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Quantized multi-task learning for context-specific representations of gene network dynamics. bioRxiv. 2024 Aug 19.
Chen H, Venkatesh MS, Ortega JG, Mahesh SV, Nandi TN, Madduri RK, Pelka K, Theodoris CV. PMID: 39229018; PMCID: PMC11370383.
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Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis. Nat Med. 2024 May; 30(5):1349-1362.
Thomas MF, Slowikowski K, Manakongtreecheep K, Sen P, Samanta N, Tantivit J, Nasrallah M, Zubiri L, Smith NP, Tirard A, Ramesh S, Arnold BY, Nieman LT, Chen JH, Eisenhaure T, Pelka K, Song Y, Xu KH, Jorgji V, Pinto CJ, Sharova T, Glasser R, Chan P, Sullivan RJ, Khalili H, Juric D, Boland GM, Dougan M, Hacohen N, Li B, Reynolds KL, Villani AC. PMID: 38724705; PMCID: PMC11673812.
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PubMed Mentions:
4 Fields:
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Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nat Immunol. 2024 Apr; 25(4):644-658.
Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N. PMID: 38503922.
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PubMed Mentions:
20 Fields:
Translation:
HumansCells
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Dual checkpoint T(h1)eamwork makes the anti-cancer dream work. Immunity. 2024 03 12; 57(3):406-408.
Dietl A, Ralser A, Pelka K. PMID: 38479356.
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PubMed Mentions: Fields:
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Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol. 2023 Sep; 41(9):1345.
Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG. PMID: 37653227.
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Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response. bioRxiv. 2023 Apr 06.
Chen JH, Nieman LT, Spurrell M, Jorgji V, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Raay KV, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee M, Korsunsky I, Mino-Kenudson M, Gainor JF, Hacohen N. PMID: 37066412; PMCID: PMC10104028.
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Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nat Protoc. 2023 05; 18(5):1416-1440.
Lareau CA, Liu V, Muus C, Praktiknjo SD, Nitsch L, Kautz P, Sandor K, Yin Y, Gutierrez JC, Pelka K, Satpathy AT, Regev A, Sankaran VG, Ludwig LS. PMID: 36792778; PMCID: PMC10317201.
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PubMed Mentions:
16 Fields:
Translation:
HumansAnimalsCells
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Combined PD-1, BRAF and MEK inhibition in BRAFV600E colorectal cancer: a phase 2 trial. Nat Med. 2023 02; 29(2):458-466.
Tian J, Chen JH, Chao SX, Pelka K, Giannakis M, Hess J, Burke K, Jorgji V, Sindurakar P, Braverman J, Mehta A, Oka T, Huang M, Lieb D, Spurrell M, Allen JN, Abrams TA, Clark JW, Enzinger AC, Enzinger PC, Klempner SJ, McCleary NJ, Meyerhardt JA, Ryan DP, Yurgelun MB, Kanter K, Van Seventer EE, Baiev I, Chi G, Jarnagin J, Bradford WB, Wong E, Michel AG, Fetter IJ, Siravegna G, Gemma AJ, Sharpe A, Demehri S, Leary R, Campbell CD, Yilmaz O, Getz GA, Parikh AR, Hacohen N, Corcoran RB. PMID: 36702949; PMCID: PMC9941044.
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PubMed Mentions:
41 Fields:
Translation:
HumansCTClinical Trials
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Targeting TBK1 to overcome resistance to cancer immunotherapy. Nature. 2023 03; 615(7950):158-167.
Sun Y, Revach OY, Anderson S, Kessler EA, Wolfe CH, Jenney A, Mills CE, Robitschek EJ, Davis TGR, Kim S, Fu A, Ma X, Gwee J, Tiwari P, Du PP, Sindurakar P, Tian J, Mehta A, Schneider AM, Yizhak K, Sade-Feldman M, LaSalle T, Sharova T, Xie H, Liu S, Michaud WA, Saad-Beretta R, Yates KB, Iracheta-Vellve A, Spetz JKE, Qin X, Sarosiek KA, Zhang G, Kim JW, Su MY, Cicerchia AM, Rasmussen MQ, Klempner SJ, Juric D, Pai SI, Miller DM, Giobbie-Hurder A, Chen JH, Pelka K, Frederick DT, Stinson S, Ivanova E, Aref AR, Paweletz CP, Barbie DA, Sen DR, Fisher DE, Corcoran RB, Hacohen N, Sorger PK, Flaherty KT, Boland GM, Manguso RT, Jenkins RW. PMID: 36634707; PMCID: PMC10171827.
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PubMed Mentions:
34 Fields:
Translation:
HumansCells
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Listening in on Multicellular Communication in Human Tissue Immunology. Front Immunol. 2022; 13:884185.
Albers JJ, Pelka K. PMID: 35634333; PMCID: PMC9136009.
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PubMed Mentions:
2 Fields:
Translation:
Humans
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Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell. 2021 12 22; 184(26):6262-6280.e26.
Chen B, Scurrah CR, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, Vega PN, Rolong A, Kim H, Sheng Q, Drewes JL, Zhou Y, Southard-Smith AN, Xu Y, Ro J, Jones AL, Revetta F, Berry LD, Niitsu H, Islam M, Pelka K, Hofree M, Chen JH, Sarkizova S, Ng K, Giannakis M, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N, Kawasaki K, Sato T, Goettel JA, Grady WM, Zheng W, Washington MK, Cai Q, Sears CL, Goldenring JR, Franklin JL, Su T, Huh WJ, Vandekar S, Roland JT, Liu Q, Coffey RJ, Shrubsole MJ, Lau KS. PMID: 34910928; PMCID: PMC8941949.
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PubMed Mentions:
108 Fields:
Translation:
HumansAnimalsCells
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Spatially organized multicellular immune hubs in human colorectal cancer. Cell. 2021 09 02; 184(18):4734-4752.e20.
Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N. PMID: 34450029; PMCID: PMC8772395.
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PubMed Mentions:
232 Fields:
Translation:
HumansCells
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Longitudinal proteomic analysis of severe COVID-19 reveals survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med. 2021 05 18; 2(5):100287.
Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. PMID: 33969320; PMCID: PMC8091031.
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PubMed Mentions:
134 Fields:
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Interaction of TLR4 and TLR8 in the Innate Immune Response against Mycobacterium Tuberculosis. Int J Mol Sci. 2021 Feb 04; 22(4).
Thada S, Horvath GL, Müller MM, Dittrich N, Conrad ML, Sur S, Hussain A, Pelka K, Gaddam SL, Latz E, Slevogt H, Schumann RR, Burkert S. PMID: 33557133; PMCID: PMC7913854.
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PubMed Mentions:
10 Fields:
Translation:
HumansCells
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Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients. bioRxiv. 2020 Nov 04.
Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB. PMID: 33173871; PMCID: PMC7654866.
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PubMed Mentions:
7
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Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23.
Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE. PMID: 32841603; PMCID: PMC7575124.
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PubMed Mentions:
86 Fields:
Translation:
HumansCells
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Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nat Biotechnol. 2021 04; 39(4):451-461.
Lareau CA, Ludwig LS, Muus C, Gohil SH, Zhao T, Chiang Z, Pelka K, Verboon JM, Luo W, Christian E, Rosebrock D, Getz G, Boland GM, Chen F, Buenrostro JD, Hacohen N, Wu CJ, Aryee MJ, Regev A, Sankaran VG. PMID: 32788668; PMCID: PMC7878580.
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PubMed Mentions:
105 Fields:
Translation:
HumansCells
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Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019 03 07; 176(6):1325-1339.e22.
Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, Pelka K, Ge W, Oren Y, Brack A, Law T, Rodman C, Chen JH, Boland GM, Hacohen N, Rozenblatt-Rosen O, Aryee MJ, Buenrostro JD, Regev A, Sankaran VG. PMID: 30827679; PMCID: PMC6408267.
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PubMed Mentions:
223 Fields:
Translation:
HumansCells
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The Chaperone UNC93B1 Regulates Toll-like Receptor Stability Independently of Endosomal TLR Transport. Immunity. 2018 05 15; 48(5):911-922.e7.
Pelka K, Bertheloot D, Reimer E, Phulphagar K, Schmidt SV, Christ A, Stahl R, Watson N, Miyake K, Hacohen N, Haas A, Brinkmann MM, Marshak-Rothstein A, Meissner F, Latz E. PMID: 29768176; PMCID: PMC6482051.
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PubMed Mentions:
63 Fields:
Translation:
HumansAnimalsCells
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Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming. Cell. 2018 01 11; 172(1-2):162-175.e14.
Christ A, Günther P, Lauterbach MAR, Duewell P, Biswas D, Pelka K, Scholz CJ, Oosting M, Haendler K, Baßler K, Klee K, Schulte-Schrepping J, Ulas T, Moorlag SJCFM, Kumar V, Park MH, Joosten LAB, Groh LA, Riksen NP, Espevik T, Schlitzer A, Li Y, Fitzgerald ML, Netea MG, Schultze JL, Latz E. PMID: 29328911; PMCID: PMC6324559.
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PubMed Mentions:
468 Fields:
Translation:
HumansAnimalsCells
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Emerging Concepts in Innate Immunity. Methods Mol Biol. 2018; 1714:1-18.
Pelka K, De Nardo D. PMID: 29177852.
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PubMed Mentions:
6 Fields:
Translation:
HumansAnimals
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Heavy Metal Enlightens Tumor Immunity. Cell. 2017 05 04; 169(4):567-569.
Chen JH, Pelka K, Hacohen N. PMID: 28475889; PMCID: PMC6597172.
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PubMed Mentions:
2 Fields:
Translation:
Humans
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TLR9 Deficiency Leads to Accelerated Renal Disease and Myeloid Lineage Abnormalities in Pristane-Induced Murine Lupus. J Immunol. 2016 08 15; 197(4):1044-53.
Bossaller L, Christ A, Pelka K, Nündel K, Chiang PI, Pang C, Mishra N, Busto P, Bonegio RG, Schmidt RE, Latz E, Marshak-Rothstein A. PMID: 27354219; PMCID: PMC5266544.
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PubMed Mentions:
37 Fields:
Translation:
AnimalsCells
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Nucleic acid-sensing TLRs and autoimmunity: novel insights from structural and cell biology. Immunol Rev. 2016 Jan; 269(1):60-75.
Pelka K, Shibata T, Miyake K, Latz E. PMID: 26683145.
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PubMed Mentions:
60 Fields:
Translation:
HumansAnimalsCells
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TLR8 Senses Bacterial RNA in Human Monocytes and Plays a Nonredundant Role for Recognition of Streptococcus pyogenes. J Immunol. 2015 Aug 01; 195(3):1092-9.
Eigenbrod T, Pelka K, Latz E, Kreikemeyer B, Dalpke AH. PMID: 26101323.
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PubMed Mentions:
40 Fields:
Translation:
HumansAnimalsCells
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Synergistic activation of Toll-like receptor 8 by two RNA degradation products. Nat Struct Mol Biol. 2015 Feb; 22(2):99-101.
Geyer M, Pelka K, Latz E. PMID: 25650902.
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PubMed Mentions:
10 Fields:
Translation:
HumansAnimals
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OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines. Genome Res. 2014 Oct; 24(10):1719-23.
Schmid-Burgk JL, Schmidt T, Gaidt MM, Pelka K, Latz E, Ebert TS, Hornung V. PMID: 25186908; PMCID: PMC4199374.
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PubMed Mentions:
72 Fields:
Translation:
HumansCells
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Cutting edge: the UNC93B1 tyrosine-based motif regulates trafficking and TLR responses via separate mechanisms. J Immunol. 2014 Oct 01; 193(7):3257-61.
Pelka K, Phulphagar K, Zimmermann J, Stahl R, Schmid-Burgk JL, Schmidt T, Spille JH, Labzin LI, Agrawal S, Kandimalla ER, Casanova JL, Hornung V, Marshak-Rothstein A, Höning S, Latz E. PMID: 25187660; PMCID: PMC4170058.
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PubMed Mentions:
20 Fields:
Translation:
HumansCells
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RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA. J Exp Med. 2013 Oct 21; 210(11):2447-63.
Sirois CM, Jin T, Miller AL, Bertheloot D, Nakamura H, Horvath GL, Mian A, Jiang J, Schrum J, Bossaller L, Pelka K, Garbi N, Brewah Y, Tian J, Chang C, Chowdhury PS, Sims GP, Kolbeck R, Coyle AJ, Humbles AA, Xiao TS, Latz E. PMID: 24081950; PMCID: PMC3804942.
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PubMed Mentions:
101 Fields:
Translation:
HumansAnimalsCells
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IRF5, IRF8, and IRF7 in human pDCs - the good, the bad, and the insignificant? Eur J Immunol. 2013 Jul; 43(7):1693-7.
Pelka K, Latz E. PMID: 23828296.
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PubMed Mentions:
18 Fields:
Translation:
HumansCells
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The Fer tyrosine kinase is important for platelet-derived growth factor-BB-induced signal transducer and activator of transcription 3 (STAT3) protein phosphorylation, colony formation in soft agar, and tumor growth in vivo. J Biol Chem. 2013 May 31; 288(22):15736-44.
Lennartsson J, Ma H, Wardega P, Pelka K, Engström U, Hellberg C, Heldin CH. PMID: 23589302; PMCID: PMC3668732.
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PubMed Mentions:
19 Fields:
Translation:
HumansAnimalsCells
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Getting closer to the dirty little secret. Immunity. 2011 Apr 22; 34(4):455-8.
Pelka K, Latz E. PMID: 21511178; PMCID: PMC3128920.
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PubMed Mentions:
12 Fields: