov 7.PMID: 37945504
  22. Diverse gut pathogens exploit the host engulfment pathway via a conserved mechanism.
    Anandachar MS, Roy S, Sinha S, Boadi A, Katkar GD, Ghosh P.J Biol Chem. 2023 Dec;299(12):105390. doi: 10.1016/j.jbc.2023.105390. Epub 2023 Oct 27.PMID: 37890785
  23. The arginine methyltransferase PRMT5 promotes mucosal defense in the intestine.
    Hernandez JE, Llorente C, Ma S, Miyamoto KT, Sinha S, Steele S, Xiao Z, Lai CJ, Zuniga EI, Ghosh P, Schnabl B, Huang WJM.Life Sci Alliance. 2023 Sep 4;6(11):e202302026. doi: 10.26508/lsa.202302026. Print 2023 Nov.PMID: 37666668
  24. Anticancer pan-ErbB inhibitors reduce inflammation and tissue injury and exert broad-spectrum antiviral effects.
    Saul S, Karim M, Ghita L, Huang PT, Chiu W, Durán V, Lo CW, Kumar S, Bhalla N, Leyssen P, Alem F, Boghdeh NA, Tran DH, Cohen CA, Brown JA, Huie KE, Tindle C, Sibai M, Ye C, Khalil AM, Chiem K, Martinez-Sobrido L, Dye JM, Pinsky BA, Ghosh P, Das S, Solow-Cordero DE, Jin J, Wikswo JP, Jochmans D, Neyts J, De Jonghe S, Narayanan A, Einav S.J Clin Invest. 2023 Oct 2;133(19):e169510. doi: 10.1172/JCI169510.PMID: 37581931
  25. Bicyclic Peptide Library Screening for the Identification of Gαi Protein Modulators.
    Pepanian A, Binbay FA, Roy S, Nubbemeyer B, Koley A, Rhodes CA, Ammer H, Pei D, Ghosh P, Imhof D.J Med Chem. 2023 Sep 14;66(17):12396-12406. doi: 10.1021/acs.jmedchem.3c00873. Epub 2023 Aug 16.PMID: 37587416
  26. Clinicopathologic Significance of Heat Shock Protein 60 as a Survival Predictor in Colorectal Cancer.
    Kang M, Jeong S, An J, Park S, Nam S, Kwon KA, Sahoo D, Ghosh P, Kim JH.Cancers (Basel). 2023 Aug 11;15(16):4052. doi: 10.3390/cancers15164052.PMID: 37627080
  27. Identification of a novel gene signature for neuroblastoma differentiation using a Boolean implication network.
    Zage PE, Huo Y, Subramonian D, Le Clorennec C, Ghosh P, Sahoo D.Genes Chromosomes Cancer. 2023 Jun;62(6):313-331. doi: 10.1002/gcc.23124. Epub 2023 Feb 13.PMID: 36680522
  28. Regulation of DNA damage response by trimeric G-proteins.
    Abd El-Hafeez AA, Sun N, Chakraborty A, Ear J, Roy S, Chamarthi P, Rajapakse N, Das S, Luker KE, Hazra TK, Luker GD, Ghosh P.iScience. 2023 Jan 13;26(2):105973. doi: 10.1016/j.isci.2023.105973. eCollection 2023 Feb 17.PMID: 36756378
  29. Identification of novel piperazine-tethered phthalazines as selective CDK1 inhibitors endowed with in vitro anticancer activity toward the pancreatic cancer.
    Akl L, Abd El-Hafeez AA, Ibrahim TM, Salem R, Marzouk HMM, El-Domany RA, Ghosh P, Eldehna WM, Abou-Seri SM.Eur J Med Chem. 2022 Dec 5;243:114704. doi: 10.1016/j.ejmech.2022.114704. Epub 2022 Aug 31.PMID: 36095992
  30. Discovery of novel thiazolyl-pyrazolines as dual EGFR and VEGFR-2 inhibitors endowed with in vitro antitumor activity towards non-small lung cancer.
    Abdelsalam EA, Abd El-Hafeez AA, Eldehna WM, El Hassab MA, Marzouk HMM, Elaasser MM, Abou Taleb NA, Amin KM, Abdel-Aziz HA, Ghosh P, Hammad SF.J Enzyme Inhib Med Chem. 2022 Dec;37(1):2265-2282. doi: 10.1080/14756366.2022.2104841.PMID: 36000167
  31. New 1,2,3-triazole linked ciprofloxacin-chalcones induce DNA damage by inhibiting human topoisomerase I& II and tubulin polymerization.
    Mohammed HHH, Abd El-Hafeez AA, Ebeid K, Mekkawy AI, Abourehab MAS, Wafa EI, Alhaj-Suliman SO, Salem AK, Ghosh P, Abuo-Rahma GEA, Hayallah AM, Abbas SH.J Enzyme Inhib Med Chem. 2022 Dec;37(1):1346-1363. doi: 10.1080/14756366.2022.2072308.PMID: 35548854
  32. 2-Arylquinolines as novel anticancer agents with dual EGFR/FAK kinase inhibitory activity: synthesis, biological evaluation, and molecular modelling insights.
    Elbadawi MM, Eldehna WM, Abd El-Hafeez AA, Somaa WR, Albohy A, Al-Rashood ST, Agama KK, Elkaeed EB, Ghosh P, Pommier Y, Abe M.J Enzyme Inhib Med Chem. 2022 Dec;37(1):349-372. doi: 10.1080/14756366.2021.2015344.PMID: 34923887
  33. Parsing the Role of PPARs in Macrophage Processes.
    Toobian D, Ghosh P, Katkar GD.Front Immunol. 2021 Dec 22;12:783780. doi: 10.3389/fimmu.2021.783780. eCollection 2021.PMID: 35003101
  34. Clinico-pathological relationship between androgen receptor and tumour infiltrating lymphocytes in triple negative breast cancer.
    Elghazawy H, Bakkach J, Helal T, Aref AM, Kelany M, Abdallah LE, Abdelbakey FS, Ali D, Ali DZ, Ahmed MO, El-Hafeez AAA, Ghosh P, Alorabi MO.Ecancermedicalscience. 2021 Nov 11;15:1317. doi: 10.3332/ecancer.2021.1317. eCollection 2021.PMID: 35047068
  35. A first-in-class anticancer dual HDAC2/FAK inhibitors bearing hydroxamates/benzamides capped by pyridinyl-1,2,4-triazoles.
    Mustafa M, Abd El-Hafeez AA, Abdelhamid D, Katkar GD, Mostafa YA, Ghosh P, Hayallah AM, Abuo-Rahma GEA.Eur J Med Chem. 2021 Oct 15;222:113569. doi: 10.1016/j.ejmech.2021.113569. Epub 2021 May 29.PMID: 34111829
  36. Functional assays with human patient-derived enteroid monolayers to assess the human gut barrier.
    Sayed IM, Tindle C, Fonseca AG, Ghosh P, Das S.STAR Protoc. 2021 Jul 17;2(3):100680. doi: 10.1016/j.xpro.2021.100680. eCollection 2021 Sep 17.PMID: 34337445
  37. FAK inhibitors as promising anticancer targets: present and future directions.
    Mustafa M, Abd El-Hafeez AA, Abdelhafeez DA, Abdelhamid D, Mostafa YA, Ghosh P, Hayallah AM, A Abuo-Rahma GE.Future Med Chem. 2021 Sep;13(18):1559-1590. doi: 10.4155/fmc-2021-0015. Epub 2021 Aug 3.PMID: 34340532 
  38. Design principles of dose-response alignment in coupled GTPase switches. Lingxia Qiao, Pradipta Ghosh, Padmini Rangamani.
    NPJ Syst Biol Appl. 2023 Jan 31;9(1):3. doi: 10.1038/s41540-023-00266-9. PMID: 36720885 - ConCISE
  39. Formation of protein-mediated bilayer tubes is governed by a snapthrough transition A. Mahapatra, P. Rangamani
    Soft Matter. 2023 Jun 14;19(23):4345-4359. doi: 10.1039/d2sm01676a. PMID: 37255421 - ConCISE
  40. Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling A. Leung, P. Rangamani
    NPJ Syst Biol Appl. 2023 Jul 17;9(1):34. doi: 10.1038/s41540-023-00295-4. PMID: 37460570 - ConCISE
  41. Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling A. Khalilimeybodi, S.I. Fraley, P. Rangamani
    J Physiol. 2023 Feb;601(3):483-515. doi: 10.1113/JP283966. Epub 2023 Jan 16. PMID: 36463416 - ConCISE
  42. 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
    Sci. Adv. 2023 Jul 7;9(27):eadg3485. doi: 10.1126/sciadv.adg3485. Epub 2023 Jul 7. PMID: 37418523 - ConCISE
  43. Modeling membrane curvature generation using mechanics and machine learning S. A. Malingen, P. Rangamani
    J R Soc Interface. 2022 Sep;19(194):20220448.doi: 10.1098/rsif.2022.0448. Epub 2022 Sep 21. PMID: 36128706 - ConCISE
  44. 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.
    EBioMedicine. 2023 Aug:94:104719. doi: 10.1016/j.ebiom.2023.104719. Epub 2023 Jul 27. PMID: 37516087 - PreCSN
  45. Morphological principles of neuronal mitochondria. Rachel Mendelsohn, Guadalupe C. Garcia, Thomas M. Bartol, Christopher T. Lee, P. Khandelwal, Emily Liu, Donald J. Spencer, Adam Husar, Eric A. Bushong, Sebastien Phan, Guy Perkins, Mark H. Ellisman, Alexander Skupin, Terrence J. Sejnowski, Padmini Rangamani.
    J Comp Neurol. 2022 Apr;530(6):886-902. doi: 10.1002/cne.25254. Epub 2021 Nov 1. PMID: 34608995 - ConCISE
  46. 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
    PNAS Nexus. 2024 Jan 25;3(2):pgae014. doi: 10.1093/pnasnexus/pgae014. eCollection 2024 Feb. PMID: 38312224 - PreCSN
  47. 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.
    Mol Syst Biol. 2023 Apr 12;19(4):e11127. doi: 10.15252/msb.202211127. Epub 2023 Mar 1. PMID: 36856068- ConCISE.
  48. Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayers. Arijit Mahapatra, David Saintillan, Padmini Rangamani.
    Soft Matter. 2021 Sep 22;17(36):8373-8386. doi: 10.1039/d1sm00502b. PMID: 34550131 - ConCISE.
  49. 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.

  50. 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.

  51. 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.

  52. 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.

  53. 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

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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.

  60. 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.

  61. 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.

  62. 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.


  63. 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.

  64. 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.

  65. 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.

  66. 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.

  67. 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.

  68. 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.

  69. 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.

  70. 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

  71. 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

  72. Modeling membrane nanotube morphology: the role of heterogeneity in composition and material properties. Haleh Alimohamadi, Ben Ovryn, Padmini Rangamani. Sci Rep. 2020 Feb 13;10(1):2527. doi: 10.1038/s41598-020-59221-x. PMID: 32054874; PMCID: PMC7018976. - ConCISE.

  73. 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.

  74. 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
  75. Transfer function for YAP/TAZ nuclear translocation revealed through spatial systems modeling. Kiersten E. Scott, Stephanie I. Fraley, Padmini 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.

  76. 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.

  77. 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.

  78. 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.

  79. 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.

  80. 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

  81. 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.

  82. 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

  83. 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

  84. 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.

  85. 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

  86. 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

  87. 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

  88. 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.

  89. 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.

  90. 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.

  91. 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

  92. 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.

  93. 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

  94. 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

  95. 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.

  96. 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

  97. 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.

  98. 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.

  99. 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

  100. 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

  101. 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

  102. 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

  103. 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

  104. 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

  105. 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

  106. 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

  107. 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

  108. 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

  109. 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

  110. 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

  111. 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

  112. 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

  113. 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

  114. 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

  115. 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

  116. 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

  117. 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

  118. 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

  119. 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

  120. 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

  121. 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

  122. 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

  123. 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

  124. 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

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  126. 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

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  131. 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

  132. 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

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  134. 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

  135. 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

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  139. 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