Doctoral Thesis Title:  Differential analysis of ScRNA-Seq dara to characterize epithelial cells in health and disease

Publications while at MIT: 

HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control.

Fardoos R, Nyquist SK, Asowata OE, Kazer SW, Singh A, Ngoepe A, Giandhari J, Mthabela N, Ramjit D, Singh S, Karim F, Buus S, Anderson F, Porterfield JZ, Sibiya AL, Bipath R, Moodley K, Kuhn W, Berger B, Nguyen S, de Oliveira T, Ndung'u T, Goulder P, Shalek AK, Leslie A, Kløverpris HN.Front Immunol. 2022 Oct 18;13:912038. doi: 10.3389/fimmu.2022.912038. eCollection 2022.PMID: 36330531 Free PMC article.

Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis).

Jaiswal S, Nyquist SK, Boyce S, Jivanjee T, Ibrahim S, Bromley JD, Gatter GJ, Gideon H, Patel K, Ganchua SK, Berger B, Fortune SM, Flynn JL, Shalek AK, Behar SM.BMC Genomics. 2022 Sep 12;23(1):647. doi: 10.1186/s12864-022-08867-0.PMID: 36096729 Free PMC article.

Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control.

Gideon HP, Hughes TK, Tzouanas CN, Wadsworth MH 2nd, Tu AA, Gierahn TM, Peters JM, Hopkins FF, Wei JR, Kummerlowe C, Grant NL, Nargan K, Phuah JY, Borish HJ, Maiello P, White AG, Winchell CG, Nyquist SK, Ganchua SKC, Myers A, Patel KV, Ameel CL, Cochran CT, Ibrahim S, Tomko JA, Frye LJ, Rosenberg JM, Shih A, Chao M, Klein E, Scanga CA, Ordovas-Montanes J, Berger B, Mattila JT, Madansein R, Love JC, Lin PL, Leslie A, Behar SM, Bryson B, Flynn JL, Fortune SM, Shalek AK.Immunity. 2022 May 10;55(5):827-846.e10. doi: 10.1016/j.immuni.2022.04.004. Epub 2022 Apr 27.PMID: 35483355 Free PMC article.

Cellular and transcriptional diversity over the course of human lactation.

Nyquist SK, Gao P, Haining TKJ, Retchin MR, Golan Y, Drake RS, Kolb K, Mead BE, Ahituv N, Martinez ME, Shalek AK, Berger B, Goods BA.Proc Natl Acad Sci U S A. 2022 Apr 12;119(15):e2121720119. doi: 10.1073/pnas.2121720119. Epub 2022 Apr 4.PMID: 35377806 Free PMC article.

Enriching and Characterizing T Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products.

Jivanjee T, Ibrahim S, Nyquist SK, Gatter GJ, Bromley JD, Jaiswal S, Berger B, Behar SM, Love JC, Shalek AK.Methods Mol Biol. 2022;2574:159-182. doi: 10.1007/978-1-0716-2712-9_7.PMID: 36087201

HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells.

Fardoos R, Asowata OE, Herbert N, Nyquist SK, Zungu Y, Singh A, Ngoepe A, Mbano IM, Mthabela N, Ramjit D, Karim F, Kuhn W, Madela FG, Manzini VT, Anderson F, Berger B, Pers TH, Shalek AK, Leslie A, Kløverpris HN.JCI Insight. 2021 Aug 23;6(16):e148920. doi: 10.1172/jci.insight.148920.PMID: 34252054 Free PMC article.

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK; NHLBI LungMap Consortium; Human Cell Atlas Lung Biological Network.Nat Med. 2021 Mar;27(3):546-559. doi: 10.1038/s41591-020-01227-z. Epub 2021 Mar 2.PMID: 33654293 Free PMC article.

Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation.

Dwyer DF, Ordovas-Montanes J, Allon SJ, Buchheit KM, Vukovic M, Derakhshan T, Feng C, Lai J, Hughes TK, Nyquist SK, Giannetti MP, Berger B, Bhattacharyya N, Roditi RE, Katz HR, Nawijn MC, Berg M, van den Berge M, Laidlaw TM, Shalek AK, Barrett NA, Boyce JA.Sci Immunol. 2021 Feb 26;6(56):eabb7221. doi: 10.1126/sciimmunol.abb7221.PMID: 33637594 Free PMC article.

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets.

Berger E, Yorukoglu D, Zhang L, Nyquist SK, Shalek AK, Kellis M, Numanagić I, Berger B.Nat Commun. 2020 Sep 16;11(1):4662. doi: 10.1038/s41467-020-18320-z.PMID: 32938926 Free PMC article.

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

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 2nd, 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 LE, Barbry P, Leslie A, Kiem HP, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Shalek AK, Ordovas-Montanes J; HCA Lung Biological Network. Electronic address: lung-network@humancellatlas.org; HCA Lung Biological Network.Cell. 2020 May 28;181(5):1016-1035.e19. doi: 10.1016/j.cell.2020.04.035. Epub 2020 Apr 27.PMID: 32413319 Free PMC article.

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection.

Kazer SW, Aicher TP, Muema DM, Carroll SL, Ordovas-Montanes J, Miao VN, Tu AA, Ziegler CGK, Nyquist SK, Wong EB, Ismail N, Dong M, Moodley A, Berger B, Love JC, Dong KL, Leslie A, Ndhlovu ZM, Ndung'u T, Walker BD, Shalek AK.Nat Med. 2020 Apr;26(4):511-518. doi: 10.1038/s41591-020-0799-2. Epub 2020 Mar 23.PMID: 32251406 Free PMC article.

Allergic inflammatory memory in human respiratory epithelial progenitor cells.

Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, Wadsworth MH 2nd, Hughes TK, Kazer SW, Yoshimoto E, Cahill KN, Bhattacharyya N, Katz HR, Berger B, Laidlaw TM, Boyce JA, Barrett NA, Shalek AK.Nature. 2018 Aug;560(7720):649-654. doi: 10.1038/s41586-018-0449-8. Epub 2018 Aug 22.PMID: 30135581 Free PMC article.

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