Publications

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All Publications

2026

Konishi S^#, Enkhbayar K^#, Liu S, Miyashita N, Kobayashi Y, Hutchison V, Sai A, Agarwal P, Witonsky J, Jackson ND, Seibold MA, Chen J, Tata A^*, Tata PR^*. TP53/TAU axis regulates microtubule bundling to control alveolar stem cell mediated regeneration. Journal of Clinical Investigation. 2026 (in press). (^# equal contribution *co-corresponding author).

2025

Pratapa A, Tata PR*, Singh R*. Transforming Biological Foundation Model Representations for Out-of-Distribution Data. bioRxiv; 2025 Dec 3. p. 2025.11.20.689462. (*co-corresponding author).

Pratapa A, Mansouri S, Nikulina N, Matuck B, Schneider MA, Byrd KM, Savai R, Tata PR*, Singh R*. SAME: Topology-flexible transforms enable robust integration of multimodal spatial omics. bioRxiv; 2025 Sept 30. p. 2025.07.12.664419. (*co-corresponding author).

Kobayashi Y, Sunadome K, Maki K, Fukunaga H, Matsubara H, Ohkubo S, Maki R, Yoshikawa M, Tata A, Tata PR, Matsumoto Kichi, Adachi T, Iwaki M, Yamamoto T, Toyoshima F. Distinct dermal fibroblasts direct mechano-chemical signaling to the epidermis during pregnancy. bioRxiv; 2025 [cited 2025 Dec 3]. p. 2025.09.11.675503.

Matuck BF, Huynh KLA, Pereira D, Easter QT, Zhang X, Kunz M, Kumar N, Pratapa A, Rupp BT, Ghodke A, Predeus AV, Szabó L, Hartmann S, Harnischfeger N, Khavandgar Z, Beach M, Perez P, Nilges B, Moreno MM, Ko KI, Singh R, Tata PR, Teichmann SA, Kimple A, Pringle S, Kretzschmar K, Warner BM, Sequeira I, Liu J, Byrd KM. The Immunoregulatory Architecture of the Adult Oral Cavity. bioRxiv; 2025 Dec 3]. p. 2024.12.01.626279.

Cosgrove BD, Bounds LR, Taylor CK, Su AL, Rizzo AJ, Barrera A, Sun T, Safi A, Song L, Whitlow T, Tata A, Iglesias N, Diao Y, Tata PR, Hoffman BD, Crawford GE, Gersbach CA. Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness. Science. 2025 Sept 25;eadl1988. PMID: 40997217

Wu S, Drive I, Luo M, Miyazaki H, Shambhu S, Popov D, Yang L, Wang J, Ma J, Guo J, Atha J, Tata A, Hoffman EA, Wang Y, Tata PR, Jensen MB, Engelhardt JF, Sontake V, Liu X. Ferret model of bleomycin-induced lung injury shares features of human idiopathic pulmonary fibrosis. bioRxiv. 2025 May 14;2025.05.08.652970. PMCID: PMC12132224

Madhurakkat Perikamana SK, Kumar V, Mogha P, Duncan L, Angel N, Tata A, Jabba SV, Jordt SE, Tata PR, Varghese S. Modeling functional responses to pollutant exposure using modular hydrogel supported vascularized alveolosphere-on-a-chip. Biomater Sci. 2025 Oct 21;13(21):6046–6057. PMCID: PMC12442856

Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber G, Misra RS, Purkerson J, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber G, Jain Y, Qaurooni D, Kong Y, Tata PR, Team HRA, Bueckle A, Herr BW. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage. bioRxiv; 2024 [cited 2024 Oct 29]. p. 2024.03.27.587041.

Nakano S, Hamele CE, Tata A, Tata PR, Heaton NS. Influenza B virus infection alters the regenerative potential of murine alveolar type 2 pneumocytes. mBio. 2025 Feb 5;16(2):e0274324. PMCID: PMC11796384.

Forrester MT, Egol JR, Ozbay S, Waddell FD, Singh R, Tata PR. Topology-Driven Discovery of Transmembrane Protein S-Palmitoylation. J Biol Chem. 2025 Feb 3;108259. PMID: 39909380.

Vose A, Birukova A, Albright M, Schlobohm A, Garantziotis S, Tata PR, Barkauskas C, Tighe R. Hyaluronan Directs Alveolar Type II Cell Response to Acute Ozone Exposure in Mice. Am J Respir Cell Mol Biol. 2025 Jan 6; PMID: 39761597.

2024

Polkoff KM, Lampe R, Gupta NK, Murphy Y, Chung J, Carter A, Simon JM, Gleason K, Moatti A, Murthy PK, Edwards L, Greenbaum A, Tata A, Tata PR, Piedrahita JA. Novel Porcine Model Reveals Two Distinct LGR5 Cell Types During Lung Development and Homeostasis. Am J Respir Cell Mol Biol. 2024 Nov 5; PMID: 39499850.

Forrester MT, Egol JR, Tata A, Tata PR, Foster MW. Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap). J Proteome Res. 2024 Aug 2;23(8):3716–3725. PMID: 39008777

Tighe RM, Birukova A, Malakhau Y, Kobayashi Y, Vose AT, Chandramohan V, Cyphert-Daly JM, Cumming RI, Fradin Kirshner H, Tata PR, Ingram JL, Gunn MD, Que LG, Yu YRA. Altered ontogeny and transcriptomic signatures of tissue-resident pulmonary interstitial macrophages ameliorate allergic airway hyperresponsiveness. Front Immunol. 2024;15:1371764. PMCID: PMC11231371

Meganck RM, Edwards CE, Mallory ML, Lee RE, Dang H, Bailey AB, Wykoff JA, Gallant SC, Zhu DR, Yount BL, Kato T, Shaffer KM, Nakano S, Cawley AM, Sontake V, Wang JR, Hagan RS, Miller MB, Tata PR, Randell SH, Tse LV, Ehre C, Okuda K, Boucher RC, Baric RS. SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia. Cell Rep. 2024 Apr 23;43(4):114076. PMCID: PMC11165423.

Chioccioli M, Liu S, Magruder S, Tata A, Borriello L, McDonough JE, Konkimalla A, Kim SH, Nouws J, Gonzalez DG, Traub B, Ye X, Yang T, Entenberg DR, Krishnaswamy S, Hendry CE, Kaminski N, Tata PR, Sauler M. Stem cell migration drives lung repair in living mice. Developmental Cell. 2024 Feb 14;S1534-5807(24)00074–1. PMID: 38377991.

2023                                                      

Konkimalla A*, Konishi S*, Macadlo L*, Kobayashi Y, Farino ZJ, Miyashita N, El Haddad L, Morowitz J, Barkauskas CE, Agarwal P, Souma T, ElMallah MK, Tata A^§, Tata PR^§. Transitional cell states sculpt tissue topology during lung regeneration. Cell Stem Cell. 2023 Nov 2;30(11):1486-1502.e9. PMCID: PMC10762634 (* equal contribution, ^§ co-corresponding author).

Vazquez-Armendariz AI, Tata PR. Recent advances in lung organoid development and applications in disease modeling. J Clin Invest. 2023 Nov 15;133(22):e170500. PMCID: PMC10645385

Hou YJ, Chiba S, Leist SR, Meganck RM, Martinez DR, Schäfer A, Catanzaro NJ, Sontake V, West A, Edwards CE, Yount B, Lee RE, Gallant SC, Zost SJ, Powers J, Adams L, Kong EF, Mattocks M, Tata A, Randell SH, Tata PR, Halfmann P, Crowe JE, Kawaoka Y, Baric RS. Host range, transmissibility and antigenicity of a pangolin coronavirus. Nat Microbiol. 2023 Oct;8(10):1820–1833. PMCID: PMC10522490

El Haddad L, Lai E, Murthy PKL, Biswas DD, Soufny R, Roger AL, Tata PR, ElMallah MK. GAA deficiency disrupts distal airway cells in Pompe disease. Am J Physiol Lung Cell Mol Physiol. 2023 Sep 1;325(3):L288–L298. PMID: 37366541

Karmaus PWF, Tata A, Meacham JM, Day F, Thrower D, Tata PR, Fessler MB. Meta-Analysis of COVID-19 Bronchoalveolar Lavage scRNA-Seq Reveals Alveolar Epithelial Transitions and Unique Alveolar Epithelial Cell Fates. Am J Respir Cell Mol Biol. 2023 Jul 31; PMID: 37523502

Conchola AS, Frum T, Xiao Z, Hsu PP, Kaur K, Downey MS, Hein RFC, Miller AJ, Tsai YH, Wu A, Holloway EM, Anand A, Murthy PKL, Glass I, Tata PR, Spence JR. Regionally distinct progenitor cells in the lower airway give rise to neuroendocrine and multiciliated cells in the developing human lung. Proc Natl Acad Sci U S A. 2023 Jun 13;120(24):e2210113120. PMCID: PMC10268599

Konkimalla A, Elmore Z, Konishi S, Macadlo L, Katsura H, Tata A, Asokan A, Tata PR. Efficient AAV Mediated Transgenesis in Alveolar Stem Cells and Associated Niches. Am J Respir Cell Mol Biol. 2023 Jun 14; PMID: 37315312

Apostolou E, Blau H, Chien K, Lancaster MA, Tata PR, Trompouki E, Watt FM, Zeng YA, Zernicka-Goetz M. Progress and challenges in stem cell biology. Nat Cell Biol. 2023 Feb;25(2):203–206. PMID: 36788378

Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, Lung Biological Network Consortium, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe’er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med. 2023 Jun 8; PMID: 37291214.

2022

Ide S, Ide K, Abe K, Kobayashi Y, Kitai H, McKey J, Strausser SA, O’Brien LL, Tata A, Tata PR, Souma T. Sex differences in resilience to ferroptosis underlie sexual dimorphism in kidney injury and repair. Cell Rep. 2022 Nov 8;41(6):111610. PMCID: PMC9795409

Konkimalla A, Konishi S, Kobayashi Y, Kadur Lakshminarasimha Murthy P, Macadlo L, Mukherjee A, Elmore Z, Kim SJ, Pendergast AM, Lee PJ, Asokan A, Knudsen L, Bravo-Cordero JJ, Tata A, Tata PR. Multi-apical polarity of alveolar stem cells and their dynamics during lung development and regeneration. iScience. 2022 Oct 21;25(10):105114. PMCID: PMC9519774.

Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, Cohen BM, Kerelsky A, Lin TY, Liberatore KM, Bulaon DK, Van Nest SJ, Koundouros N, Kastenhuber ER, Mercadante MN, Shobana-Ganesh K, He L, Schwartz RE, Chen S, Weinstein H, Elemento O, Piskounova E, Nilsson-Payant BE, Lee G, Trimarco JD, Burke KN, Hamele CE, Chaparian RR, Harding AT, Tata A, Zhu X, Tata PR, Smith CM, Possemato AP, Tkachev SL, Hornbeck PV, Beausoleil SA, Anand SK, Aguet F, Getz G, Davidson AD, Heesom K, Kavanagh-Williamson M, Matthews DA, tenOever BR, Cantley LC, Blenis J, Heaton NS. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication. Sci Signal. 2022 Oct 25;15(757):eabm0808. PMCID: PMC9830954

DeBenedittis P, Karpurapu A, Henry A, Thomas MC, McCord TJ, Brezitski K, Prasad A, Baker CE, Kobayashi Y, Shah SH, Kontos CD, Tata PR, Lumbers RT, Karra R. Coupled myovascular expansion directs cardiac growth and regeneration. Development. 2022 Sep 15;149(18):dev200654. PMID: 36134690

Leinroth AP, Mirando AJ, Rouse D, Kobayahsi Y, Tata PR, Rueckert HE, Liao Y, Long JT, Chakkalakal JV, Hilton MJ. Identification of distinct non-myogenic skeletal-muscle-resident mesenchymal cell populations. Cell Rep. 2022 May 10;39(6):110785. PMID: 35545045.

Murthy P*, Sontake V*, Tata A, Kobayashi Y, Macadlo L, Okuda K, Conchola AS, Nakano S, Gregory S, Miller LA, Spence JR, Engelhardt JF, Boucher RC, Rock JR, Randell SH, Tata PR^§. Human distal lung maps and lineage hierarchies reveal a bipotent progenitor. Nature. 604, pages111–119 (2022). PMCID: PMC9169066(* equal contribution).

Konishi S, Tata A^§, Tata PR^§. Defined conditions for long-term expansion of murine and human alveolar epithelial stem cells in 3-dimensional culture. STAR Protocols 2022 Jun10;3(2):101447.PMCID: PMC9192963.

Kadur Lakshminarasimha Murthy P, Xi R, Arguijo D, Everitt JI, Kocak DD, Kobayashi Y, Bozec A, Vicent S, Ding S, Crawford GE, Hsu D, Tata PR, Reddy T, Shen X. Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity. Dev Cell. 2022 Feb 7;57(3):310-328.e9. PMCID: PMC8938988

Kumar V, Madhurakkat Perikamana SK, Tata A, Hoque J, Gilpin A, Tata PR, Varghese S. An In Vitro Microfluidic Alveolus Model to Study Lung Biomechanics. Front Bioeng Biotechnol. 2022;10:848699. PMCID: PMC8895303

2021

Konkimalla A, Tata A, Tata PR. Lung Regeneration: Cells, Models, and Mechanisms. Cold Spring Harb Perspect Biol. 2021 Nov 8;a040873. PMID: 34750172

Wang L, Wang E, Prado Balcazar J, Wu Z, Xiang K, Wang Y, Huang Q, Negrete M, Chen KY, Li W, Fu Y, Dohlman A, Mines R, Zhang L, Kobayashi Y, Chen T, Shi G, Shen JP, Kopetz S, Tata PR, Moreno V, Gersbach C, Crawford G, Hsu D, Huang E, Bu P, Shen X. Chromatin Remodeling of Colorectal Cancer Liver Metastasis is Mediated by an HGF-PU.1-DPP4 Axis. Adv Sci (Weinh). 2021 Aug 10;e2004673. PMID: 34378358

Tata A, Chow RD, Tata PR. Epithelial cell plasticity: breaking boundaries and changing landscapes. EMBO Rep. 2021 Jun 6;e51921. PMID: 34096150

Ide S, Kobayashi Y, Ide K, Strausser SA, Abe K, Herbek S, O’Brien LL, Crowley SD, Barisoni L, Tata A, Tata PR, Souma T. Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair. eLife. 2021 Jul 19;10:e68603. PMCID: PMC8318592

Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT-Y, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe’er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani A-C, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021 Apr 29; PMID: 33915569

Bui LT, Winters NI, Chung M-I, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE, Human Cell Atlas Lung Biological Network. Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Nat Commun. 2021 Jul 14;12(1):4314. PMCID: PMC8280215

Plate M, Kobayashi Y, Chambers R, Tata PR. Epithelial stem cells at the intersection of tissue regeneration and pulmonary fibrosis. European Respiratory Society, Book Chapter 2021. p. 290–305.

2020

Okuda K, Dang H, Kobayashi Y, Carraro G, Nakano S, Chen G, Kato T, Asakura T, Gilmore RC, Morton LC, Lee RE, Mascenik T, Yin W-N, Barbosa Cardenas SM, O’Neal YK, Minnick CE, Chua M, Quinney NL, Gentzsch M, Anderson CW, Ghio A, Matsui H, Nagase T, Ostrowski LE, Grubb BR, Olsen JC, Randell SH, Stripp BR, Tata PR, O’Neal WK, Boucher RC. Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia. Am J Respir Crit Care Med. 2020 Dec 15; PMID: 33321047

Moiseenko A, Vazquez-Armendariz AI, Kheirollahi V, Chu X, Tata A, Rivetti S, Günther S, Lebrigand K, Herold S, Braun T, Mari B, De Langhe S, Kwapiszewska G, Günther A, Chen C, Seeger W, Tata PR, Zhang J-S, Bellusci S, El Agha E. Identification of a Repair-Supportive Mesenchymal Cell Population during Airway Epithelial Regeneration. Cell Rep. 2020 Dec 22;33(12):108549. PMID: 33357434

Sapoznik E, Chang B-J, Huh J, Ju RJ, Azarova EV, Pohlkamp T, Welf ES, Broadbent D, Carisey AF, Stehbens SJ, Lee K-M, Marin A, Hanker AB, Schmidt JC, Arteaga CL, Yang B, Kobayashi Y, Tata PR, Kruithoff R, Dubrovinski K, Shepherd DP, Millet-Sikking A, York AG, Dean KM, Fiolka RP. A versatile Oblique Plane Microscope for large-scale and high-resolution imaging of subcellular dynamics. eLife. 2020 Nov 12;9. PMID: 33179596

Katsura H, Sontake V, Tata A, Kobayashi Y, Edwards CE, Heaton BE, Konkimalla A, Asakura T, Mikami Y, Fritch EJ, Lee PJ, Heaton NS, Boucher RC, Randell SH, Baric RS, Tata PR. Human Lung Stem Cell-Based Alveolospheres Provide Insights into SARS-CoV-2-Mediated Interferon Responses and Pneumocyte Dysfunction. Cell Stem Cell. 2020 Oct 21; PMCID: PMC7577733

Tucker NR, Chaffin M, Bedi KC, Papangeli I, Akkad A-D, Arduini A, Hayat S, Eraslan G, Muus C, Bhattacharyya RP, Stegmann CM, Kropski JA, Theis FJ, Schiller HB, Zaragosi L-E, Barbry P, Leslie A, Kiem H-P, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Banovich NE, Barbry P, Brazma A, Desai T, Duong TE, Eickelberg O, Falk C, Farzan M, Glass I, Haniffa M, Horvath P, Hung D, Kaminski N, Krasnow M, Kuhnemund M, Lafyatis R, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer K, Misharin A, Nawijn M, Nikolic MZ, Pe’er D, Powell J, Quake S, Rajagopal J, Tata PR, Rawlins EL, Regev A, Reyfman PA, Rojas M, Rosen O, Saeb-Parsy K, Samakovlis C, Schultze JL, Siebold MA, Shepherd D, Spence J, Spira A, Sun X, Teichmann S, Tsankov A, Berge M, Papen M, Whitsett J, Xavier R, Xu Y, Zaragosi L, Zhang K, Shalek AK, Margulies KB, Ellinor PT. Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis. Circulation. 2020 18;142(7):708–710. PMCID: PMC7424896

Sontake V, Tata PR. BALO: a “mini lung” model to study cell-cell interactions. EMBO J. 2020 Oct 1;e106697. PMID: 33001445 (Preview article – not peer reviewed)

Kobayashi Y, Tata A, Konkimalla A, Katsura H, Lee RF, Ou J, Banovich NE, Kropski JA, Tata PR. Persistence of a novel regeneration-associated transitional cell state in pulmonary fibrosis. Nature Cell Biology. 2020 Jul 13; PMID: 32661339.

Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Wang JP, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre JMS, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi L-E, Barbry P, Leslie A, Kiem H-P, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Banovich NE, Barbry P, Brazma A, Desai T, Duong TE, Eickelberg O, Falk C, Farzan M, Glass I, Haniffa M, Horvath P, Hung D, Kaminski N, Krasnow M, Kuhnemund M, Lafyatis R, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer K, Misharin A, Nawijn M, Nikolic MZ, Pe’er D, Powell J, Quake S, Rajagopal J, Tata PR, Rawlins EL, Regev A, Reyfman PA, Rojas M, Rosen O, Saeb-Parsy K, Samakovlis C, Schultze JL, Siebold MA, Shepherd D, Spence J, Spira A, Sun X, Teichmann S, Tsankov A, Berge M, Papen M, Whitsett J, Xavier R, Xu Y, Zaragosi L, Zhang K, Shalek AK, Ordovas-Montanes J. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell. 2020 28;181(5):1016-1035.e19. PMCID: PMC7252096

Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, Banovich NE, Barbry P, Brazma A, Desai T, Duong TE, Eickelberg O, Falk C, Farzan M, Glass I, Haniffa M, Horvath P, Hung D, Kaminski N, Krasnow M, Kuhnemund M, Lafyatis R, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer K, Misharin A, Nawijn M, Nikolic MZ, Pe’er D, Powell J, Quake S, Rajagopal J, Tata PR, Rawlins EL, Regev A, Reyfman PA, Rojas M, Rosen O, Saeb-Parsy K, Samakovlis C, Schultze JL, Siebold MA, Shepherd D, Spence J, Spira A, Sun X, Teichmann S, Tsankov A, Berge M, Papen M, Whitsett J, Xavier R, Xu Y, Zaragosi L, Zhang K. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine. 2020;26(5):681–687. PMID: 32327758

Hou YJ, Okuda K, Edwards CE, Martinez DR, Asakura T, Dinnon KH, Kato T, Lee RE, Yount BL, Mascenik TM, Chen G, Olivier KN, Ghio A, Tse LV, Leist SR, Gralinski LE, Schäfer A, Dang H, Gilmore R, Nakano S, Sun L, Fulcher ML, Livraghi-Butrico A, Nicely NI, Cameron M, Cameron C, Kelvin DJ, de Silva A, Margolis DM, Markmann A, Bartelt L, Zumwalt R, Martinez FJ, Salvatore SP, Borczuk A, Tata PR, Sontake V, Kimple A, Jaspers I, O’Neal WK, Randell SH, Boucher RC, Baric RS. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell. 2020 May 27; PMCID: PMC7250779

2019

Uezu A, Hisey E, Kobayashi Y, Gao Y, Bradshaw TW, Devlin P, Rodriguiz R, Tata PR, Soderling S. Essential role for InSyn1 in dystroglycan complex integrity and cognitive behaviors in mice. eLife. 2019 Dec 12;8. PMCID: PMC6944460

Hogan B, Tata PR. Cellular organization and biology of the respiratory system. Nature Cell Biology. 2019 Jul 25; PMID: 31346286

Katsura H, Kobayashi Y, Tata PR§, Hogan BLM§. IL-1 and TNFα Contribute to the Inflammatory Niche to Enhance Alveolar Regeneration. Stem Cell Rep. 2019 Mar 12; PMCID: PMC6450459. (§ co-corresponding autor).

Khatri A, Kraft BD, Tata PR, Randell SH, Piantadosi CA, Pendergast AM. ABL kinase inhibition promotes lung regeneration through expansion of an SCGB1A1+ SPC+ cell population following bacterial pneumonia. Proc Natl Acad Sci U S A. 2019 Jan 17; PMID: 30655340

2018

Montoro DT, Haber AL, Biton M, Vinarsky V, Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, Rogel N, Burgin G, Tsankov AM, Waghray A, Slyper M, Waldman J, Nguyen L, Dionne D, Rozenblatt-Rosen O, Tata PR, Mou H, Shivaraju M, Bihler H, Mense M, Tearney GJ, Rowe SM, Engelhardt JF, Regev A, Rajagopal J. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature. 2018 Aug;560(7718):319–324. PMID: 30069044

Kobayashi Y, Tata PR^§. Pulmonary Neuroendocrine Cells: Sensors and Sentinels of the Lung. Developmental Cell. 2018 May 21;45(4):425–426. PMID: 29787707. (§ – indicates corresponding author)

Tata A, Kobayashi Y, Ryan DZ, Tran J, Desai A, Massri AJ, McCord TJ, Gunn MD, Tata PR^§. Myoepithelial cells of submucosal glands can function as reserve stem cells to regenerate airways after injury. Cell Stem Cell. 2018 May 3;22(5):668-683.e6. PMID: 29656943.

(§ – indicates corresponding author)

Tata PR*^§, Chow RD*, Saladi SV, Tata A, Konkimalla A, Bara A, Montoro D, Hariri LP, Shih AR, Mino-Kenudson M, Mou H, Kimura S, Ellisen LW, Rajagopal J. Developmental History Provides a Roadmap for the Emergence of Tumor Plasticity. Developmental Cell. 2018 Mar 26;44(6):679-693.e5. PMID: 29587142. (*- indicates equal contribution; §- indicates corresponding author)

Taylor MS, Chivukula RR, Myers LC, Jeck WR, Waghray A, Tata PR, Selig MK, O’Donnell WJ, Farver CF, Thompson BT, Rajagopal J, Kradin RL. A Conserved Distal Lung Regenerative Pathway in Acute Lung Injury. American Journal of Pathology. 2018 Feb 21; PMID: 29476724

2017

Konkimalla, A., and Tata, PR^§. Plasticity in Olfactory Epithelium: Is It a Sniffer or Shape Shifter? Cell Stem Cell. 2017 December 13;21, 707–708. (§ – indicates corresponding author)

Taylor MS, Chivukula RR, Myers LC, Jeck WR, Tata PR, O’Donnell WJ, Farver CF, Thompson BT, Rajagopal J, Kradin RL. Delayed Alveolar Epithelization: A Distinct Pathology in Diffuse Acute Lung Injury. Am J Respir Crit Care Med. 2017 Jul 11; PMID: 28696778

Tata PR, Rajagopal J. Plasticity in the lung: making and breaking cell identity. Development. 2017 Mar 1;144(5):755–766. PMID: 28246210

Hempel A, Kühl SJ, Rothe M, Tata PR, Sirbu IO, Vainio SJ, Kühl M. The CapZ interacting protein Rcsd1 is required for cardiogenesis downstream of Wnt11a in Xenopus laevis. Developmental Biology. 2017 Feb 22; PMID: 28237811

Saladi SV, Ross K, Karaayvaz M, Tata PR, Mou H, Rajagopal J, Ramaswamy S, Ellisen LW. ACTL6A Is Co-Amplified with p63 in Squamous Cell Carcinoma to Drive YAP Activation, Regenerative Proliferation, and Poor Prognosis. Cancer Cell. 2017 Jan 9;31(1):35–49. PMCID: PMC5225026

Prior to 2017

Tata PR, Rajagopal J. Regulatory Circuits and Bi-directional Signaling between Stem Cells and Their Progeny. Cell Stem Cell. 2016 Dec 1;19(6):686–689. PMID: 27912089

Tata PR, Rajagopal J. Cellular plasticity: 1712 to the present day. Curr Opin Cell Biol. 2016 Jul 30;43:46-54. PubMed PMID: 27485353.

Mou H, Vinarsky V, Tata PR, Brazauskas K, Choi SH, Crooke AK, Zhang B, Solomon GM, Turner B, Bihler H, Harrington J, Lapey A, Channick C, Keyes C, Freund A, Artandi S, Mense M, Rowe S, Engelhardt JF, Hsu Y-C, Rajagopal J. Dual SMAD Signaling Inhibition Enables Long-Term Expansion of Diverse Epithelial Basal Cells. Cell Stem Cell. 2016 Jun 15; PMID: 27320041

Pardo-Saganta A*, Tata P.R.*, Law, B.M., Saez, B., Chow, R.D.-W., Prabhu, M., Gridley, T., Rajagopal, J., 2015. Parent stem cells can serve as niches for their daughter cells. Nature 523, 597–601 (highlighted in Cell Leading Edge Select) (*equal contribution).

Pardo-Saganta A, Law B.M., Tata P.R., Villoria J, Saez B, Mou H, Zhao R, Rajagopal J. Injury Induces Direct Lineage Segregation of Functionally Distinct Airway Basal Stem/Progenitor Cell Subpopulations. Cell Stem Cell. 2015 Feb 5;16(2):184-197. Previewed in Cell Stem Cell, 107-109. PMID: 25658372.

Tata PR, Mou H, Pardo-Saganta A, Zhao R, Prabhu M, Law BM, Vinarsky V, Cho JL, Breton S, Sahay A, Medoff BD, Rajagopal J. Dedifferentiation of committed luminal epithelial cells into functional stem cells in vivo. Nature, 2013;503; 218-223 (highlighted in Nature News and Views, featured in Cell Leading Edge Select and a Cell Stem Cell preview, selected as a prime article by Faculty 1000). PMID: 24196716.

Weidgang C.E.*, Russell R. *, Tata P.R.*, Kühl S.J., Illing A., Müller M., Lin Q., Brunner C., Boeckers T.M., Bauer K., Kartikasari A.P., Guo Y., Radenz M., Berneman C., Weiss M., Seufferlein T., Zenke M., Iacovino M., Kyba M., Scholer H. R., Kühl M., Liebau S., Kleger A. 2013. TBX3 directs cell-fate decision toward mesendoderm. Stem Cell Reports, 1, 248–265. PubMed PMID: 24319661(*equal contribution).

Tata PR, Pardo-Saganta A, Prabhu M, Vinarsky V, Law BM, Fontaine BA, Tager AM, Rajagopal J.Airway specific inducible transgene expression using aerosolized doxycycline. Am J Respir Cell Mol Biol. 2013 Am J Respir Cell Mol Biol. 2013; Dec: 49(6): 1048-1056. PMID: 23848320

H. Watanabe, J. M. Francis, M. S. Woo, B. Etemad, W. Lin, D. F. Fries, S. Peng, E. L. Snyder, Tata P.R., F. Izzo, A. C. Schinzel, J. Cho, P. S. Hammerman, R. G. Verhaak, W. C. Hahn, J. Rajagopal, T. Jacks, and M. Meyerson, “Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target. Genes and Development, vol. 27, no. 2, pp. 197–210 (2013).

Kleger, A., Weidgang, C., Tata P.R., Müller, M., Schöler, H., Seufferlein, T., and Liebau, S. Tbx3 directs cell fate decision towards mesendoderm, pancreas and liver in mouse embryonic stem cells. Z. Für Gastroenterol. 50 (2012).

Tata P.R., Tata N.R., Kühl M., and Sirbu I.O. 2011. Identification of a novel epigenetic regulatory region within the pluripotency associated microRNA cluster, EEmiRC. Nucleic Acids Research. 39, 3574–3581. PubMed PMID: 21247880

Tata P.R., Kühl M., 2010. An updated overview on Wnt signaling pathways: a prelude for more. Circulation Research. 106, 1798–1806. Pubmed PMID: 20576942.