SYSTEMS BIOLOGY OF
MAMMALIAN TISSUES
SYSTEMS BIOLOGY OF
MAMMALIAN TISSUES
Harnik, Y., Yakubovsky, O., Hoefflin, R., Novoselsky R., Bahar Halpern K., Barkai T., Korem Kohanim Y., Egozi A., Golani O., Addadi Y., Kedmi M., Keidar Haran T., Levin Y., Savidor A., Keren-Shaul H., Mayer C., Pencovich N., Pery R., Shouval D., Tirosh I., Nachmany I & Itzkovitz S. A spatial expression atlas of the adult human proximal small intestine. Nature. August 07, (2024). pdf.
Buchauer L. & Itzkovitz S. cellanneal: A User-Friendly Deconvolution Software for Transcriptomics Data. Journal of Open Source Software. January 12, (2024). pdf
Bahar Halpern K., Korem Kohanim Y., Biram A., Harnik Y., Egozi A., Yakubovsky O., Shulman Z. & Itzkovitz S. The cellular states and fates of shed intestinal cells. Nature Metabolism. October 19, (2023). pdf. See also preview.
Egozi A., Olaloye O., Werner L., Silva T., McCourt B., Pierce W. R., An X., Wang F., Chen K., Pober S. J., Shouval D., Itzkovitz S. & Konnikova L. Single-cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis. Plos Biology. May 19, (2023). pdf.
Dan S., Ungar B., Ben-Moshe S., Bahar Halpern K., Yavzori M., Fudim E., Picard O., Mushka Abitbol C., Harnik S., Barshack I., Kopylov U., Ben-Horin S. & Itzkovitz S. Distal fecal wash host transcriptomics identifies inflammation throughout the colon and terminal ileum. CMGH. February 13, (2023). pdf. See also: CMGH.
Afriat A., Zuzarte-Luís V., Bahar Halpern K., Buchauer L., Marques S., Ferreira Chora Â., Lahree A., Amit I., Mota MM. & Itzkovitz S. A spatiotemporally resolved single-cell atlas of the Plasmodium liver stage. Nature. November 9 (2022). pdf. See also: Nature.
Ben-Moshe S., Veg T., Manco R., Dan S., Papinutti D., Lifshitz A., Kolodziejczyk A.A., Bahar Halpern K., Elinav E. & Itzkovitz S. The spatiotemporal program of zonal liver regeneration following acute injury. Cell Stem Cell. June 2 (2022). pdf. See also: Cell Stem Cell
Ungar B., Yavzori M., Fudim E., Picard O., Kopylov U., Eliakim R., Shouval D., Levin Y., Savidor A., Ben-Moshe S., Manco R., Dan S., Egozi A., Bahar Halpern K., Mayer C., Barshack I., Ben-Horin S. & Itzkovitz S. Host transcriptome signatures in human faecal-washes predict histological remission in patients with IBD. Gut. January 19 (2022). pdf
Harnik Y., Buchauer L., Ben-Moshe S., Averbukh I., Levin Y., Savidor A., Eilam R., Moor AE & Itzkovitz S. Spatial discordances between mRNAs and proteins in the intestinal epithelium. Nature Metabolism. December 20 (2021). pdf
Egozi A., Llivichuzhca-Loja D., McCourt BT., Bahar Halpern K., Farack L., An X., Wang F., Chen K., Konnikova L. & Itzkovitz S. Insulin is expressed by enteroendocrine cells during human fetal development. Nature Medicine. December 9 (2021). pdf
Cohen N., Massalha H., Ben-Moshe S., Egozi A., Rozenberg M., Bahar Halpern K. & Itzkovitz S. Spatial gene expression maps of the intestinal lymphoid follicle and associated epithelium identify zonated expression programs. PLOS Biology. October 11 (2021). pdf
Manco R.*, Averbukh I.*, Porat Z., Bahar Halpern K., Amit I. & Itzkovitz S. Clump sequencing exposes the spatial expression programs of intestinal secretory cells. Nature Communications. May 24 (2021). (* equal contribution) pdf
Droin, C., El Kholtei, J., Bahar Halpern, K., Hurni, C., Rozenberg, M., Muvkadi, S., Itzkovitz, S. & Naef, F. Space-time logic of liver gene expression at sub-lobular scale. Nature Metabolism Jan 11 (2021). pdf See also: Nature Metabolism
Massalha, H., Bahar Halpern, K., Abu-Gazala, S., Jana, T., Massasa, EE., Moor AE., Buchauer, L., Rozenberg, M., Pikarsky, E., Amit, I., Zamir, G. & Itzkovitz, S., A single cell atlas of the human liver tumor microenvironment, Molecular Systems Biology, December 17 (2020). pdf
Manco, R. & Itzkovitz, S., Liver Zonation, Journal of Hepatology, December 11 (2020). pdf
Egozi, A. Bahar Halpern, K., Farack, L., Rotem, H. & Itzkovitz, S., Zonation of Pancreatic Acinar Cells in Diabetic Mice, Cell Reports, August 18 (2020). pdf
Bahar Halpern, K., Massalha, H., Zwick RK., Moor, AE., Castillo-Azofeifa D., Rozenberg, M., Farack, L., Egozi, A., Miller, DR., Averbukh, I., Harnik, Y., Weinberg-Corem, N., de Sauvage FJ., Amit, I., Klein, OD., Shoshkes-Carmel, M., & Itzkovitz, S. Lgr5+ telocytes are a signaling source at the intestinal villus tip, Nature Communications, April 22 (2020). pdf
Ben-Moshe S*, Shapira Y*, Moor A E, Manco R, Veg T, Bahar Halpern K & Itzkovitz S, Spatial sorting enables comprehensive characterization of liver zonation, Nature Metabolism, September 16 (2019). (* equal contribution). pdf
Ben-Moshe S & Itzkovitz S, Spatial heterogeneity in the mammalian liver, Nature reviews gastroenterology & hepatology, April 1 (2019). pdf
Farack L*, Golan M*, Egozi A, Dezorella N, Bahar Halpern K, Ben-Moshe S, Garzilli I, Tóth B, Roitman L, Krizhanovsky V & Itzkovitz S, Transcriptional heterogeneity of beta cells in the intact pancreas, Developmental Cell, November 29 (2018). (* equal contribution) pdf See also: Developmental Cell
Farack L*, Egozi A* & Itzkovitz S, Single molecule approaches for studying gene regulation in metabolic tissues, Diabetes, Obesity and Metabolism, September 19 (2018). (* equal contribution) pdf
Moor A E, Harnik Y, Ben-Moshe S, Massasa E E, Rozenberg M, Eilam R, Bahar-Halpern K & Itzkovitz S, Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis, cell, September 27 (2018). pdf. See also: Nature Reviews Gastroenterology & Hepatology
Bahar-Halpern K*, Shenhav R*, Massalha H, Toth B, Egozi A, Massasa E E, Medgalia C, David E, Giladi A, Moor A E, Porat Z, Amit I & Itzkovitz S, Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells, Nature Biotechnology, September 17 (2018). (* equal contribution) pdf
Garzilli, I. & Itzkovitz, S. Design principles of the paradoxical feedback between pancreatic alpha and beta cells. Scientific Reports Jul 16 (2018). pdf
Moor A E, Golan M, Massasa E E, Lemze D, Weizman T, Shenhav R, Baydatch S, Mizrahi O, Winkler R, Golani O, Stern-Ginossar N & Itzkovitz S, Global mRNA polarization regulates translation efficiency in the intestinal epithelium. Science August 10 (2017). pdf See also: Science, Developmental Cell, F1000.
Moor A E & Itzkovitz S, Spatial transcriptomics: paving the way for tissue-level systems biology. Current Opinion in Biotechnology March 24 (2017). pdf
Bahar-Halpern K*, Shenhav R*, Matcovitch-Natan O, Tóth B, Lemze D, Golan M, Massasa E., Baydatch S, Landen S, Moor A, Brandis A, Giladi A, Stokar-Avihail A, David E, Amit I & Itzkovitz S, Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature Feb 6 (2017). (* equal contribution) pdf See also: Nature Reviews Gastroenterology & Hepatology, Nature News, Liver Zonation Table
Tóth B*, Ben-Moshe S*, Gavish A*, Barkai N & Itzkovitz S, Early commitment and robust differentiation in colonic crypts. Molecular Systems Biology Jan 3 (2017). (* equal contribution) pdf See also: Cover image
Tanami S, Ben-Moshe S, Mayo A, Bahar Halpern K, Itzkovitz S, Dynamic zonation of liver polyploidy. Cell and Tissue Research June 15 (2016).pdf
Bahar Halpern K, Caspi I, Lemze D, Levy M, Landen S, Elinav E, Ulitsky I, Itzkovitz S, Nuclear Retention of mRNA in Mammalian Tissues. Cell Reports 13 (2015). See also: Nature Reviews Molecular Cell Biology. pdf
Bahar Halpern K, Itzkovitz S, Single Molecule approaches for quantifying transcription and
degradation rates in intact mammalian tissues. Methods (2015). pdf. Download TransQuant.
Bahar Halpern K, Tanami S, Landen S, Chapal M, Szlak L, Hutzler A, Nizhberg A, Itzkovitz S, Bursty Gene Expression in the Intact Mammalian Liver. Molecular Cell, 58 (2015). See also: Developmental Cell. pdf
Itzkovitz S, Blat I, Jacks T, Clevers H, van Oudenaarden A, Optimality in the development of intestinal crypts. Cell, 148(3) (2012). See also: HFSP preview. pdf
Itzkovitz S, Lyubimova A, Blat I, Maynard M, van Es J, Lees J, Jacks T, Clevers H, van Oudenaarden A, Single molecule transcript counting of stem cell markers in the mouse intestine. Nature Cell Biology, 14(1) (2011). See also: HFSP preview, Protocol. pdf
Itzkovitz S, van Oudenaarden A, Validating transcripts with probes and imaging technology. Nature Methods 8, S12-S19 (2011). pdf
Reizel Y*, Itzkovitz S*, Adar R*, Elbaz J, Jinich A, Chapal Ilani N, Maruvka YE, Nevo N, Marx Z, Horovitz I, Wasserstrom A, Mayo A, Shur I, Benayahu D, Skorecki K, Segal E, Dekel N, Shapiro S, Cell lineage analysis of the mammalian female germline. Plos Genetics, 8(2) (2012). (* equal contribution) pdf
Itzkovitz S*, Hodis E*, Segal E, Overlapping codes within protein-coding sequences. Genome Research 20, 1582-1589 (2010) (* equal contribution). See also: Nature Reviews Genetics, Nature Methods. pdf
Zaslaver A, Kaplan S, Bren A, Jinich A, Mayo A, Dekel E, Alon U, Itzkovitz S, Invariant Distribution of Promoter Activities in Escherichia coli. Plos Computational Biology 5 (2009). pdf
Itzkovitz S*, Baruch L*, Shapiro E, Segal E, Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code. Proceedings of the National Academy of Sciences USA 105, 9278-9283 (2008). (* equal contribution) pdf
Itzkovitz S, Shlush LI, Gluck D, Skorecki K, Population mixture model for nonlinear telomere dynamics.Physical Review E 78, 060902 (2008). pdf
Itzkovitz S, Alon U, The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Research 17, 405-412 (2007). See also: Genome Research, Nature Reviews Genetics. pdf
Itzkovitz S, Tlusty T, Alon U, Coding limits on the number of transcription factors. BMC Genomics 7 (2006). pdf
Itzkovitz S, Milo R, Kashtan N, Levitt R, Lahav A, Alon, U, Recurring harmonic walks and network motifs in Western music. Advances in Complex Systems 9, 121-132 (2006). pdf
Itzkovitz S, Alon U, Subgraphs and network motifs in geometric networks. Physical Review E 71, 026117 (2005). pdf
Itzkovitz S, Levitt R., Kashtan N, Milo R, Itzkovitz M. and Alon U, Coarse-graining and self-dissimilarity of complex networks. Physical Review E 71, 016127 (2005). pdf
Itzkovitz S, Milo R, Kashtan N, Ziv G, Alon U, Subgraphs in random networks. Physical Review E 68, 026127 (2003). pdf