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1

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

Hilsenbeck, Oliver, Schwarzfischer, Michael, Skylaki, Stavroula, Schauberger, Bernhard, Hoppe, Philipp S, Loeffler, Dirk, Kokkaliaris, Konstantinos D, Hastreiter, Simon, Skylaki, Eleni, Filipczyk, Ada

Journal:

Nature Biotechnology

Year:

2016

Language:

english

File:

PDF, 2.15 MB

english, 2016

2

Network plasticity of pluripotency transcription factors in embryonic stem cells

Filipczyk, Adam, Marr, Carsten, Hastreiter, Simon, Feigelman, Justin, Schwarzfischer, Michael, Hoppe, Philipp S., Loeffler, Dirk, Kokkaliaris, Konstantinos D., Endele, Max, Schauberger, Bernhard, Hils

Journal:

Nature Cell Biology

Year:

2015

Language:

english

File:

PDF, 21.94 MB

english, 2015

3

Multicolor quantitative confocal imaging cytometry

Coutu, Daniel L, Kokkaliaris, Konstantinos D, Kunz, Leo, Schroeder, Timm

Journal:

Year:

2017

Language:

english

File:

PDF, 9.84 MB

english, 2017

4

HOXB4 Can Enhance the Differentiation of Embryonic Stem Cells by Modulating the Hematopoietic Niche

Melany Jackson, Richard A. Axton, A. Helen Taylor, Julie A. Wilson, Sabrina A.M. Gordon-Keylock, Konstantinos D. Kokkaliaris, Joshua M. Brickman, Herbert Schulz, Oliver Hummel, Norbert Hubner, Lesley

Journal:

Year:

2012

Language:

english

File:

PDF, 1.34 MB

english, 2012

5

Wnt to Notch Relay Signaling Induces Definitive Hematopoiesis

Dirk Loeffler, Konstantinos D. Kokkaliaris, Timm Schroeder

Journal:

Year:

2011

Language:

english

File:

PDF, 376 KB

english, 2011

6

Drosophila oogenesis as a bio-marker responding to EMF sources

Margaritis, Lukas H., Manta, Areti K., Kokkaliaris, Konstantinos D., Schiza, Dimitra, Alimisis, Konstantinos, Barkas, Georgios, Georgiou, Eleana, Giannakopoulou, Olympia, Kollia, Ioanna, Kontogianni,

Journal:

Electromagnetic Biology and Medicine

Year:

2014

Language:

english

File:

PDF, 2.41 MB

english, 2014

7

Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level

Swiers, Gemma, Baumann, Claudia, O’Rourke, John, Giannoulatou, Eleni, Taylor, Stephen, Joshi, Anagha, Moignard, Victoria, Pina, Cristina, Bee, Thomas, Kokkaliaris, Konstantinos D., Yoshimoto, Momoko,

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 1.09 MB

english, 2013

8

Molecular control of hematopoietic stem cell behavior by the microenvironment

Kokkaliaris, Konstantinos, Moore, Kateri, Schroeder, Timm

Journal:

Experimental Hematology

Year:

2014

Language:

english

File:

PDF, 50 KB

english, 2014

9

Bloody signals: From birth to disease and death

Trompouki, Eirini, King, Katherine Y., Will, Britta, Lessard, Julie, Flores-Figueroa, Eugenia, Kokkaliaris, Konstantinos D., Bowman, Teresa

Journal:

Experimental Hematology

Year:

2014

Language:

english

File:

PDF, 225 KB

english, 2014

10

Advances in tracking hematopoiesis at the single-cell level

Kokkaliaris, Konstantinos D., Loeffler, Dirk, Schroeder, Timm

Journal:

Current Opinion in Hematology

Year:

2012

Language:

english

File:

PDF, 287 KB

english, 2012

11

Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation

Yilmaz, Atilgan, Engeler, Rachel, Constantinescu, Simona, Kokkaliaris, Konstantinos D., Dimitrakopoulos, Christos, Schroeder, Timm, Beerenwinkel, Niko, Paro, Renato

Journal:

Stem Cell Research

Year:

2015

Language:

english

File:

PDF, 1.53 MB

english, 2015

12

Understanding hematopoiesis from a single-cell standpoint

Kokkaliaris, Konstantinos D., Lucas, Daniel, Beerman, Isabel, Kent, David G., Perié, Leila

Journal:

Experimental Hematology

Year:

2016

Language:

english

File:

PDF, 878 KB

english, 2016

13

Three-dimensional multicolor imaging of bone marrow cell populations

Kokkaliaris, Konstantinos, Coutu, Daniel, Kunz, Leo, Schroeder, Timm

Journal:

Experimental Hematology

Year:

2015

Language:

english

File:

PDF, 50 KB

english, 2015

14

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

Hoppe, Philipp S., Schwarzfischer, Michael, Loeffler, Dirk, Kokkaliaris, Konstantinos D., Hilsenbeck, Oliver, Moritz, Nadine, Endele, Max, Filipczyk, Adam, Gambardella, Adriana, Ahmed, Nouraiz, Etzrod

Journal:

Year:

2016

Language:

english

File:

PDF, 5.44 MB

english, 2016

15

Three-dimensional multicolor quantitative imaging of bone marrow niches

Kokkaliaris, Konstantinos, Coutu, Daniel, Kunz, Leo, Schroeder, Timm

Journal:

Experimental Hematology

Year:

2016

Language:

english

File:

PDF, 48 KB

english, 2016

16

A microfluidic platform for dynamic cell culture and quantitative time-lapse imaging of non-adherent cells

Dettinger, Philip, Etzrodt, Martin, Frank, Tino, Ahmed, Nouraiz, Reimann, Andreas, Trenzinger, Christoph, Skylaki, Laura, Hilsenbeck, Oliver, Loeffler, Dirk, Kokkaliaris, Konstantinos, Tay, Savas, Sch

Journal:

Experimental Hematology

Year:

2016

Language:

english

File:

PDF, 46 KB

english, 2016

17

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

Endele, Max, Loeffler, Dirk, Kokkaliaris, Konstantinos D., Hilsenbeck, Oliver, Skylaki, Stavroula, Hoppe, Philipp S., Schambach, Axel, Stanley, E. Richard, Schroeder, Timm

Journal:

Year:

2017

Language:

english

File:

PDF, 1.69 MB

english, 2017

18

Prospective identification of hematopoietic lineage choice by deep learning

Buggenthin, Felix, Buettner, Florian, Hoppe, Philipp S, Endele, Max, Kroiss, Manuel, Strasser, Michael, Schwarzfischer, Michael, Loeffler, Dirk, Kokkaliaris, Konstantinos D, Hilsenbeck, Oliver, Schroe

Journal:

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

19

Three-dimensional multicolor quantitative imaging of hematopoietic cells in their bone marrow niche

Kokkaliaris, Konstantinos, Coutu, Daniel, Kunz, Leo, Schroeder, Timm

Journal:

Experimental Hematology

Year:

2017

Language:

english

File:

PDF, 222 KB

english, 2017

20

On the statistical analysis of single cell lineage trees

Stadler, Tanja, Skylaki, Stavroula, D, Konstantinos, Kokkaliaris,, Schroeder, Timm

Journal:

Journal of Theoretical Biology

Year:

2017

Language:

english

File:

PDF, 767 KB

english, 2017

21

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

Hastreiter, Simon, Skylaki, Stavroula, Loeffler, Dirk, Reimann, Andreas, Hilsenbeck, Oliver, Hoppe, Philipp S., Coutu, Daniel L., Kokkaliaris, Konstantinos D., Schwarzfischer, Michael, Anastassiadis,

Journal:

Stem Cell Reports

Year:

2018

Language:

english

File:

PDF, 2.23 MB

english, 2018

22

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

Bourgine, Paul E., Klein, Thibaut, Paczulla, Anna M., Shimizu, Takafumi, Kunz, Leo, Kokkaliaris, Konstantinos D., Coutu, Daniel L., Lengerke, Claudia, Skoda, Radek, Schroeder, Timm, Martin, Ivan

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 1.84 MB

english, 2018

23

HSC-Explorer: A Curated Database for Hematopoietic Stem Cells

Montrone, Corinna, Kokkaliaris, Konstantinos D., Loeffler, Dirk, Lechner, Martin, Kastenmüller, Gabi, Schroeder, Timm, Ruepp, Andreas, Bunting, Kevin D.

Journal:

Year:

2013

Language:

english

File:

PDF, 617 KB

english, 2013

24

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

Strasser, Michael K., Hoppe, Philipp S., Loeffler, Dirk, Kokkaliaris, Konstantinos D., Schroeder, Timm, Theis, Fabian J., Marr, Carsten

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 814 KB

english, 2018

25

Automated Microfluidic System for Dynamic Stimulation and Tracking of Single Cells

Dettinger, Philip, Frank, Tino, Etzrodt, Martin, Ahmed, Nouraiz, Reimann, Andreas, Trenzinger, Christoph, Loeffler, Dirk, Kokkaliaris, Konstantinos D., Schroeder, Timm, Tay, Savaş

Journal:

Analytical Chemistry

Year:

2018

Language:

english

File:

PDF, 3.19 MB

english, 2018

26

Quantitative Bone-Marrow Imaging Reveals Niche Signatures of Distinct Types of Adult and Juvenile Hematopoietic Stem Cells

Kokkaliaris, Konstantinos, Kunz, Leo, Cabezas-Wallscheid, Nina, Coutu, Daniel, Trumpp, Andreas, Schroeder, Timm

Journal:

Experimental Hematology

Year:

2018

Language:

english

File:

PDF, 55 KB

english, 2018

27

Inflammatory signals directly instruct PU.1 in HSCs via TNF

Etzrodt, Martin, Ahmed, Nouraiz, Hoppe, Philipp S., Loeffler, Dirk, Skylaki, Stavroula, Hilsenbeck, Oliver, Kokkaliaris, Konstantinos D., Kaltenbach, Hans-Michael, Stelling, Jörg, Nerlov, Claus, Schro

Journal:

Year:

2018

Language:

english

File:

PDF, 418 KB

english, 2018

28

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

Severe, Nicolas, Karabacak, Nezihi Murat, Gustafsson, Karin, Baryawno, Ninib, Courties, Gabriel, Kfoury, Youmna, Kokkaliaris, Konstantinos D., Rhee, Catherine, Lee, Dongjun, Scadden, Elizabeth W., Gar

Journal:

Year:

2019

Language:

english

File:

PDF, 4.21 MB

english, 2019

29

Asymmetric lysosome inheritance predicts activation of haematopoietic stem cells

Loeffler, Dirk, Wehling, Arne, Schneiter, Florin, Zhang, Yang, Müller-Bötticher, Niklas, Hoppe, Philipp S., Hilsenbeck, Oliver, Kokkaliaris, Konstantinos D., Endele, Max, Schroeder, Timm

Journal:

Year:

2019

Language:

english

File:

PDF, 47.03 MB

english, 2019

30

Publisher Correction: Asymmetric lysosome inheritance predicts activation of haematopoietic stem cells

Loeffler, Dirk, Wehling, Arne, Schneiter, Florin, Zhang, Yang, Müller-Bötticher, Niklas, Hoppe, Philipp S., Hilsenbeck, Oliver, Kokkaliaris, Konstantinos D., Endele, Max, Schroeder, Timm

Journal:

Year:

2019

File:

PDF, 307 KB

2019

31

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

Bourgine, Paul E., Fritsch, Kristin, Pigeot, Sebastien, Takizawa, Hitoshi, Kunz, Leo, Kokkaliaris, Konstantinos D., Coutu, Daniel L., Manz, Markus G., Martin, Ivan, Schroeder, Timm

Journal:

Year:

2019

Language:

english

File:

PDF, 4.60 MB

english, 2019

32

Publisher Correction: Asymmetric lysosome inheritance predicts activation of haematopoietic stem cells

Loeffler, Dirk, Wehling, Arne, Schneiter, Florin, Zhang, Yang, Müller-Bötticher, Niklas, Hoppe, Philipp S., Hilsenbeck, Oliver, Kokkaliaris, Konstantinos D., Endele, Max, Schroeder, Timm

Journal:

Year:

2019

File:

PDF, 307 KB

2019

33

Dissecting the spatial bone marrow microenvironment of hematopoietic stem cells

Kokkaliaris, Konstantinos D.

Journal:

Current Opinion in Oncology

Year:

2020

Language:

english

File:

PDF, 236 KB

english, 2020

34

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

Kokkaliaris, Konstantinos, Kunz, Leo, Cabezas-Wallscheid, Nina, Christodoulou, Constantina, Renders, Simon, Camargo, Fernando, Trumpp, Andreas, Scadden, David T, Schroeder, Timm

Journal:

Year:

2020

File:

PDF, 2.43 MB

2020

35

Cell interactions in the bone marrow microenvironment affecting myeloid malignancies

Kokkaliaris, Konstantinos D., Scadden, David T.

Journal:

Year:

2020

File:

PDF, 1.10 MB

2020

36

Erratum to âOn the statistical analysis of single cell lineage treesâ [J. Theor. Biol. 439 (2018) 160â165]

Stadler, Tanja, Skylaki, Stavroula, Kokkaliaris, Konstantinos D., Schroeder, Timm

Journal:

Journal of Theoretical Biology

Year:

2020

File:

PDF, 201 KB

2020