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*Lab members are shown in bold.


Bone marrow niches for hematopoietic stem cells: Lifespan dynamics and adaptation to acute stress.

Hofmann J and Kokkaliaris KD

Blood. In press

Variation in Mesenchymal KITL/SCF and IGF1 Expression at Middle Age Underlies Steady-State Hematopoietic Stem Cell Aging.

Young KA, Telpoukhovskaia MA, Hofmann J, Mistry JJ, Kokkaliaris KD, Trowbridge JJ.

Blood. In press


Feasibility of Next-generation Sequencing of Liquid Biopsy (Circulating Tumor DNA) Samples and Tumor Tissue from Patients with Metastatic Prostate Cancer in a Real-world Clinical Setting in Germany

Mandel P, Hoeh B, Humke C, Doering C, Wenzel M, Cano Garcia C, Fuhr N, Koll F, Fassl A, Tilki D, Steuber T, Faull I, Jeroch J, Ebner S, Schmitt C, Reis H, Köllermann J, Kokkaliaris KD, Demes MC, Chun FKH, Wild PJ.

European Urology Focus. 15:S2405-4569(24)00043-9.


The Brain Pre-Metastatic Niche: Biological and Technical Advancements

Geissler M, Jia W, Kiraz EN, Kulacz I, Liu X, Rombach A, Prinz V, Jussen D, Kokkaliaris KD, Medyouf H, Sevenich L, Czabanka M, Broggini T.

International Journal of Molecular Sciences 24(12):10055.

B lymphocyte-derived acetylcholine restrains steady-state and emergency hematopoiesis.

Schloss MJ, Hulsmans M, Rohde D, Lee H, Severe N, Foy B, Pulous F, Zhang S, Kokkaliaris KD, Frodermann V, Courties C, Yang C, Iwamoto Y, Knudsen A, McAlpineC, Yamazoe M, Schmidt S, Wojtkiewicz G, Masson G, Gustafsson K, Capen D, Brown D, Higgins J, Scadden DT, Libby P, Swirski F, Naxerova K, Nahrendorf M.

Nature Immunology. 23(4):605-618.


Human prostate cancer bone metastases have an actionable immunosuppressive microenvironment.

Kfoury Y, Baryawno N, Severe N, Mei S, Gustafsson K, Hirz T, Brouse T, Scadden EW, Igolkina AA, Kokkaliaris K, Choi BD, Barkas N, Randolph MA, Shin JH, Saylor PJ, Scadden DT, Sykes DB, Kharchenko PV; as part of the Boston Bone Metastases Consortium.

Cancer Cell. 39(11):1464-1478.

tiRNA signaling via stress-regulated vesicle transfer in the hematopoietic niche.

Kfoury YS, Ji F, Mazzola M, Sykes DB, Scherer AK, Anselmo A, Akiyama Y, Mercier F, Severe N, Kokkaliaris KD, Zhao T, Brouse T, Saez B, Seidl J, Papazian A, Ivanov P, Mansour MK, Sadreyev RI, Scadden DT.

​Cell Stem Cell. 28(12):2090-2103.


Adult blood stem cell localization reflects the abundance of reported bone marrow niche cell types and their combinations.

Kokkaliaris KD*, Kunz L, Cabezas-Wallscheid N, Christodoulou C, Renders S, Camargo F, Trumpp A, Scadden DT, Schroeder T*.

Blood. 136(20):2296-2307.

*co-corresponding authors, Cover story

Cell interactions in the bone marrow microenvironment affecting myeloid malignancies.

Kokkaliaris KD and Scadden DT.

Blood Advances. 4(15):3795-3803.

Cover story

Live-animal imaging of native haematopoietic stem and progenitor cells.

Christodoulou C, Spencer JA, Yeh SA, Turcotte R, Kokkaliaris KD, Panero R, Ramos A, Guo G, Seyedhassantehrani N, Esipova TV, Vinogradov SA, Rudzinskas S, Zhang Y, Perkins AS, Orkin SH, Calogero RA, Schroeder T, Lin CP, Camargo FD.

Nature. 578(7794):278-283.

Dissecting the spatial bone marrow microenvironment of hematopoietic stem cells.

Kokkaliaris KD.

Curr Opin Oncol. 32(2):154-161.


Asymmetric lysosome inheritance predicts blood stem cell activation.

Loeffler D, Wehling A, Schneiter F, Zhang Y, Müller-Bötticher N, Hoppe PS, Hilsenbeck O, Kokkaliaris KD, Endele M, Schroeder T.

Nature. 573(7774):426-429.

Stress-Induced Changes in Bone Marrow Stromal Cell Populations Revealed through Single-Cell Protein Expression Mapping.

Severe N, Karabacak NM, Gustafsson K, Baryawno N, Courties G, Kfoury Y, Kokkaliaris KD, Rhee C, Lee D, Scadden EW, Garcia-Robledo JE, Brouse T, Nahrendorf M, Toner M, Scadden DT.

Cell Stem Cell. 25(4):570-583.

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia.

Baryawno N, Przybylski D, Kowalczyk MS, Kfoury Y, Severe N, Gustafsson K, Kokkaliaris KD, Mercier F, Tabaka M, Hofree M, Dionne D, Papazian A, Lee D, Ashenberg O, Subramanian A, Vaishnav ED, Rozenblatt-Rosen O, Regev A, Scadden DT.

Cell. 177(7):1915-1932.

Inflammatory signals directly instruct PU.1 in HSCs via TNF.

Etzrodt M, Ahmed N, Hoppe PS, Loeffler D, Skylaki S, Hilsenbeck O, Kokkaliaris KD, Kaltenbach HM, Stelling J, Nerlov C and Schroeder T.

Blood. 133(8): 816-9.

Fate Distribution and Regulatory Role of Human Mesenchymal Stromal Cells in Engineered Hematopoietic Bone Organs.

Bourgine PE, Fritsch K, Pigeot S, Takiawa H, Kunz L, Kokkaliaris KD, Coutu DL, Manz M, Martin I, Schroeder T.

iScience. 19:504-513.


Automated Microfluidic System for Dynamic Stimulation and Tracking of Single Cells.

Dettinger P, Frank T, Etzrodt M, Ahmed N, Reimann A, Trenzinger C, Loeffler D, Kokkaliaris KD, Schroeder T, Tay S.

Analytical Chemistry. 90(18):10695-10700.

Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm.

Strasser MK, Hoppe P, Loeffler D, Kokkaliaris KD, Schroeder T, Theis FJ and Marr C.

Nature Communications, 12;9(1):2697.

In vitro biomimetic engineering of a human hematopoietic niche with functional properties.

Bourgine PE, Klein T, Paczulla AM, Shimizu T, Kunz L, Kokkaliaris KD, Coutu DL, Lengerke C, Skoda R, Schroeder T, Martin I.

Proc Natl Acad Sci U S A. 115(25):E5688-E5695.

Inductive and Selective Effects of GSK3 and MEK Inhibition on Nanog Heterogeneity in Embryonic Stem Cells.

Hastreiter S, Skylaki S, Loeffler D, Reimann A, Hilsenbeck O, Hoppe PS, Coutu DL, Kokkaliaris KD, Schwarzfischer M, Anastassiadis K, Theis FJ, Schroeder T.

Stem Cell Reports. 11(1):58-69.


On the statistical analysis of cell lineage trees.

Stadler T, Skylaki S, Kokkaliaris KD, Schroeder T.

Journal of Theoretical Biology. 14;439:160-165.

Multicolor quantitative confocal imaging cytometry.

Coutu D+, Kokkaliaris KD+, Kunz L+, Schroeder T.

Nature Methods, 15: 39-46.

+co-first authors


Three-dimensional map of nonhematopoietic bone and bone-marrow cells and molecules.

Coutu D+, Kokkaliaris KD+, Kunz L, Schroeder T.

Nature Biotechnology, 35(12):1202-1210.
+co-first authors, Cover story

Prospective identification of hematopoietic lineage choice by deep learning.

Buggenthin F, Buettner F, Hoppe PS, Endele M, Kroiss M, Strasser M, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Schroeder T, Theis FJ and Marr C.

Nature Methods, 14:403-406.

CSF-1 induced Src signaling can instruct monocytic lineage choice.

Endele M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Skylaki S, Hoppe PS, Schambach A, Stanley RE and Schroeder T.

Blood, 23:1691-1701.


Identification of factors promoting ex vivo maintenance of mouse hematopoietic stem cells by long-term single-cell quantification.  

Kokkaliaris KD, Drew E, Endele M, Loeffler D, Hoppe PS, Hilsenbeck O, Schauberger B, Hinzen C, Skylaki S, Theodorou M, Kieslinger M, Lemischka I, Moore K and Schroeder T.

Blood, 128(9): 1181-92.

                        Previewed: Palis J (2016) Behaving better: stem cells singled out. Blood. 128(9):1157-8.

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios.

Hoppe PS, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Moritz N, Endele M, Filipczyk AA, Gambardella A, Ahmed N, Etzrodt M, Coutu DL, Rieger MA, Marr C, Strasser M, Schauberger B, Burtscher I, Ermakova O, Bürger A, Lickert H, Nerlov C, Theis FJ and Schroeder T.

Nature, 535(7611):299-302.

Software tools for single-cell tracking and quantification of cellular and molecular properties.

Hilsenbeck O+, Schwarzfischer M+, Skylaki S+, Schauberger B, Hoppe PS, Loeffler D, Kokkaliaris KD, Hastreiter S, Skylaki E, Filipczyk A, Strasser M, Buggenthin F, Feigelman JS, Krumsiek J, van den Berg AJJ, Endele M, Etzrodt M, Marr C, Theis FJ and Schroeder T.

Nature Biotechnology, 34(7):703-6.

Understanding hematopoiesis from a single-cell standpoint.

Kokkaliaris KD+, Lucas D+, Beerman I+, Kent DG, Perié L.

Experimental Hematology. 44(6):447-50.

+co-first authors


​Network Plasticity of Pluripotency Transcription Factors in Embryonic Stem Cells.

Filipczyk A, Marr C, Hastreiter S, Feigelman J, Schwarzfischer M, Hoppe PS, Loeffler D, Kokkaliaris KD, Endele M, Schauberger B, Hilsenbeck O, Skylaki S, Hasenauer J, Anastassiadis K, Theis FJ, Schroeder T.

Nature Cell Biology, (10):1235-46.

CCND1-CDK4-mediated cell cycle progression provides a competitive advantage for human hematopoietic stem cells in vivo.

Mende N, Kuchen EE, Lesche M, Grinenko T, Kokkaliaris KD, Hanenberg H, Lindemann D, Dahl A, Platz A, Höfer T, Calegari F, Waskow C.

Journal of Experimental Medicine, 212: 1171-1183.

Ectopic expression of msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation.

Yilmaz A, Engeler R, Constantinescu S, Kokkaliaris KD, Dimitrakopoulos C, Schroeder T, Beerenwinkel N, Paro R.

Stem Cell Research, 15(3):542-53.

Clonal evolution of pre-leukemic hematopoietic stem cells in acute myeloid leukemia.

Sykes SM+, Kokkaliaris KD+, Milsom MD+, Levine RL, Majeti R.

Experimental Hematology, 43(12):989-92.

+co-first authors


Bloody signals: From birth to disease and death.

Trompouki E, King KY, Will B, Lessard J, Flores-Figueroa E, Kokkaliaris KD, Bowman T.

Experimental Hematology, 42(12):989-94.


Early dynamic fate changes in haemogenic endothelium characterised at the single cell level.

Swiers G, Baumann C, O'Rourke J, Giannoulatou E, Taylor S, Joshi A, Moignard V, Pina C, Bee T, Kokkaliaris KD, Yoshimoto M, Yoder MC, Frampton J, Schroeder T, Enver T, Göttgens B, de Bruijn MF.

Nature Communications, 4:2924.


HSC-Explorer: A Curated Database for Hematopoietic Stem Cells.

Montrone C, Kokkaliaris KD, Loeffler D, Lechner M, Kastenmüller G, Schroeder T, Ruepp A.

PLoS One, 8(7): e70348.


Drosophila oogenesis as a bio-marker responding to EMF sources.

Margaritis LH, Manta AK, Kokkaliaris KD, Schiza D, Alimisis K, Barkas G, Georgiou E, Giannakopoulou O, Kollia I, Kontogianni G, Kourouzidou A, Myari A, Roumelioti F, Skouroliakou A, Sykioti V, Varda G, Xenos K, Ziomas K.

Electromagnetic Biology & Medicine. 33(3):165-8


HOXB4 can enhance the differentiation of embryonic stem cells by modulating the hematopoietic niche.

Jackson M, Axton RA, Taylor AH, Wilson JA, Gordon-Keylock SA, Kokkaliaris KD, Brickman JM, Schulz H, Hummel O, Hubner N, Forrester LM.

Stem Cells, 30:150-160.


Advances in tracking hematopoiesis at the single cell level.

Kokkaliaris KD, Loeffler D, Schroeder T.

Current Opinion in Hematology, 19(4):243-9.


Wnt to Notch relay signaling induces definitive hematopoiesis.

Loeffler D, Kokkaliaris KD, Schroeder T.

Cell Stem Cell, 9(1): 2-4

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