Publications

PUBLICATIONS

  1. Nobs SP*, Kolodziejczyk AA*, Adler L, Horesh N, Botscharnikow C, Herzog E, Mohapatra G, Hejndorf S, Hodgetts RJ, Spivak I, Schorr L, Fluhr L, Kviatcovsky D, Zacharia A, Njuki S, Barasch D, Stettner N, Dori-Bachash M, Harmelin A, Brandis A, Mehlman T, Erez A, He Y, Ferrini S, Puschhof J, Shapiro H, Kopf M, Moussaieff A, Abdeen SK, Elinav E. (2023) Lung dendritic-cell metabolism underlies susceptibility to viral infection in diabetes. Nature, 624, 645–652.
  2. Schneor L, Kaltenbach S, Fridman S, Nissan Y, Shuler G, Fraimovitch E, Weinberg M, Kolodziejczyk AA, Donati G, Teeling EC, Yovel Y, Hagai T. (2023) Comparison of antiviral responses in two bat species reveals conserved and divergent innate immune pathways. iScience 26, 107435.
  3. Javitt A*, Shmueli MD*, Kramer MP, Kolodziejczyk AA, Cohen I, Kamer I, Litchfield K, Bab-Dinitz E, Zadok O, Welk V, Ulman A, Radomir L, Wolf-Levy H, Eisenberg-Lerner A, Kacen A, Alon M, Toste Rêgo A, Stacher-Priehse E, Lindner M, Koch I, Bar J, Swanton C, Samuels Y, Levin Y, da Fonseca PAC, Elinav E, Friedman N, Meiners S, Merbl Y. (2023) The proteasome regulator PSME4 drives immune evasion and abrogates anti-tumor immunity in NSCLC. Nature Cancer,  4, 629–647.
  4. Zheng D*, Mohapatra G*, Kern L*, Ye Y, Valdés-Mas R, Kolodziejczyk A, Shorr L, Hertel F, Lee Y, Camacho M, Ceddaha E, Hodgetts R, Dori-Bachash M, Kleimeyer C, Goldenberg K, Heinemenn M, Shapiro H, Puschhof J, Abdeen S, Elinav E. (2023) Epithelial Nlrp10 inflammasome mediates protection against intestinal auto-inflammation. Nature Immunology 24, 585–594.
  5. Ben-Moshe S, Veg T, Manco R, Dan S, Bahar Halpern K, Kolodziejczyk AA, Elinav E, Itzkovitz S. (2022) The spatio-temporal program of liver zonal regeneration. Cell Stem Cell 29 (6), 973-989.
  6. Fluhr L*, Mor U*, Kolodziejczyk AA, Dori-Bachash M, Leshem A, Itav S, Cohen Y, Suez J, Moresi C, Molina S, Ayalon N, Valdés-Mas R, Hornstein S, Karbi H, Kviatcovsky D, Livne A, Bukimer A, Eliyahu-Miller S, Metz A, Brandis A, Mehlman T, Kuperman Y, Tsoory M, Stettner N, Harmelin A, Shapiro H, Elinav E. (2021) Gut microbiota modulates weight gain in mice after discontinued smoke exposure. Nature 600 (7890), 713-719.
  7. Winick-Ng W, Kukalev A, Harabulā I, Zea L Redondo, Meijer M, Serebreni L, Bianco S, Szabo D, Chiariello AM, Azcarate II, Fiorillo L, Musella F, Thieme C, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Castelo-Branco G, Pombo A. (2021) Cell-type specialization is encoded by specific chromatin topologies. Nature 599 (7886), 684-691.
  8. Kern L*, Abdeen S*, Kolodziejczyk AA*, Elinav E. (2021) Commensal inter-bacterial interactions shaping the microbiota. Curr. Opin. Microbiol. 63, 158-17.
  9. Kolodziejczyk AA, Federici S, Zmora N, Mohapatra G, Dori-Bachash M, Hornstein S, Leshem A, Reuveni D, Zigmond E, Meir Salame T, Harmelin A, Tobar A, Shlomai A, Shapiro H, Amit I, Elinav E. (2020) Acute liver failure is regulated by Myc- and microbiome dependent programs. Nat Med. 26 (12), 1899-1911.
  10. Kolodziejczyk AA*, Zheng D*, Elinav E. (2019) Diet–microbiota interactions and personalized nutrition. Nat. Rev. Microbiol. 17 (12), 742-753.
  11. Kolodziejczyk AA*, Zheng D*, Shibolet O, Elinav E. (2019) The role of the microbiome in NAFLD and NASH. EMBO Mol. Med. 11 (2).
  12. Shapiro H*, Kolodziejczyk AA*, Halstuch D*, Elinav E. (2018) Bile acids in glucose metabolism in health and disease. J. Exp. Med. 215 (2), 383-396.
  13. Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. (2017) Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression. Nat Commun. 8 (1), 36.
  14. Kolodziejczyk AA, T Lönnberg T. (2017) Global and targeted approaches to single-cell transcriptome characterization. Brief. Funct. Genomics 17 (4) 209–219.
  15. Natarajan KN, Teichmann SA, Kolodziejczyk AA. (2017) Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation. Curr. Opin. Genet. Dev. 46, 66-76.
  16. Yang J, Ryan D, Wang W, Tsang CHJ, Lan G, Gao X, Antunes L, Clifford Wilkinson A, Yu Y, Kolodziejczyk AA, Campos L, Wang J, Yang F, Tanaka Y, Eckersley-Maslin M,l Woods M, Bussell J, Ramirez-Solis R, Reik W, Gottgens B, Zou X, Lu L, Wang C, Masaki H, White J, Nakauchi H, Zhong Z, Teichmann SA, Fu B, Zhu Z, Liu P. (2017) Establishment of mouse expanded potential stem cells. Nature 550 (7676), 393-39.
  17. Levy M*, Kolodziejczyk AA*, Thaiss CA*, Elinav E. (2017) Dysbiosis and the immune system. Nat. Rev. Immunol. 17 (4), 219-232.
  18. Martinez-Jimenez CP*, Eling N*, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT. (2017) Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science 355 (6332), 1433-1436.
  19. Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy D, Marioni JC, Teichmann SA. (2016) Classification of low quality cells from single cell RNA-seq data. Genome Biol. 17 (1), 1.
  20. Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. (2015) Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat. Commun. 6, 8687.
  21. Kolodziejczyk AA*, Kim JK*, Tsang JCH, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA. (2015) Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation. Cell Stem Cell 17 (4), 471-485.
  22. Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA. (2015) The Technology and Biology of Single-Cell RNA Sequencing. Mol. Cell 58 (4), 610-620.
  23. Tsang JCH, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L, Liu L. (2015) Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. Genome Biol. 16 (1), 1-16.
  24. Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L, Taylor AE, Hebenstreit D, Dingler FA, Moignard V, Göttgens B, Arlt W, McKenzie ANJ, Teichmann SA. (2014) Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis. Cell Rep. 22;7(4):1130-42.
  25. Brennecke P*, Anders S*, Kim JK*, Kolodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. (2013) Accounting for technical noise in single-cell RNA-seq experiments. Nat. Meth. 10: 1093–1095.