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Pan-cancer analysis of whole genomes.

Nature 578 (7793): 82-93. 6 February 2020

Computational pan-genomics: status, promises and challenges.

Briefings in Bioinformatics 19 (1): 118-135. January 2018

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing.
Abay, T., Stickels, R.R., Takizawa, M.T., Nalbant, B.N., Hsieh, Y.H., Hwang, S., Snopkowski, C., Yu, K.K.H., Abou-Mrad, Z., Tabar, V., Howitt, B.E, Ludwig, L.S., Chaligné, R., Satpathy, A.T and Lareau, C.A.
Nature Genetics 8 January 2025 (In Press)

Phylogenetic ctDNA analysis depicts early stage lung cancer evolution.
Abbosh, C., Birkbak, N.J., Wilson, G.A., Jamal-Hanjani, M., Constantin, T., Salari, R., Quesne, J.L., Moore, D.A., Veeriah, S., Rosenthal, R., Marafioti, T., Kirkizlar, E., Watkins, T.B.K., McGranahan, N., Ward, S., Martinson, L., Riley, J., Fraioli, F., Bakir, M.A., Grönroos, E., Zambrana, F., Endozo, R., Bi, W.L., Fennessy, F.M., Sponer, N., Johnson, D., Laycock, J., Shafi, S., Czyzewska-Khan, J., Rowan, A., Chambers, T., Matthews, N., Turajlic, S., Hiley, C., Lee, S.M., Forster, M.D., Ahmad, T., Falzon, M., Borg, E., Lawrence, D., Hayward, M., Kolvekar, S., Panagiotopoulos, N., Janes, S.M., Thakrar, R., Ahmed, A., Blackhall, F., Summers, Y., Hafez, D., Naik, A., Ganguly, A., Kareht, S., Shah, R., Joseph, L., Quinn, A.M., Crosbie, P., Naidu, B., Middleton, G., Langman, G., Trotter, S., Nicolson, M., Remmen, H., Kerr, K., Chetty, M., Gomersall, L., Fennell, D.A., Nakas, A., Rathinam, S., Anand, G., Khan, S., Russell, P., Ezhil, V., Ismail, B., Irvin-Sellers, M., Prakash, V., Lester, J.F., Kornaszewska, M., Attanoos, R., Adams, H., Davies, H., Oukrif, D., Akarca, A.U., Hartley, J.A., Lowe, H.L., Lock, S., Iles, N., Bell, H., Ngai, Y., Elgar, G., Szallasi, Z., Schwarz, R.F., Herrero, J., Stewart, A., Quezada, S.A., Van Loo, P., Dive, C., Lin, C.J., Rabinowitz, M., Aerts, H.J.W.L., Hackshaw, A., Shaw, J.A., Zimmermann, B.G. and Swanton, C.
Nature 545 (7655): 446-451. 25 May 2017

Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA.
Abbosh, C., Frankell, A.M., Harrison, T., Kisistok, J., Garnett, A., Johnson, L., Veeriah, S., Moreau, M., Chesh, A., Chaunzwa, T.L., Weiss, J., Schroeder, M.R., Ward, S., Grigoriadis, K., Shahpurwalla, A., Litchfield, K., Puttick, C., Biswas, D., Karasaki, T., Black, J.R.M., Martínez-Ruiz, C., Bakir, M.A.l., Pich, O., Watkins, T.B.K., Lim, E.L., Huebner, A., Moore, D.A., Godin-Heymann, N., L'Hernault, A., Bye, H., Odell, A., Roberts, P., Gomes, F., Patel, A.J., Manzano, E., Hiley, C.T., Carey, N., Riley, J., Cook, D.E., Hodgson, D., Stetson, D., Barrett, J.C., Kortlever, R.M., Evan, G.I., Hackshaw, A., Daber, R.D., Shaw, J.A., Aerts, H.J.W.L., Licon, A., Stahl, J., Jamal-Hanjani, M., Birkbak, N.J., McGranahan, N. and Swanton, C.
Nature 616 (7957): 553-562. 20 April 2023

Impaired human hematopoiesis due to a cryptic intronic splicing mutation.
Abdulhay, N.J., Fiorini, C., Verboon, J.M., Ludwig, L.S., Ulirsch, J.C., Zieger, B., Lareau, C.A., Mi, X., Roy, A., Obeng, E.A., Erlacher, M., Gupta, N., Gabriel, S.B., Ebert, B.L., Niemeyer, C.M., Khoriaty, R.N., Ancliff, P., Gazda, H.T., Wlodarski, M.W. and Sankaran, V.G.
Journal of Experimental Medicine 216 (5): 1050-1060. 6 May 2019

Screening of well-established drugs targeting cancer metabolism: reproducibility of the efficacy of a highly effective drug combination in mice.
Abolhassani, M., Guais, A., Sanders, E., Campion, F., Fichtner, I., Bonte, J., Baronzio, G., Fiorentini, G., Israel, M. and Schwartz, L.
Investigational New Drugs 30 (4): 1331-1342. August 2012

Biochemical analysis of TREX complex recruitment to intronless and intron-containing yeast genes.
Abruzzi, K.C., Lacadie, S. and Rosbash, M.
EMBO Journal 23 (13): 2620-2631. 7 July 2004

Comparative evaluation of the biological properties of reducible and acid-sensitive folate prodrugs of a highly potent doxorubicin derivative.
Abu Ajaj, K., El-Abadla, N., Welker, P., Azab, S., Zeisig, R., Fichtner, I. and Kratz, F.
European Journal of Cancer 48 (13): 2054-2065. September 2012

In vitro and in vivo study of an albumin-binding prodrug of doxorubicin that is cleaved by cathepsin B.
Abu Ajaj, K., Graeser, R., Fichtner, I. and Kratz, F.
Cancer Chemotherapy and Pharmacology 64 (2): 413-418. July 2009

MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange.
Abualrous, E.T., Stolzenberg, S., Sticht, J., Wieczorek, M., Roske, Y., Günther, M., Dähn, S., Boesen, B.B., Calvo, M.M., Biese, C., Kuppler, F., Medina-García, Á., Álvaro-Benito, M., Höfer, T., Noé, F. and Freund, C.
Nature Chemical Biology 19 (10): 1196-1204. October 2023

Malaria-specific antibody responses and parasite persistence after infection of mice with Plasmodium chabaudi chabaudi.
Achtman, A.H., Stephens, R., Cadman, E.T., Harrison, V. and Langhorne, J.
Parasite Immunology 29 (9): 435-444. September 2007

CCR7-deficient mice develop atypically persistent germinal centers in response to thymus-independent type 2 antigens.
Achtman, A.H., Höpken, U.E., Bernert, C. and Lipp, M.
Journal of Leukocyte Biology 85 (3): 409-417. March 2009

C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice.
Ackermann, T., Hartleben, G., Müller, C., Mastrobuoni, G., Groth, M., Sterken, B.A., Zaini, M.A., Youssef, S.A., Zuidhof, H.R., Krauss, S.R., Kortman, G., de Haan, G., de Bruin, A., Wang, Z.Q., Platzer, M., Kempa, S. and Calkhoven, C.F.
Communications Biology 2 : 208. 14 June 2019

Genetic determinants of micronucleus formation in vivo.
Adams, D.J., Barlas, B., McIntyre, R.E., Salguero, I., van der Weyden, L., Barros, A., Vicente, J.R., Karimpour, N., Haider, A., Ranzani, M., Turner, G., Thompson, N.A., Harle, V., Olvera-León, R., Robles-Espinoza, C.D., Speak, A.O., Geisler, N., Weninger, W.J., Geyer, S.H., Hewinson, J., Karp, N.A., Fu, B., Yang, F., Kozik, Z., Choudhary, J., Yu, L., van Ruiten, M.S., Rowland, B.D., Lelliott, C.J., Del Castillo Velasco-Herrera, M., Verstraten, R., Bruckner, L., Henssen, A.G., Rooimans, M.A., de Lange, J., Mohun, T.J., Arends, M.J., Kentistou, K.A., Coelho, P.A., Zhao, Y., Zecchini, H., Perry, J.R.B., Jackson, S.P. and Balmus, G.
Nature 627 (8002): 130-136. 7 March 2024

Cell cycle effects of fatty acid derivatives of cytarabine, CP-4055, and of gemcitabine, CP-4126, as basis for the interaction with oxaliplatin and docetaxel.
Adema, A.D., Laan, A.C., Myhren, F., Fichtner, I., Verheul, H.M., Sandvold, M.L. and Peters, G.J.
International Journal of Oncology 36 (1): 285-294. 1 January 2010

[S3-Guidelines "Exocrine pancreatic cancer" 2007.] S3-Leitlinie "Exokrines Pankreaskarzinom" 2007.
Adler, G., Seufferlein, T., Bischoff, S.C., Brambs, H.J., Feuerbach, S., Grabenbauer, G., Hahn, S., Heinemann, V., Hohenberger, W., Langrehr, J.M., Lutz, M.P., Neuhaus, H., Neuhaus, P., Oettle, H., Schlag, P.M., Schmid, R., Schmiegel, W., Schlottmann, K., Werner, J., Wiedenmann, B. and Kopp, I.
Zeitschrift fuer Gastroenterologie 45 : 487-523. June 2007

SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8(+) T cell responses.
Agerer, B., Koblischke, M., Gudipati, V., Montaño-Gutierrez, L.F., Smyth, M., Popa, A., Genger, J.W., Endler, L., Florian, D.M., Mühlgrabner, V., Graninger, M., Aberle, S.W., Husa, A.M., Shaw, L.E., Lercher, A., Gattinger, P., Torralba-Gombau, R., Trapin, D., Penz, T., Barreca, D., Fae, I., Wenda, S., Traugott, M., Walder, G., Pickl, W.F., Thiel, V., Allerberger, F., Stockinger, H., Puchhammer-Stöckl, E., Weninger, W., Fischer, G., Hoepler, W., Pawelka, E., Zoufaly, A., Valenta, R., Bock, C., Paster, W., Geyeregger, R., Farlik, M., Halbritter, F., Huppa, J.B., Aberle, J.H. and Bergthaler, A.
Science Immunology 6 (57): eabg6461. March 2021

T cell homing to tumors detected by 3D-coordinated positron emission tomography and magnetic resonance imaging.
Agger, R., Petersen, M.S., Petersen, C.C., Hansen, S.B., Stodkilde-Jorgensen, H., Skands, U., Blankenstein, T., Andersen, T.E., Hulgaard, E.F., Jorgensen, J.T., Marqversen, J., Gundersen, H.J. and Hokland, M.E.
Journal of Immunotherapy 30 (1): 29-39. January 2007

A Notch/STAT3-driven Blimp-1/c-Maf-dependent molecular switch induces IL-10 expression in human CD4(+) T cells and is defective in Crohn's disease patients.
Ahlers, J., Mantei, A., Lozza, L., Stäber, M., Heinrich, F., Bacher, P., Hohnstein, T., Menzel, L., Yüz, S.G., Alvarez-Simon, D., Bickenbach, A.R., Weidinger, C., Mockel-Tenbrinck, N., Kühl, A.A., Siegmund, B., Maul, J., Neumann, C. and Scheffold, A.
Mucosal Immunology 15 (3): 480-490. May 2022

Nicotine strongly activates dendritic cell-mediated adaptive immunity - Potential role for progression of atherosclerotic lesions.
Aicher, A., Heeschen, C., Mohaupt, M., Cooke, J.P., Zeiher, A.M. and Dimmeler, S.
Circulation 107 (4): 604-611. 4 February 2003

1H, 15N and 13C assignments of the cysteine protease inhibitor Chagasin from Trypanosoma cruzi.
Aido-Machado, R., Salmon, D., Diehl, A., Leidert, M., Schmetzer, O., de Lima, A.P.C.A., Scharfstein, J., Oschkinat, H. and Pires, J.R.
Journal of Biomolecular NMR 36 (Suppl) (1): 30. December 2006

Gab1 and Mapk signaling are essential in the hair cycle and hair follicle stem cell quiescence.
Akilli Öztürk, Ö., Pakula, H., Chmielowiec, J., Qi, J., Stein, S., Lan, L., Sasaki, Y., Rajewsky, K. and Birchmeier, W.
Cell Reports 13 (3): 561-572. 20 October 2015

The evolution of non-small cell lung cancer metastases in TRACERx.
Al Bakir, M., Huebner, A., Martínez-Ruiz, C., Grigoriadis, K., Watkins, T.B.K., Pich, O., Moore, D.A., Veeriah, S., Ward, S., Laycock, J., Johnson, D., Rowan, A., Razaq, M., Akther, M., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Hessey, S., Dietzen, M., Colliver, E., Frankell, A.M., Bunkum, A., Lim, E.L., Karasaki, T., Abbosh, C., Hiley, C.T., Hill, M.S., Cook, D.E., Wilson, G.A., Salgado, R., Nye, E., Stone, R.K., Fennell, D.A., Price, G., Kerr, K.M., Naidu, B., Middleton, G., Summers, Y., Lindsay, C.R., Blackhall, F.H., Cave, J., Blyth, K.G., Nair, A., Ahmed, A., Taylor, M.N., Procter, A.J., Falzon, M., Lawrence, D., Navani, N., Thakrar, R.M., Janes, S.M., Papadatos-Pastos, D., Forster, M.D., Lee, S.M., Ahmad, T., Quezada, S.A., Peggs, K.S., Van Loo, P., Dive, C., Hackshaw, A., Birkbak, N.J., Zaccaria, S., Jamal-Hanjani, M., McGranahan, N. and Swanton, C.
Nature 616 (7957): 534-542. April 2023

Body composition and lung cancer-associated cachexia in TRACERx.
Al-Sawaf, O., Weiss, J., Skrzypski, M., Lam, J.M., Karasaki, T., Zambrana, F., Kidd, A.C., Frankell, A.M., Watkins, T.B.K., Martínez-Ruiz, C., Puttick, C., Black, J.R.M., Huebner, A., Bakir, M.A., Sokač, M., Collins, S., Veeriah, S., Magno, N., Naceur-Lombardelli, C., Prymas, P., Toncheva, A., Ward, S., Jayanth, N., Salgado, R., Bridge, C.P., Christiani, D.C., Mak, R.H., Bay, C., Rosenthal, M., Sattar, N., Welsh, P., Liu, Y., Perrimon, N., Popuri, K., Beg, M.F., McGranahan, N., Hackshaw, A., Breen, D.M., O'Rahilly, S., Birkbak, N.J., Aerts, H.J.W.L., Jamal-Hanjani, M. and Swanton, C.
Nature Medicine 29 (4): 846-858. April 2023

Chlamydia trachomatis prevents apoptosis via activation of PDPK1-MYC and enhanced mitochondrial binding of hexokinase II.
Al-Zeer, M.A., Xavier, A., Abu Lubad, M., Sigulla, J., Kessler, M., Hurwitz, R. and Meyer, T.F.
EBioMedicine 23 : 100-110. September 2017

The metabolic background is a global player in Saccharomyces gene expression epistasis.
Alam, M.T., Zelezniak, A., Mülleder, M., Shliaha, P., Schwarz, R., Capuano, F., Vowinckel, J., Radmaneshfar, E., Krüger, A., Calvani, E., Michel, S., Börno, S., Christen, S., Patil, K.R., Timmermann, B., Lilley, K.S. and Ralser, M.
Nature Microbiology 1 : 15030. 1 February 2016

From operating table to laboratory bench: the path toward metastasis research from the clinical setting.
Alberto Vilchez, M. and Rau, B.
Methods in Molecular Biology 2294 : 325-333. 2021

Distinct functional properties of the TAP subunits coordinate the nucleotide-dependent transport cycle.
Alberts, P., Daumke, O., Deverson, E.V., Howard, J.C. and Knittler, M.R.
Current Biology 11 (4): 242-51. 20 February 2001

MYCN mediates cysteine addiction and sensitizes neuroblastoma to ferroptosis.
Alborzinia, H., Flórez, A.F., Kreth, S., Brückner, L.M., Yildiz, U., Gartlgruber, M., Odoni, D.I., Poschet, G., Garbowicz, K., Shao, C., Klein, C., Meier, J., Zeisberger, P., Nadler-Holly, M., Ziehm, M., Paul, F., Burhenne, J., Bell, E., Shaikhkarami, M., Würth, R., Stainczyk, S.A., Wecht, E.M., Kreth, J., Büttner, M., Ishaque, N., Schlesner, M., Nicke, B., Stresemann, C., Llamazares-Prada, M., Reiling, J.H., Fischer, M., Amit, I., Selbach, M., Herrmann, C., Wölfl, S., Henrich, K.O., Höfer, T., Trumpp, A. and Westermann, F.
Nature Cancer 3 (4): 471-485. 28 April 2022

Spontaneous non-sustained ventricular tachycardia and premature ventricular contractions and their prognostic relevance in patients with cancer in routine care.
Albrecht, A., Porthun, J., Eucker, J., Coats, A.J.S., von Haehling, S., Pezzutto, A., Karakas, M., Riess, H., Keller, U., Landmesser, U., Haverkamp, W., Anker, S.D. and Anker, M.S.
Cancers 13 (10): 2303. 12 May 2021

Clinically relevant glioblastoma patient-derived xenograft models to guide drug development and identify molecular signatures.
Alcaniz, J., Winkler, L., Dahlmann, M., Becker, M., Orthmann, A., Haybaeck, J., Krassnig, S., Skofler, C., Kratzsch, T., Kuhn, S.A., Jödicke, A., Linnebacher, M., Fichtner, I., Walther, W. and Hoffmann, J.
Frontiers in Oncology 13 : 1129627. 11 April 2023

Characterization of protein-binding to the spinach chloroplast psbA mRNA 5' untranslated region.
Alexander, C., Faber, N. and Klaff, P.
Nucleic Acids Research 26 (10): 2265-2272. 15 May 1998

Tumor-derived extracellular vesicles impair CD171-specific CD4(+) CAR T cell efficacy.
Ali, S., Toews, K., Schwiebert, S., Klaus, A., Winkler, A., Grunewald, L., Oevermann, L., Deubzer, H.E., Tüns, A., Jensen, M.C., Henssen, A.G., Eggert, A., Schulte, J.H., Schwich, E., Rebmann, V., Schramm, A. and Künkele, A.
Frontiers in Immunology 11 : 531. 31 March 2020

Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J., Karaiskos, N., Praktiknjo, S.D., Grosswendt, S., Wahle, P., Ruffault, P.L., Ayoub, S., Schreyer, L., Boltengagen, A., Birchmeier, C., Zinzen, R., Kocks, C. and Rajewsky, N.
BMC Biology 15 (1): 44. 19 May 2017

Inter-individual and inter-strain differences in cognitive and social abilities of Dark Agouti and Wistar Han rats.
Alonso, L., Peeva, P., Ramos-Prats, A., Alenina, N., Winter, Y. and Rivalan, M.
Behavioural Brain Research 377 : 112188. 13 January 2020

Response prediction by FDG-PET after neoadjuvant radiochemotherapy and combined regional hyperthermia of rectal cancer: correlation with endorectal ultrasound and histopathology.
Amthauer, H., Denecke, T., Rau, B., Hildebrandt, B., Huenerbein, M., Ruf, J., Schneider, U., Gutberlet, M., Schlag, P.M., Felix, R. and Wust, P.
European Journal of Nuclear Medicine and Molecular Imaging 31 (6): 811-819. 1 January 2004

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.
Anania, C., Acemel, R.D., Jedamzick, J., Bolondi, A., Cova, G., Brieske, N., Kühn, R., Wittler, L., Real, F.M. and Lupiáñez, D.G.
Nature Genetics 54 (7): 1026-1036. July 2022

Molecular pathways: comparing the effects of drugs and T cells to effectively target oncogenes.
Anders, K. and Blankenstein, T.
Clinical Cancer Research 19 (2): 320-326. 15 January 2013

Depot formation of doxycycline impairs Tet-regulated gene expression in vivo.
Anders, K., Buschow, C., Charo, J. and Blankenstein, T.
Transgenic Research 21 (5): 1099-1107. October 2012

Oncogene-targeting T cells reject large tumors while oncogene inactivation selects escape variants in mouse models of cancer.
Anders, K., Buschow, C., Herrmann, A., Milojkovic, A., Loddenkemper, C., Kammertoens, T., Daniel, P., Yu, H., Charo, J. and Blankenstein, T.
Cancer Cell 20 (6): 755-767. 13 December 2011

Microarray meta-analysis defines global angiogenesis-related gene expression signatures in human carcinomas.
Anders, M., Fehlker, M., Wang, Q., Wissmann, C., Pilarsky, C., Kemmner, W. and Hoecker, M.
Molecular Carcinogenesis 52 (1): 29-38. January 2013

Loss of the coxsackie and adenovirus receptor contributes to gastric cancer progression.
Anders, M., Vieth, M., Roecken, C., Ebert, M., Pross, M., Gretschel, S., Schlag, P.M., Wiedenmann, B., Kemmner, W. and Hoecker, M.
British Journal of Cancer 100 (2): 352-359. 27 January 2009

The immune system prevents recurrence of transplanted but not autochthonous antigenic tumors after oncogene inactivation therapy.
Anders, K., Kershaw, O., Larue, L., Gruber, A.D. and Blankenstein, T.
International Journal of Cancer 141 (12): 2551-2561. 15 December 2017

CD171- and GD2-specific CAR-T cells potently target retinoblastoma cells in preclinical in vitro testing.
Andersch, L., Radke, J., Klaus, A., Schwiebert, S., Winkler, A., Schumann, E., Grunewald, L., Zirngibl, F., Flemmig, C., Jensen, M.C., Rossig, C., Joussen, A., Henssen, A., Eggert, A., Schulte, J.H. and Künkele, A.
BMC Cancer 19 (1): 895. 9 September 2019

Phosphorylation-dependent down-regulation of c-Myb DNA binding is abrogated by a point mutation in the v-myb oncogene.
Andersson, K.B., Kowenz-Leutz, E., Brendeford, E.M., Tygsett, A.H.H., Leutz, A. and Gabrielsen, O.S.
Journal of Biological Chemistry 278 (6): 3816-3824. 7 February 2003

Mining the literature: new methods to exploit keyword profiles.
Andrade-Navarro, M.A.
Genome Medicine 4 (10): 81. 30 October 2012

A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations.
Andrade-Navarro, M.A., Kanji, F., Palii, C.G., Brand, M., Atkins, H. and Perez-Iratxeta, C.
BMC Biotechnology 13 (1): 80. 3 October 2013

De novo whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome, an animal model for severe/critical COVID-19.
Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L.G., Landthaler, M., Bieniara, M., Trimpert, J. and Wyler, E.
Genome Biology and Evolution 14 (7): evac100. July 2022

An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers.
Andres, D., Gohlke, U., Broeker, N.K., Schulze, S., Rabsch, W., Heinemann, U., Barbirz, S. and Seckler, R.
Glycobiology 23 (4): 486-494. April 2013

Tail morphology controls DNA release in two Salmonella phages with one lipopolysaccharide receptor recognition system.
Andresen, D., Roske, Y., Doering, C., Heinemann, U., Seckler, R. and Barbirz, S.
Molecular Microbiology 83 (6): 1244-1253. March 2012

CAR affinity modulates the sensitivity of CAR-T cells to PD-1/PD-L1-mediated inhibition.
Andreu-Saumell, I., Rodriguez-Garcia, A., Mühlgrabner, V., Gimenez-Alejandre, M., Marzal, B., Castellsagué, J., Brasó-Maristany, F., Calderon, H., Angelats, L., Colell, S., Nuding, M., Soria-Castellano, M., Barbao, P., Prat, A., Urbano-Ispizua, A., Huppa, J.B. and Guedan, S.
Nature Communications 15 (1): 3552. 26 April 2024

destiny: diffusion maps for large-scale single-cell data in R.
Angerer, P., Haghverdi, L., Büttner, M., Theis, F.J., Marr, C. and Buettner, F.
Bioinformatics 32 (8): 1241-1243. 15 April 2016

Downregulation of odd-skipped related 2, a novel regulator of epithelial-mesenchymal transition, enables efficient somatic cell reprogramming.
Anh, L.P.H., Nishimura, K., Kuno, A., Nguyen, T.L., Kato, T., Ohtaka, M., Nakanishi, M., Sugihara, E., Sato, T.A., Hayashi, Y., Fukuda, A. and Hisatake, K.
Stem Cells 40 (4): 397-410. 29 April 2022

New cardiovascular biomarkers in patients with advanced cancer – a prospective study comparing MR-proADM, MR-proANP, copeptin, high-sensitivity troponin T and NT-proBNP.
Anker, M.S., Lück, L.C., Khan, M.S., Porthun, J., Hadzibegovic, S., Lena, A., Wilkenshoff, U., Weinländer, P., Evertz, R., Totzeck, M., Mahabadi, A.A., Rassaf, T., Anker, S.D., Bullinger, L., Keller, U., Karakas, M., Landmesser, U., Butler, J. and von Haehling, S.
European Journal of Heart Failure 26 November 2024 (In Press)

Patient-reported ability to walk 4 m and to wash: New clinical endpoints and predictors of survival in patients with pre-terminal cancer.
Anker, M.S., Lena, A., Roeland, E.J., Porthun, J., Schmitz, S., Hadzibegovic, S., Sikorski, P., Wilkenshoff, U., Fröhlich, A.K., Ramer, L.V., Rose, M., Eucker, J., Rassaf, T., Totzeck, M., Lehmann, L.H., von Haehling, S., Coats, A.J.S., Friede, T., Butler, J., Anker, S.D., Riess, H., Landmesser, U., Bullinger, L., Keller, U. and Ahn, J.
Journal of Cachexia Sarcopenia and Muscle 14 (4): 1670-1681. August 2023

Cardiovascular health-related quality of life in cancer: a prospective study comparing the ESC HeartQoL and EORTC QLQ-C30 questionnaire.
Anker, M.S., Potthoff, S.K., Lena, A., Porthun, J., Hadzibegovic, S., Evertz, R., Denecke, C., Fröhlich, A.K., Sonntag, F., Regitz-Zagrosek, V., Rosen, S.D., Lyon, A.R., Lüscher, T.F., Spertus, J.A., Anker, S.D., Karakas, M., Bullinger, L., Keller, U., Landmesser, U., Butler, J. and von Haehling, S.
European Journal of Heart Failure 25 (9): 1635-1647. September 2023

B-Myb, a repressed trans-activating protein.
Ansieau, S., Kowenz-Leutz, E., Dechend, R. and Leutz, A.
Journal of Molecular Medicine 75 (11-12): 815-819. November 1997

Early life stress regulates cardiac development through an IL4-glucocorticoid signaling balance.
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Functionalized bead assay to measure three-dimensional traction forces during T-cell activation.
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Nano Letters 21 (1): 507-514. 13 January 2021

CD38 low IgG-secreting cells are precursors of various CD38 high-expressing plasma cell populations.
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Clonal hematopoiesis is associated with improved survival in patients with metastatic colorectal cancer from the FIRE-3 trial.
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Hematopoietic lineage distribution and evolutionary dynamics of clonal hematopoiesis.
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Leukemia 32 (9): 1908-1919. September 2018

Dynamics of clonal hematopoiesis under DNA-damaging treatment in patients with ovarian cancer.
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Associations of clonal hematopoiesis with recurrent vascular events and death in patients with incident ischemic stroke.
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Eukaryotic expression: developments for structural proteomics.
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Acta Crystallographica Section D 62 (Pt. 10): 1114-1124. October 2006

Colon cancer metastasis: MACC1 and Met as metastatic pacemakers.
Arlt, F. and Stein, U.
International Journal of Biochemistry and Cell Biology 41 (12): 2356-2359. December 2009

Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle, independently of its on-target effect.
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Journal of Enzyme Inhibition and Medicinal Chemistry 36 (1): 1282-1289. 30 June 2021

Inhibiting phosphoglycerate dehydrogenase counteracts chemotherapeutic efficacy against MYCN-amplified neuroblastoma.
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International Journal of Cancer 148 (5): 1219-1232. 1 March 2021

SETD1A protects HSCs from activation-induced functional decline in vivo.
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Blood 131 (12): 1311-1324. 22 March 2018

Reactivating TP53 signaling by the novel MDM2 inhibitor DS-3032b as a therapeutic option for high-risk neuroblastoma.
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Oncotarget 9 (2): 2304-2319. 2018

The germinal center response is impaired in the absence of T cell-expressed CXCR5.
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European Journal of Immunology 37 (1): 100-109. January 2007

Analysis of NTRK expression in gastric and esophageal adenocarcinoma (AGE) with pan-TRK immunohistochemistry.
Arnold, A., Daum, S., von Winterfeld, M., Berg, E., Hummel, M., Horst, D., Rau, B., Stein, U. and Treese, C.
Pathology Research and Practice 215 (11): 152662. November 2019

Prognostic impact of Claudin 18.2 in gastric and esophageal adenocarcinomas.
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Clinical and Translational Oncology 22 (12): 2357-2363. December 2020

Immunohistochemical analysis of nicotinamide phosphoribosyltransferase expression in gastric and esophageal adenocarcinoma (AEG).
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Gastrointestinal Disorders 4 (4): 333-340. 13 December 2022

Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers.
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Nature Communications 7 : 13047. 20 October 2016

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
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Bioinformatics 26 (17): 2109-2115. 1 September 2010

Prospective tracking of donor-reactive T-cell clones in the circulation and rejecting human kidney allografts.
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Frontiers in Immunology 12 : 750005. 14 October 2021

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
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Genome Medicine 13 (1): 7. 13 January 2021

Post-COVID exercise intolerance is associated with capillary alterations and immune dysregulations in skeletal muscles.
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Conserved beta-hairpin recognition by the GYF domains of Smy2 and GIGYF2 in mRNA surveillance and vesicular transport complexes.
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Increased MACC1 levels in tissues and blood identify colon adenoma patients at high risk.
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Journal of Translational Medicine 14 (1): 215. 20 July 2016

Saffron: The golden spice with therapeutic properties on digestive diseases.
Ashktorab, H., Soleimani, A., Singh, G., Amr, A., Tabtabaei, S., Latella, G., Stein, U., Akhondzadeh, S., Solanki, N., Gondré-Lewis, M.C., Habtezion, A. and Brim, H.
Nutrients 11 (5): 943. 26 April 2019

Histone methyltransferase DOT1L controls state-specific identity during B cell differentiation.
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CXXC5 (Retinoid-Inducible Nuclear Factor, RINF) is a potential therapeutic target in high-risk human acute myeloid leukemia.
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Oncotarget 4 (9): 1438-1448. September 2013

REG1A expression is a prognostic marker in colorectal cancer and associated with peritoneal carcinomatosis.
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International Journal of Cancer 123 (2): 409-413. 15 July 2008

Loss of epidermal Evi/Wls results in a phenotype resembling psoriasiform dermatitis.
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Journal of Experimental Medicine 210 (9): 1761-1777. 26 August 2013

IKK phosphorylates RelB to modulate its promoter specificity and promote fibroblast migration downstream of TNF receptors.
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Proceedings of the National Academy of Sciences of the United States of America 111 (41): 14794-14799. 14 October 2014

The magnitude of germinal center reactions is restricted by a fixed number of preexisting niches.
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Proceedings of the National Academy of Sciences of the United States of America 118 (30): e2100576118. 27 July 2021

Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface.
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Crystal structure of human sex hormone-binding globulin in complex with 2-methoxyestradiol reveals the molecular basis for high affinity interactions with C-2 derivatives of estradiol.
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Determination of interaction kinetics between the T cell receptor and peptide-loaded MHC class II via single-molecule diffusion measurements.
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Biophysical Journal 103 (2): L17-9. 18 July 2012

Single molecule fluorescence microscopy on planar supported bilayers.
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Journal of Visualized Experiments (105): e53158. 31 October 2015

Measuring TCR-pMHC binding in situ using a FRET-based microscopy assay.
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Journal of Visualized Experiments (105): e53157. 30 October 2015

Structure and function of the Bacillus hybrid enzyme GluXyn-1: Native-like jellyroll fold preserved after insertion of autonomous globular domain.
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Proceedings of the National Academy of Sciences of the United States of America 95 (12): 6613-6618. 9 June 1998

Steady state migratory RelB(+) Langerin(+) dermal dendritic cells mediate peripheral induction of antigen-specific CD4(+) CD25(+) Foxp3(+) regulatory T cells.
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European Journal of Immunology 41 (5): 1420-1434. May 2011

A rapid embryonic stem cell-based mouse model for B-cell lymphomas driven by Epstein-Barr virus protein LMP1.
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Loss of m(1)acp(3)Ψ ribosomal RNA modification is a major feature of cancer.
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Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome.
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Nucleic Acids Research 37 (4): 1141-1151. March 2009

Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization.
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Nature Cell Biology 22 (1): 38-48. January 2020

Development of resistance towards artesunate in MDA-MB-231 human breast cancer cells.
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PLoS ONE 6 (5): e20550. 26 May 2011

STAT3 activation in Th17 and Th22 cells controls IL-22-mediated epithelial host defense during infectious colitis.
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RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation.
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Suppression of peripheral pain by blockade of voltage-gated calcium 2.2 channels in nociceptors induces RANKL and impairs recovery from inflammatory arthritis in a mouse model.
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Arthritis & Rheumatology 67 (6): 1657-1667. June 2015

A chronic model of arthritis supported by a strain-specific periarticular lymph node in BALB/c mice.
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Nature Communications 4 : 1644. 2013

Cytotoxic T cells modulate inflammation and endogenous opioid analgesia in chronic arthritis.
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Journal of Neuroinflammation 14 (1): 30. 6 February 2017

Apoptosis-induced cleavage of keratin 15 and keratin 17 in a human breast epithelial cell line.
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Ubiquitin binding by a CUE domain regulates ubiquitin chain formation by ERAD E3 ligases.
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Molecular Cell 50 (4): 528-539. 23 May 2013

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey, M.H., Meyerson, W.U., Dursi, L.J., Wang, L.B., Dong, G., Liang, W.W., Weerasinghe, A., Li, S., Li, Y., Kelso, S., Saksena, G., Ellrott, K., Wendl, M.C., Wheeler, D.A., Getz, G., Simpson, J.T., Gerstein, M.B. and Ding, Li
Nature Communications 11 (1): 4748. 21 September 2020

Essential role of c-myc in ara-C-induced differentiation of human erythroleukemia cells.
Baker, S.J., Pawlita, M., Leutz, A. and Hoelzer, D.
Leukemia 8 (8): 1309-1317. August 1994

In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia.
Bakina, O., Conrad, T., Mitic, N., Vidal, R.O., Obrusnik, T., Sai, S., Nolte, C., Semtner, M. and Kettenmann, H.
PLoS ONE 19 (7): e0302376. 11 July 2024

Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region.
Balasubramanian, S., Andreani, M., Goncalves Andrade, J., Saha, T., Sundaravinayagam, D., Garzón, J., Zhang, W., Popp, O., Hiraga, S., Rahjouei, A., Rosen, D.B., Mertins, P., Chait, B.T., Donaldson, A.D. and Di Virgilio, M.
eLife 11 : e75047. 13 April 2022

Binding of Drosophila ORC proteins to anaphase chromosomes requires cessation of mitotic cyclin-dependent kinase activity.
Baldinger, T. and Gossen, M.
Molecular and Cellular Biology 29 (1): 140-149. January 2009

Immune phenotypes and checkpoint molecule expression of clonally expanded lymph node-infiltrating T cells in classical Hodgkin lymphoma.
Ballhausen, A., Ben Hamza, A., Welters, C., Dietze, K., Bullinger, L., Rahn, H.P., Hartmann, S., Hansmann, M.L. and Hansmann, L.
Cancer Immunology Immunotherapy 72 (2): 515-521. February 2023

Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR.
Balyschew, N., Yushkevich, A., Mikirtumov, V., Sanchez, R.M., Sprink, T. and Kudryashev, M.
Nature Communications 14 (1): 6543. 17 October 2023

Role of β-catenin in synaptic vesicle localization and presynaptic assembly.
Bamji, S.X., Shimazu, K., Kimes, N., Huelsken, J., Birchmeier, W., Lu, B. and Reichardt, L.F.
Neuron 40 (4): 719-731. November 2003

Common mode of remodeling AAA ATPases p97/CDC48 by their disassembling cofactors ASPL/PUX1.
Banchenko, S., Arumughan, A., Petrović, S., Schwefel, D., Wanker, E.E., Roske, Y. and Heinemann, U.
Structure 27 (12): 1830-1841. 3 December 2019

First steps towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high biomedical value.
Banci, L., Bertini, I., Cusack, S., de Jong, R.N., Heinemann, U., Jones, E.Y., Kozielski, F., Maskos, K., Messerschmidt, A., Owens, R., Perrakis, A., Poterszman, A., Schneider, G., Siebold, C., Silman, I., Sixma, T., Stewart-Jones, G., Sussman, J.L., Thierry, J.C. and Moras, D.
Acta Crystallographica Section D 62 (Pt. 10): 1208-1217. October 2006

Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases.
Bandapalli, O.R., Geheeb, M., Kobelt, D., Kuehnle, K., Elezkurtaj, S., Herrmann, J., Gressner, A.M., Weiskirchen, R., Beule, D., Blüthgen, N., Herzel, H., Franke, C. and Brand, K.
International Journal of Cancer 118 : 74-89. 1 January 2006

Substituted titanocenes induce caspase-dependent apoptosis in human epidermoid carcinoma cells in vitro and exhibit antitumour activity in vivo.
Bannon, J.H., Fichtner, I., O'Neill, A., Pampillon, C., Sweeney, N.J., Strohfeldt, K., Watson, R.W., Tacke, M. and McGee, M.M.
British Journal of Cancer 97 (9): 1234-1241. 5 November 2007

Epithelial OPA1 links mitochondrial fusion to inflammatory bowel disease.
Bao, L.L., Yu, Y.Q., González-Acera, M., Patankar, J.V., Giessl, A., Sturm, G., Kühl, A.A., Atreya, R., Erkert, L., Gámez-Belmonte, R., Krug, S.M., Schmid, B., Tripal, P., Chiriac, M.T., Hildner, K., Siegmund, B., Wirtz, S., Stürzl, M., Mohamed Abdou, M., Trajanoski, Z., Neurath, M.F., Zorzano, A. and Becker, C.
Science Translational Medicine 17 (781): eadn8699. January 2025

In contrast to Western diet, a plant-based, high-fat, low-sugar diet does not exacerbate retinal endothelial injury in streptozotocin-induced diabetes.
Barakat, A., Nakao, S., Zandi, S., Sun, D., Schmidt-Ullrich, R., Hayes, K.C. and Hafezi-Moghadam, A.
FASEB Journal 33 (9): 10327-10338. September 2019

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C, Daub, C.O., Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

Dynamics of the ligand binding domain layer during AMPA receptor activation.
Baranovic, J., Chebli, M., Salazar, H., Carbone, A.L., Faelber, K., Lau, A.Y., Daumke, O. and Plested, A.J.R.
Biophysical Journal 110 (4): 896-911. 23 February 2016

Subsequent malignancies among long-term survivors of Hodgkin lymphoma and non-Hodgkin lymphoma: a pooled analysis of German cancer registry data (1990-2012).
Baras, N., Dahm, S., Haberland, J., Janz, M., Emrich, K., Kraywinkel, K. and Salama, A.
British Journal of Haematology 177 (2): 226-242. April 2017

Crystal structure of Escherichia coli phage HK620 tailspike: podoviral tailspike endoglycosidase modules are evolutionarily related.
Barbirz, S., Mueller, J.J., Uetrecht, C., Clark, A.J., Heinemann, U. and Seckler, R.
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PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
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Constitutive nuclear factor-kappaB-RelA activation is required for proliferation and survival of Hodgkin's disease tumor cells.
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Characterization of a novel Hodgkin cell-line, HD-MyZ, HD-Myr, with myelomonocytic features mimicking Hodgkin's disease in severe combined immunodeficient mice.
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Blocking of transcription factor E2F/DP by dominant-negative mutants in a normal breast epithelial cell line efficiently inhibits apoptosis and induces tumor growth in scid mice.
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Overexpression of the death-promoting gene bax-alpha which is downregulated in breast cancer restores sensitivity to different apoptotic stimuli and reduces tumor growth in SCID mice.
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Experimental observation of a fundamental length scale of waves in random media.
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Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells.
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OPA1 functionally interacts with MIC60 but is dispensable for crista junction formation.
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Short-chain fatty acid propionate protects from hypertensive cardiovascular damage.
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The Myb leucine zipper is essential for leukemogenicity of the v-Myb protein.
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Contrasting requirements during disease evolution identify EZH2 as a therapeutic target in AML.
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Enhancement of CRISPR-Cas9 induced precise gene editing by targeting Histone H2A-K15 ubiquitination.
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CD40 activity on mesenchymal cells negatively regulates OX40L to maintain bone marrow immune homeostasis under stress conditions.
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Identification of TTLL8, POTEE, and PKMYT1 as immunogenic cancer-associated antigens and potential immunotherapy targets in ovarian cancer.
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Synergistic activity of bortezomib and HDACis in preclinical models of B-cell precursor acute lymphoblastic leukemia via modulation of p53, PI3K/AKT and NF-κB.
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Extraembryonic gut endoderm cells undergo programmed cell death during development.
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Adenine nucleotide translocase-1, a component of the permeability transition pore, can dominantly induce apoptosis.
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Feedback, mass conservation and reaction kinetics impact the robustness of cellular oscillations.
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State-of-the-art analytical methods of viral infections in human lung organoids.
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Investigating the role of GLUL as a survival factor in cellular adaptation to glutamine depletion via targeted stable isotope resolved metabolomics.
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Proteomic profiling of colorectal adenomas identifies a predictive risk signature for development of metachronous advanced colorectal neoplasia.
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Monosomal karyotype and chromosome 17p loss or TP53 mutations in decitabine-treated patients with acute myeloid leukemia.
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The anticancer phytochemical rocaglamide inhibits Rho GTPase activity and cancer cell migration.
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The traditional Chinese medical compound Rocaglamide protects nonmalignant primary cells from DNA damage-induced toxicity by inhibition of p53 expression.
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The mTOR pathway inhibitor RAD001 (everolimus) is highly efficacious in tamoxifen-sensitive and -resistant breast cancer xenografts.
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Structural identification of the VPS18 β-propeller reveals a critical role in the HOPS complex stability and function.
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Claudin-targeted suicide gene therapy for claudin-overexpressing tumor cells by using modified clostridium perfringens enterotoxin (CPE).
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A new measure to assess the difficulty of liver resection.
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Feasibility of navigated resection of liver tumors using multiplanar visualization of intraoperative 3-dimensional ultrasound data.
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Image-guided surgery of liver metastases by three-dimensional ultrasound-based optoelectronic navigation.
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CD95 (APO-1/Fas) mutations in childhood T-lineage acute lymphoblastic leukemia.
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Smac mimetic and glucocorticoids synergize to induce apoptosis in childhood ALL by promoting ripoptosome assembly.
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Impact of patient- and disease-specific factors on SLNB in breast cancer patients. Are current guidelines justified?
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Sentinel-Node-Biopsie : Definition, historische Entwicklung und methodisches Vorgehen.
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Chirurg 75 (8): 761-766. 1 January 2004

Presence of mature DC-Lamp(+) dendritic cells in sentinel and non-sentinel lymph nodes of breast cancer patients.
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European Journal of Surgical Oncology 34 (5): 514-518. May 2008

Sentinel lymph node biopsy in rectal cancer - not yet ready for routine clinical use.
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Surgery 135 (5): 498-505. May 2004

Detection of lymph node micrometastases and isolated tumor cells in sentinel and nonsentinel lymph nodes of colon cancer patients.
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Optimierung des Staging beim Kolonkarzinom durch Sentinel-Lymphknoten-Biopsie. Aktuelle Aspekte [Optimization of staging in colon cancer using sentinel lymph node biopsy].
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Sentinel lymph node biopsy in colon cancer: A prospective multicenter trial.
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A kinome of 2600 in the ciliate Paramecium tetraurelia.
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Virus-reactive T cells expanded in aplastic anemia eliminate hematopoietic progenitor cells by molecular mimicry.
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gen.ethix. Multimediales Online-Spiel zum aktuellen Bioethik-Diskurs.
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Modeling Wnt/β-catenin target gene expression in APC and Wnt gradients under wild type and mutant conditions.
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Frontiers in Physiology 4 : 21. 25 February 2013

Disentangling pro-mitotic signaling during cell cycle progression using time-resolved single-cell imaging.
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Leveraging large language models for decision support in personalized oncology.
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Mathematical modelling of promoter occupancies in MYC-dependent gene regulation.
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Controlling nuclear NF-κB dynamics by β-TrCP-insights from a computational model.
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