Pesquisa | BVS Doenças Infecciosas e Parasitárias

1.

Toward Minimal Residual Disease-Directed Therapy in Melanoma.

Rambow, Florian; Rogiers, Aljosja; Marin-Bejar, Oskar; Aibar, Sara; Femel, Julia; Dewaele, Michael; Karras, Panagiotis; Brown, Daniel; Chang, Young Hwan; Debiec-Rychter, Maria; Adriaens, Carmen; Radaelli, Enrico; Wolter, Pascal; Bechter, Oliver; Dummer, Reinhard; Levesque, Mitchell; Piris, Adriano; Frederick, Dennie T; Boland, Genevieve; Flaherty, Keith T; van den Oord, Joost; Voet, Thierry; Aerts, Stein; Lund, Amanda W; Marine, Jean-Christophe.

Cell ; 174(4): 843-855.e19, 2018 08 09.

Artigo em Inglês | MEDLINE | ID: mdl-30017245

2.

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain.

Davie, Kristofer; Janssens, Jasper; Koldere, Duygu; De Waegeneer, Maxime; Pech, Uli; Kreft, Lukasz; Aibar, Sara; Makhzami, Samira; Christiaens, Valerie; Bravo González-Blas, Carmen; Poovathingal, Suresh; Hulselmans, Gert; Spanier, Katina I; Moerman, Thomas; Vanspauwen, Bram; Geurs, Sarah; Voet, Thierry; Lammertyn, Jeroen; Thienpont, Bernard; Liu, Sha; Konstantinides, Nikos; Fiers, Mark; Verstreken, Patrik; Aerts, Stein.

Cell ; 174(4): 982-998.e20, 2018 08 09.

Artigo em Inglês | MEDLINE | ID: mdl-29909982

3.

Cell-type-directed design of synthetic enhancers.

Taskiran, Ibrahim I; Spanier, Katina I; Dickmänken, Hannah; Kempynck, Niklas; Pancíková, Alexandra; Eksi, Eren Can; Hulselmans, Gert; Ismail, Joy N; Theunis, Koen; Vandepoel, Roel; Christiaens, Valerie; Mauduit, David; Aerts, Stein.

Nature ; 626(7997): 212-220, 2024 Feb.

Artigo em Inglês | MEDLINE | ID: mdl-38086419

4.

Decoding gene regulation in the fly brain.

Janssens, Jasper; Aibar, Sara; Taskiran, Ibrahim Ihsan; Ismail, Joy N; Gomez, Alicia Estacio; Aughey, Gabriel; Spanier, Katina I; De Rop, Florian V; González-Blas, Carmen Bravo; Dionne, Marc; Grimes, Krista; Quan, Xiao Jiang; Papasokrati, Dafni; Hulselmans, Gert; Makhzami, Samira; De Waegeneer, Maxime; Christiaens, Valerie; Southall, Tony; Aerts, Stein.

Nature ; 601(7894): 630-636, 2022 01.

Artigo em Inglês | MEDLINE | ID: mdl-34987221

5.

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks.

Bravo González-Blas, Carmen; De Winter, Seppe; Hulselmans, Gert; Hecker, Nikolai; Matetovici, Irina; Christiaens, Valerie; Poovathingal, Suresh; Wouters, Jasper; Aibar, Sara; Aerts, Stein.

Nat Methods ; 20(9): 1355-1367, 2023 09.

Artigo em Inglês | MEDLINE | ID: mdl-37443338

6.

LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky, Nikolaus; Almouzni, Geneviève; Gorski, Stanislaw A; Aerts, Stein; Amit, Ido; Bertero, Michela G; Bock, Christoph; Bredenoord, Annelien L; Cavalli, Giacomo; Chiocca, Susanna; Clevers, Hans; De Strooper, Bart; Eggert, Angelika; Ellenberg, Jan; Fernández, Xosé M; Figlerowicz, Marek; Gasser, Susan M; Hubner, Norbert; Kjems, Jørgen; Knoblich, Jürgen A; Krabbe, Grietje; Lichter, Peter; Linnarsson, Sten; Marine, Jean-Christophe; Marioni, John C; Marti-Renom, Marc A; Netea, Mihai G; Nickel, Dörthe; Nollmann, Marcelo; Novak, Halina R; Parkinson, Helen; Piccolo, Stefano; Pinheiro, Inês; Pombo, Ana; Popp, Christian; Reik, Wolf; Roman-Roman, Sergio; Rosenstiel, Philip; Schultze, Joachim L; Stegle, Oliver; Tanay, Amos; Testa, Giuseppe; Thanos, Dimitris; Theis, Fabian J; Torres-Padilla, Maria-Elena; Valencia, Alfonso; Vallot, Céline; van Oudenaarden, Alexander; Vidal, Marie; Voet, Thierry.

Nature ; 587(7834): 377-386, 2020 11.

Artigo em Inglês | MEDLINE | ID: mdl-32894860

7.

Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning.

Atak, Zeynep Kalender; Taskiran, Ibrahim Ihsan; Demeulemeester, Jonas; Flerin, Christopher; Mauduit, David; Minnoye, Liesbeth; Hulselmans, Gert; Christiaens, Valerie; Ghanem, Ghanem-Elias; Wouters, Jasper; Aerts, Stein.

Genome Res ; 31(6): 1082-1096, 2021 06.

Artigo em Inglês | MEDLINE | ID: mdl-33832990

8.

Cross-species analysis of enhancer logic using deep learning.

Minnoye, Liesbeth; Taskiran, Ibrahim Ihsan; Mauduit, David; Fazio, Maurizio; Van Aerschot, Linde; Hulselmans, Gert; Christiaens, Valerie; Makhzami, Samira; Seltenhammer, Monika; Karras, Panagiotis; Primot, Aline; Cadieu, Edouard; van Rooijen, Ellen; Marine, Jean-Christophe; Egidy, Giorgia; Ghanem, Ghanem-Elias; Zon, Leonard; Wouters, Jasper; Aerts, Stein.

Genome Res ; 30(12): 1815-1834, 2020 12.

Artigo em Inglês | MEDLINE | ID: mdl-32732264

9.

14q32 rearrangements deregulating BCL11B mark a distinct subgroup of T-lymphoid and myeloid immature acute leukemia.

Di Giacomo, Danika; La Starza, Roberta; Gorello, Paolo; Pellanera, Fabrizia; Kalender Atak, Zeynep; De Keersmaecker, Kim; Pierini, Valentina; Harrison, Christine J; Arniani, Silvia; Moretti, Martina; Testoni, Nicoletta; De Santis, Giovanna; Roti, Giovanni; Matteucci, Caterina; Bassan, Renato; Vandenberghe, Peter; Aerts, Stein; Cools, Jan; Bornhauser, Beat; Bourquin, Jean-Pierre; Piazza, Rocco; Mecucci, Cristina.

Blood ; 138(9): 773-784, 2021 09 02.

Artigo em Inglês | MEDLINE | ID: mdl-33876209

10.

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.

Bravo González-Blas, Carmen; Minnoye, Liesbeth; Papasokrati, Dafni; Aibar, Sara; Hulselmans, Gert; Christiaens, Valerie; Davie, Kristofer; Wouters, Jasper; Aerts, Stein.

Nat Methods ; 16(5): 397-400, 2019 05.

Artigo em Inglês | MEDLINE | ID: mdl-30962623

11.

Melanoma addiction to the long non-coding RNA SAMMSON.

Leucci, Eleonora; Vendramin, Roberto; Spinazzi, Marco; Laurette, Patrick; Fiers, Mark; Wouters, Jasper; Radaelli, Enrico; Eyckerman, Sven; Leonelli, Carina; Vanderheyden, Katrien; Rogiers, Aljosja; Hermans, Els; Baatsen, Pieter; Aerts, Stein; Amant, Frederic; Van Aelst, Stefan; van den Oord, Joost; de Strooper, Bart; Davidson, Irwin; Lafontaine, Denis L J; Gevaert, Kris; Vandesompele, Jo; Mestdagh, Pieter; Marine, Jean-Christophe.

Nature ; 531(7595): 518-22, 2016 Mar 24.

Artigo em Inglês | MEDLINE | ID: mdl-27008969

12.

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine.

Rajewsky, Nikolaus; Almouzni, Geneviève; Gorski, Stanislaw A; Aerts, Stein; Amit, Ido; Bertero, Michela G; Bock, Christoph; Bredenoord, Annelien L; Cavalli, Giacomo; Chiocca, Susanna; Clevers, Hans; De Strooper, Bart; Eggert, Angelika; Ellenberg, Jan; Fernández, Xosé M; Figlerowicz, Marek; Gasser, Susan M; Hubner, Norbert; Kjems, Jørgen; Knoblich, Jürgen A; Krabbe, Grietje; Lichter, Peter; Linnarsson, Sten; Marine, Jean-Christophe; Marioni, John C; Marti-Renom, Marc A; Netea, Mihai G; Nickel, Dörthe; Nollmann, Marcelo; Novak, Halina R; Parkinson, Helen; Piccolo, Stefano; Pinheiro, Inês; Pombo, Ana; Popp, Christian; Reik, Wolf; Roman-Roman, Sergio; Rosenstiel, Philip; Schultze, Joachim L; Stegle, Oliver; Tanay, Amos; Testa, Giuseppe; Thanos, Dimitris; Theis, Fabian J; Torres-Padilla, Maria-Elena; Valencia, Alfonso; Vallot, Céline; van Oudenaarden, Alexander; Vidal, Marie; Voet, Thierry.

Nature ; 592(7852): E8, 2021 Apr.

Artigo em Inglês | MEDLINE | ID: mdl-33731935

13.

Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-like Domains.

Ravenscroft, Thomas A; Janssens, Jasper; Lee, Pei-Tseng; Tepe, Burak; Marcogliese, Paul C; Makhzami, Samira; Holmes, Todd C; Aerts, Stein; Bellen, Hugo J.

J Neurosci ; 40(42): 7999-8024, 2020 10 14.

Artigo em Inglês | MEDLINE | ID: mdl-32928889

14.

Amniotic ectoderm expansion in mouse occurs via distinct modes and requires SMAD5-mediated signalling.

Dobreva, Mariya P; Abon Escalona, Vanesa; Lawson, Kirstie A; Sanchez, Marina N; Ponomarev, Ljuba C; Pereira, Paulo N G; Stryjewska, Agata; Criem, Nathan; Huylebroeck, Danny; Chuva de Sousa Lopes, Susana M; Aerts, Stein; Zwijsen, An.

Development ; 145(13)2018 07 02.

Artigo em Inglês | MEDLINE | ID: mdl-29884675

15.

Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics.

Bravo González-Blas, Carmen; Quan, Xiao-Jiang; Duran-Romaña, Ramon; Taskiran, Ibrahim Ihsan; Koldere, Duygu; Davie, Kristofer; Christiaens, Valerie; Makhzami, Samira; Hulselmans, Gert; de Waegeneer, Maxime; Mauduit, David; Poovathingal, Suresh; Aibar, Sara; Aerts, Stein.

Mol Syst Biol ; 16(5): e9438, 2020 05.

Artigo em Inglês | MEDLINE | ID: mdl-32431014

16.

How regulatory sequences learn cell representations.

Aerts, Stein.

Nat Methods ; 19(9): 1041-1043, 2022 09.

Artigo em Inglês | MEDLINE | ID: mdl-35941240

17.

SCENIC: single-cell regulatory network inference and clustering.

Aibar, Sara; González-Blas, Carmen Bravo; Moerman, Thomas; Huynh-Thu, Vân Anh; Imrichova, Hana; Hulselmans, Gert; Rambow, Florian; Marine, Jean-Christophe; Geurts, Pierre; Aerts, Jan; van den Oord, Joost; Atak, Zeynep Kalender; Wouters, Jasper; Aerts, Stein.

Nat Methods ; 14(11): 1083-1086, 2017 Nov.

Artigo em Inglês | MEDLINE | ID: mdl-28991892

18.

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks.

Moerman, Thomas; Aibar Santos, Sara; Bravo González-Blas, Carmen; Simm, Jaak; Moreau, Yves; Aerts, Jan; Aerts, Stein.

Bioinformatics ; 35(12): 2159-2161, 2019 06 01.

Artigo em Inglês | MEDLINE | ID: mdl-30445495

19.

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic.

Verfaillie, Annelien; Svetlichnyy, Dmitry; Imrichova, Hana; Davie, Kristofer; Fiers, Mark; Kalender Atak, Zeynep; Hulselmans, Gert; Christiaens, Valerie; Aerts, Stein.

Genome Res ; 26(7): 882-95, 2016 07.

Artigo em Inglês | MEDLINE | ID: mdl-27197205

20.

dachshund Potentiates Hedgehog Signaling during Drosophila Retinogenesis.

Brás-Pereira, Catarina; Potier, Delphine; Jacobs, Jelle; Aerts, Stein; Casares, Fernando; Janody, Florence.

PLoS Genet ; 12(7): e1006204, 2016 07.

Artigo em Inglês | MEDLINE | ID: mdl-27442438

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