| Year |
Citation |
Score |
| 2023 |
Bravo González-Blas C, De Winter S, Hulselmans G, Hecker N, Matetovici I, Christiaens V, Poovathingal S, Wouters J, Aibar S, Aerts S. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nature Methods. PMID 37443338 DOI: 10.1038/s41592-023-01938-4 |
0.418 |
|
| 2023 |
Mohylyak I, Bengochea M, Pascual-Caro C, Asfogo N, Fonseca-Topp S, Danda N, Atak ZK, De Waegeneer M, Plaçais PY, Preat T, Aerts S, Corti O, de Juan-Sanz J, Hassan BA. Developmental transcriptional control of mitochondrial homeostasis is required for activity-dependent synaptic connectivity. Biorxiv : the Preprint Server For Biology. PMID 37333418 DOI: 10.1101/2023.06.11.544500 |
0.575 |
|
| 2023 |
Floc'hlay S, Balaji R, Stanković D, Christiaens VM, Bravo González-Blas C, De Winter S, Hulselmans GJ, De Waegeneer M, Quan X, Koldere D, Atkins M, Halder G, Uhlirova M, Classen A, Aerts S. Shared enhancer gene regulatory networks between wound and oncogenic programs. Elife. 12. PMID 37133250 DOI: 10.7554/eLife.81173 |
0.778 |
|
| 2023 |
Praschberger R, Kuenen S, Schoovaerts N, Kaempf N, Singh J, Janssens J, Swerts J, Nachman E, Calatayud C, Aerts S, Poovathingal S, Verstreken P. Neuronal identity defines α-synuclein and tau toxicity. Neuron. PMID 36948206 DOI: 10.1016/j.neuron.2023.02.033 |
0.561 |
|
| 2022 |
Li H, Janssens J, De Waegeneer M, Kolluru SS, Davie K, Gardeux V, Saelens W, David FPA, Brbić M, Spanier K, Leskovec J, McLaughlin CN, Xie Q, Jones RC, Brueckner K, ... ... Aerts S, et al. Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science (New York, N.Y.). 375: eabk2432. PMID 35239393 DOI: 10.1126/science.abk2432 |
0.604 |
|
| 2022 |
De Rop FV, Ismail JN, Bravo González-Blas C, Hulselmans GJ, Flerin CC, Janssens J, Theunis K, Christiaens VM, Wouters J, Marcassa G, de Wit J, Poovathingal S, Aerts S. Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads. Elife. 11. PMID 35195064 DOI: 10.7554/eLife.73971 |
0.591 |
|
| 2022 |
Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier KI, De Rop FV, González-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, ... ... Aerts S, et al. Decoding gene regulation in the fly brain. Nature. PMID 34987221 DOI: 10.1038/s41586-021-04262-z |
0.684 |
|
| 2021 |
Atak ZK, Taskiran II, Demeulemeester J, Flerin C, Mauduit D, Minnoye L, Hulselmans G, Christiaens V, Ghanem GE, Wouters J, Aerts S. Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning. Genome Research. PMID 33832990 DOI: 10.1101/gr.260851.120 |
0.335 |
|
| 2020 |
Ravenscroft TA, Janssens J, Lee PT, Tepe B, Marcogliese PC, Makhzami S, Holmes TC, Aerts S, Bellen HJ. voltage-gated sodium channels are only expressed in active neurons and are localized to distal axonal initial segment-like domains. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 32928889 DOI: 10.1523/Jneurosci.0142-20.2020 |
0.66 |
|
| 2020 |
Wouters J, Kalender-Atak Z, Minnoye L, Spanier KI, De Waegeneer M, Bravo González-Blas C, Mauduit D, Davie K, Hulselmans G, Najem A, Dewaele M, Pedri D, Rambow F, Makhzami S, Christiaens V, ... ... Aerts S, et al. Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma. Nature Cell Biology. 22: 986-998. PMID 32753671 DOI: 10.1038/S41556-020-0547-3 |
0.361 |
|
| 2020 |
Minnoye L, Taskiran II, Mauduit D, Fazio M, Van Aerschot L, Hulselmans G, Christiaens V, Makhzami S, Seltenhammer M, Karras P, Primot A, Cadieu E, van Rooijen E, Marine JC, Egidy G, ... ... Aerts S, et al. Cross-species analysis of enhancer logic using deep learning. Genome Research. PMID 32732264 DOI: 10.1101/Gr.260844.120 |
0.412 |
|
| 2020 |
Van de Sande B, Flerin C, Davie K, De Waegeneer M, Hulselmans G, Aibar S, Seurinck R, Saelens W, Cannoodt R, Rouchon Q, Verbeiren T, De Maeyer D, Reumers J, Saeys Y, Aerts S. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nature Protocols. 15: 2247-2276. PMID 32561888 DOI: 10.1038/S41596-020-0336-2 |
0.454 |
|
| 2020 |
Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, ... ... Aerts S, et al. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications. 11: 2631. PMID 32457347 DOI: 10.1038/S41467-020-16284-8 |
0.39 |
|
| 2020 |
Bravo González-Blas C, Quan XJ, Duran-Romaña R, Taskiran II, Koldere D, Davie K, Christiaens V, Makhzami S, Hulselmans G, de Waegeneer M, Mauduit D, Poovathingal S, Aibar S, Aerts S. Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics. Molecular Systems Biology. 16: e9438. PMID 32431014 DOI: 10.15252/Msb.20209438 |
0.468 |
|
| 2019 |
Moya IM, Castaldo SA, Van den Mooter L, Soheily S, Sansores-Garcia L, Jacobs J, Mannaerts I, Xie J, Verboven E, Hillen H, Algueró-Nadal A, Karaman R, Van Haele M, Kowalczyk W, De Waegeneer M, ... ... Aerts S, et al. Peritumoral activation of the Hippo pathway effectors YAP and TAZ suppresses liver cancer in mice. Science (New York, N.Y.). 366: 1029-1034. PMID 31754005 DOI: 10.1126/Science.Aaw9886 |
0.309 |
|
| 2019 |
Bonnefont J, Tiberi L, van den Ameele J, Potier D, Gaber ZB, Lin X, Bilheu A, Herpoel A, Velez Bravo FD, Guillemot F, Aerts S, Vanderhaeghen P. Cortical Neurogenesis Requires Bcl6-Mediated Transcriptional Repression of Multiple Self-Renewal-Promoting Extrinsic Pathways. Neuron. PMID 31353074 DOI: 10.1016/J.Neuron.2019.06.027 |
0.404 |
|
| 2019 |
Bravo González-Blas C, Minnoye L, Papasokrati D, Aibar S, Hulselmans G, Christiaens V, Davie K, Wouters J, Aerts S. cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data. Nature Methods. PMID 30962623 DOI: 10.1038/S41592-019-0367-1 |
0.416 |
|
| 2019 |
Varum S, Baggiolini A, Zurkirchen L, Atak ZK, Cantù C, Marzorati E, Bossart R, Wouters J, Häusel J, Tuncer E, Zingg D, Veen D, John N, Balz M, Levesque MP, ... ... Aerts S, et al. Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation. Cell Stem Cell. 24: 637-653.e9. PMID 30951662 DOI: 10.1016/J.Stem.2019.03.011 |
0.402 |
|
| 2019 |
Bates AS, Janssens J, Jefferis GS, Aerts S. Neuronal cell types in the fly: single-cell anatomy meets single-cell genomics. Current Opinion in Neurobiology. 56: 125-134. PMID 30703584 DOI: 10.1016/J.Conb.2018.12.012 |
0.631 |
|
| 2018 |
Moerman T, Aibar S, González-Blas CB, Simm J, Moreau Y, Aerts J, Aerts S. GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks. Bioinformatics (Oxford, England). PMID 30445495 DOI: 10.1093/Bioinformatics/Bty916 |
0.414 |
|
| 2018 |
Rambow F, Rogiers A, Marin-Bejar O, Aibar S, Femel J, Dewaele M, Karras P, Brown D, Chang YH, Debiec-Rychter M, Adriaens C, Radaelli E, Wolter P, Bechter O, Dummer R, ... ... Aerts S, et al. Toward Minimal Residual Disease-Directed Therapy in Melanoma. Cell. PMID 30017245 DOI: 10.1016/J.Cell.2018.06.025 |
0.37 |
|
| 2018 |
Lambrechts D, Wauters E, Boeckx B, Aibar S, Nittner D, Burton O, Bassez A, Decaluwé H, Pircher A, Van den Eynde K, Weynand B, Verbeken E, De Leyn P, Liston A, Vansteenkiste J, ... ... Aerts S, et al. Phenotype molding of stromal cells in the lung tumor microenvironment. Nature Medicine. PMID 29988129 DOI: 10.1038/S41591-018-0096-5 |
0.382 |
|
| 2018 |
Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo González-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, ... ... Aerts S, et al. A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain. Cell. PMID 29909982 DOI: 10.1016/J.Cell.2018.05.057 |
0.629 |
|
| 2018 |
Jacobs J, Atkins M, Davie K, Imrichova H, Romanelli L, Christiaens V, Hulselmans G, Potier D, Wouters J, Taskiran II, Paciello G, González-Blas CB, Koldere D, Aibar S, Halder G, ... Aerts S, et al. The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes. Nature Genetics. PMID 29867222 DOI: 10.1038/S41588-018-0140-X |
0.778 |
|
| 2018 |
Fiers MWEJ, Minnoye L, Aibar S, Bravo González-Blas C, Kalender Atak Z, Aerts S. Mapping gene regulatory networks from single-cell omics data. Briefings in Functional Genomics. PMID 29342231 DOI: 10.1093/Bfgp/Elx046 |
0.405 |
|
| 2018 |
Bornschein S, Demeyer S, Stirparo R, Gielen O, Vicente C, Geerdens E, Ghesquière B, Aerts S, Cools J, de Bock CE. Defining the molecular basis of oncogenic cooperation between TAL1 expression and Pten deletion in T-ALL using a novel pro-T-cell model system. Leukemia. 32: 941-951. PMID 29151585 DOI: 10.1038/Leu.2017.328 |
0.36 |
|
| 2018 |
Aerts S. Decision letter: Genome-wide quantification of the effects of DNA methylation on human gene regulation Elife. DOI: 10.7554/Elife.37513.045 |
0.342 |
|
| 2017 |
Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S. SCENIC: single-cell regulatory network inference and clustering. Nature Methods. PMID 28991892 DOI: 10.1038/Nmeth.4463 |
0.443 |
|
| 2017 |
Pascual J, Jacobs J, Sansores-Garcia L, Natarajan M, Zeitlinger J, Aerts S, Halder G, Hamaratoglu F. Hippo Reprograms the Transcriptional Response to Ras Signaling. Developmental Cell. 42: 667-680.e4. PMID 28950103 DOI: 10.1016/J.Devcel.2017.08.013 |
0.329 |
|
| 2017 |
Kalender Atak Z, Imrichova H, Svetlichnyy D, Hulselmans G, Christiaens V, Reumers J, Ceulemans H, Aerts S. Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks. Genome Medicine. 9: 80. PMID 28854983 DOI: 10.1186/S13073-017-0464-7 |
0.41 |
|
| 2017 |
Spanier KI, Jansen M, Decaestecker E, Hulselmans G, Becker D, Colbourne JK, Orsini L, De Meester L, Aerts S. Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia. Genome Biology and Evolution. 9: 1821-1842. PMID 28854641 DOI: 10.1093/Gbe/Evx127 |
0.505 |
|
| 2017 |
Neto M, Naval-Sánchez M, Potier D, Pereira PS, Geerts D, Aerts S, Casares F. Nuclear receptors connect progenitor transcription factors to cell cycle control. Scientific Reports. 7: 4845. PMID 28687780 DOI: 10.1038/S41598-017-04936-7 |
0.442 |
|
| 2017 |
Olvedy M, Tisserand JC, Luciani F, Boeckx B, Wouters J, Lopez S, Rambow F, Aibar S, Thienpont B, Barra J, Köhler C, Radaelli E, Tartare-Deckert S, Aerts S, Dubreuil P, et al. Comparative oncogenomics identifies tyrosine kinase FES as a tumor suppressor in melanoma. The Journal of Clinical Investigation. PMID 28463229 DOI: 10.1172/Jci91291 |
0.347 |
|
| 2017 |
Wouters J, Kalender Atak Z, Aerts S. Decoding transcriptional states in cancer. Current Opinion in Genetics & Development. 43: 82-92. PMID 28129557 DOI: 10.1016/J.Gde.2017.01.003 |
0.472 |
|
| 2016 |
Atkins M, Potier D, Romanelli L, Jacobs J, Mach J, Hamaratoglu F, Aerts S, Halder G. An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model. Current Biology : Cb. PMID 27476594 DOI: 10.1016/J.Cub.2016.06.035 |
0.79 |
|
| 2016 |
Brás-Pereira C, Potier D, Jacobs J, Aerts S, Casares F, Janody F. dachshund Potentiates Hedgehog Signaling during Drosophila Retinogenesis. Plos Genetics. 12: e1006204. PMID 27442438 DOI: 10.1371/Journal.Pgen.1006204 |
0.381 |
|
| 2016 |
Adriaens C, Standaert L, Barra J, Latil M, Verfaillie A, Kalev P, Boeckx B, Wijnhoven PW, Radaelli E, Vermi W, Leucci E, Lapouge G, Beck B, van den Oord J, Nakagawa S, ... ... Aerts S, et al. p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity. Nature Medicine. PMID 27376578 DOI: 10.1038/Nm.4135 |
0.334 |
|
| 2016 |
Verfaillie A, Svetlichnyy D, Imrichova H, Davie K, Fiers M, Kalender Atak Z, Hulselmans G, Christiaens V, Aerts S. Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic. Genome Research. PMID 27197205 DOI: 10.1101/Gr.204149.116 |
0.413 |
|
| 2016 |
Jin M, Aibar S, Ge Z, Chen R, Aerts S, Mardon G. Identification of Novel Direct Targets of Drosophila Sine Oculis by Integration of Genome-wide Data Sets. Developmental Biology. PMID 27178668 DOI: 10.1016/J.Ydbio.2016.05.007 |
0.434 |
|
| 2016 |
Leucci E, Vendramin R, Spinazzi M, Laurette P, Fiers M, Wouters J, Radaelli E, Eyckerman S, Leonelli C, Vanderheyden K, Rogiers A, Hermans E, Baatsen P, Aerts S, Amant F, et al. Melanoma addiction to the long non-coding RNA SAMMSON. Nature. 531: 518-22. PMID 27008969 DOI: 10.1038/Nature17161 |
0.381 |
|
| 2015 |
Verfaillie A, Imrichova H, Janky R, Aerts S. iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 52: 2.16.1-2.16.39. PMID 26678384 DOI: 10.1002/0471250953.Bi0216S52 |
0.501 |
|
| 2015 |
Svetlichnyy D, Imrichova H, Fiers M, Kalender Atak Z, Aerts S. Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models. Plos Computational Biology. 11: e1004590. PMID 26562774 DOI: 10.1371/Journal.Pcbi.1004590 |
0.362 |
|
| 2015 |
Naval-Sánchez M, Potier D, Hulselmans G, Christiaens V, Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Molecular Biology and Evolution. PMID 25944915 DOI: 10.1093/Molbev/Msv107 |
0.437 |
|
| 2015 |
Imrichová H, Hulselmans G, Kalender Atak Z, Potier D, Aerts S. i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. Nucleic Acids Research. 43: W57-64. PMID 25925574 DOI: 10.1093/Nar/Gkv395 |
0.456 |
|
| 2015 |
Verfaillie A, Imrichova H, Atak ZK, Dewaele M, Rambow F, Hulselmans G, Christiaens V, Svetlichnyy D, Luciani F, Van den Mooter L, Claerhout S, Fiers M, Journe F, Ghanem GE, Herrmann C, ... ... Aerts S, et al. Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. Nature Communications. 6: 6683. PMID 25865119 DOI: 10.1038/Ncomms7683 |
0.438 |
|
| 2015 |
Laurette P, Strub T, Koludrovic D, Keime C, Le Gras S, Seberg H, Van Otterloo E, Imrichova H, Siddaway R, Aerts S, Cornell RA, Mengus G, Davidson I. Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells. Elife. 4. PMID 25803486 DOI: 10.7554/Elife.06857 |
0.431 |
|
| 2015 |
Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G, Aerts S. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. Plos Genetics. 11: e1004994. PMID 25679813 DOI: 10.1371/Journal.Pgen.1004994 |
0.791 |
|
| 2015 |
Oliva C, Molina-Fernandez C, Maureira M, Candia N, López E, Hassan B, Aerts S, Cánovas J, Olguín P, Sierralta J. Hindsight regulates photoreceptor axon targeting through transcriptional control of jitterbug/Filamin and multiple genes involved in axon guidance in Drosophila. Developmental Neurobiology. PMID 25652545 DOI: 10.1002/Dneu.22271 |
0.63 |
|
| 2015 |
Laurette P, Strub T, Koludrovic D, Keime C, Gras SL, Seberg H, Otterloo EV, Imrichova H, Siddaway R, Aerts S, Cornell RA, Mengus G, Davidson I. Author response: Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells Elife. DOI: 10.7554/Elife.06857.025 |
0.376 |
|
| 2014 |
Potier D, Davie K, Hulselmans G, Naval Sanchez M, Haagen L, Huynh-Thu VA, Koldere D, Celik A, Geurts P, Christiaens V, Aerts S. Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. Cell Reports. 9: 2290-303. PMID 25533349 DOI: 10.1016/J.Celrep.2014.11.038 |
0.466 |
|
| 2014 |
Hattori H, Janky R, Nietfeld W, Aerts S, Madan Babu M, Venkitaraman AR. p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. Cell Cycle (Georgetown, Tex.). 13: 2572-86. PMID 25486198 DOI: 10.4161/15384101.2015.942209 |
0.335 |
|
| 2014 |
Janky R, Verfaillie A, Imrichová H, Van de Sande B, Standaert L, Christiaens V, Hulselmans G, Herten K, Naval Sanchez M, Potier D, Svetlichnyy D, Kalender Atak Z, Fiers M, Marine JC, Aerts S. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. Plos Computational Biology. 10: e1003731. PMID 25058159 DOI: 10.1371/Journal.Pcbi.1003731 |
0.514 |
|
| 2014 |
Potier D, Seyres D, Guichard C, Iche-Torres M, Aerts S, Herrmann C, Perrin L. Identification of cis-regulatory modules encoding temporal dynamics during development. Bmc Genomics. 15: 534. PMID 24972496 DOI: 10.1186/1471-2164-15-534 |
0.498 |
|
| 2014 |
Neville MC, Nojima T, Ashley E, Parker DJ, Walker J, Southall T, Van de Sande B, Marques AC, Fischer B, Brand AH, Russell S, Ritchie MG, Aerts S, Goodwin SF. Male-specific fruitless isoforms target neurodevelopmental genes to specify a sexually dimorphic nervous system. Current Biology : Cb. 24: 229-41. PMID 24440396 DOI: 10.1016/J.Cub.2013.11.035 |
0.397 |
|
| 2013 |
Atak ZK, Gianfelici V, Hulselmans G, De Keersmaecker K, Devasia AG, Geerdens E, Mentens N, Chiaretti S, Durinck K, Uyttebroeck A, Vandenberghe P, Wlodarska I, Cloos J, Foà R, Speleman F, ... ... Aerts S, et al. Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. Plos Genetics. 9: e1003997. PMID 24367274 DOI: 10.1371/Journal.Pgen.1003997 |
0.424 |
|
| 2013 |
Menoret D, Santolini M, Fernandes I, Spokony R, Zanet J, Gonzalez I, Latapie Y, Ferrer P, Rouault H, White KP, Besse P, Hakim V, Aerts S, Payre F, Plaza S. Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization. Genome Biology. 14: R86. PMID 23972280 DOI: 10.1186/Gb-2013-14-8-R86 |
0.498 |
|
| 2013 |
Aerts S, Cools J. Cancer: Mutations close in on gene regulation. Nature. 499: 35-6. PMID 23823789 DOI: 10.1038/499035A |
0.39 |
|
| 2013 |
Vanden Broeck L, Naval-Sánchez M, Adachi Y, Diaper D, Dourlen P, Chapuis J, Kleinberger G, Gistelinck M, Van Broeckhoven C, Lambert JC, Hirth F, Aerts S, Callaerts P, Dermaut B. TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila. Cell Reports. 3: 160-72. PMID 23333275 DOI: 10.1016/J.Celrep.2012.12.014 |
0.37 |
|
| 2013 |
van den Berghe V, Stappers E, Vandesande B, Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, ... ... Aerts S, et al. Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1. Neuron. 77: 70-82. PMID 23312517 DOI: 10.1016/J.Neuron.2012.11.009 |
0.303 |
|
| 2013 |
De Keersmaecker K, Atak ZK, Li N, Vicente C, Patchett S, Girardi T, Gianfelici V, Geerdens E, Clappier E, Porcu M, Lahortiga I, Lucà R, Yan J, Hulselmans G, Vranckx H, ... ... Aerts S, et al. Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia. Nature Genetics. 45: 186-90. PMID 23263491 DOI: 10.1038/Ng.2508 |
0.582 |
|
| 2013 |
Naval-Sánchez M, Potier D, Haagen L, Sánchez M, Munck S, Van de Sande B, Casares F, Christiaens V, Aerts S. Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions. Genome Research. 23: 74-88. PMID 23070853 DOI: 10.1101/Gr.140426.112 |
0.474 |
|
| 2013 |
Gianfelici V, Chiaretti S, Atak ZK, Brugnoletti F, Monica M, Hulselmans G, Keersmaecker Kd, Geerdens E, Mancini M, Vitale A, Elia L, Matarazzo M, Rossi D, Gaidano G, Guarini A, ... Aerts S, et al. Whole Transcriptome Sequencing In Refractory T-Cell Acute Lymphoblastic Leukemia Blood. 122: 350-350. DOI: 10.1182/Blood.V122.21.350.350 |
0.42 |
|
| 2013 |
Yesilyurt BT, Zhao H, Sagaert X, Coenegrachts L, Kalender Z, Garcia D, Keersmaker KD, Matthijs G, Thienpont B, Aerts S, Cools J, Amant F, Lambrechts D. Abstract 2006: Sequencing of mismatch repair deficient tumors identifies a synthetic lethal interaction with other DNA repair pathways. Cancer Research. 73: 2006-2006. DOI: 10.1158/1538-7445.Am2013-2006 |
0.311 |
|
| 2012 |
Youssef KK, Lapouge G, Bouvrée K, Rorive S, Brohée S, Appelstein O, Larsimont JC, Sukumaran V, Van de Sande B, Pucci D, Dekoninck S, Berthe JV, Aerts S, Salmon I, del Marmol V, et al. Adult interfollicular tumour-initiating cells are reprogrammed into an embryonic hair follicle progenitor-like fate during basal cell carcinoma initiation. Nature Cell Biology. 14: 1282-94. PMID 23178882 DOI: 10.1038/Ncb2628 |
0.366 |
|
| 2012 |
Herrmann C, Van de Sande B, Potier D, Aerts S. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Research. 40: e114. PMID 22718975 DOI: 10.1093/Nar/Gks543 |
0.464 |
|
| 2012 |
Kalender Atak Z, De Keersmaecker K, Gianfelici V, Geerdens E, Vandepoel R, Pauwels D, Porcu M, Lahortiga I, Brys V, Dirks WG, Quentmeier H, Cloos J, Cuppens H, Uyttebroeck A, Vandenberghe P, ... ... Aerts S, et al. High accuracy mutation detection in leukemia on a selected panel of cancer genes. Plos One. 7: e38463. PMID 22675565 DOI: 10.1371/Journal.Pone.0038463 |
0.357 |
|
| 2012 |
Aerts S. Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets. Current Topics in Developmental Biology. 98: 121-45. PMID 22305161 DOI: 10.1016/B978-0-12-386499-4.00005-7 |
0.516 |
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| 2012 |
Spans L, Atak ZK, Van Nieuwerburgh F, Deforce D, Lerut E, Aerts S, Claessens F. Variations in the exome of the LNCaP prostate cancer cell line. The Prostate. 72: 1317-27. PMID 22213130 DOI: 10.1002/Pros.22480 |
0.347 |
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| 2012 |
Potier D, Atak ZK, Sanchez MN, Herrmann C, Aerts S. Using cisTargetX to predict transcriptional targets and networks in Drosophila. Methods in Molecular Biology (Clifton, N.J.). 786: 291-314. PMID 21938634 DOI: 10.1007/978-1-61779-292-2_18 |
0.517 |
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| 2012 |
Spans L, Kalender Z, Aerts S, Claessens F. Abstract B33: Flexibility of the exome of the LNCaP cell line(s): Differences in heterozygocity and heterogeneity Cancer Research. 72: B33-B33. DOI: 10.1158/1538-7445.Prca2012-B33 |
0.373 |
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| 2011 |
Kleppe M, Tousseyn T, Geissinger E, Kalender Atak Z, Aerts S, Rosenwald A, Wlodarska I, Cools J. Mutation analysis of the tyrosine phosphatase PTPN2 in Hodgkin's lymphoma and T-cell non-Hodgkin's lymphoma. Haematologica. 96: 1723-7. PMID 21791476 DOI: 10.3324/Haematol.2011.041921 |
0.336 |
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| 2011 |
Aerts S, Hassan B. Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation. Fly. 5: 221-3. PMID 21471735 DOI: 10.4161/Fly.5.3.15542 |
0.69 |
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| 2011 |
Aerts S, Hassan BA. Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation Fly. 5: 1-3. |
0.625 |
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| 2010 |
Aerts S, Quan XJ, Claeys A, Naval Sanchez M, Tate P, Yan J, Hassan BA. Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. Plos Biology. 8: e1000435. PMID 20668662 DOI: 10.1371/Journal.Pbio.1000435 |
0.686 |
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| 2009 |
Bossuyt W, De Geest N, Aerts S, Leenaerts I, Marynen P, Hassan BA. The atonal proneural transcription factor links differentiation and tumor formation in Drosophila. Plos Biology. 7: e40. PMID 19243220 DOI: 10.1371/Journal.Pbio.1000040 |
0.662 |
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| 2009 |
Aerts S, Vilain S, Hu S, Tranchevent LC, Barriot R, Yan J, Moreau Y, Hassan BA, Quan XJ. Integrating computational biology and forward genetics in Drosophila. Plos Genetics. 5: e1000351. PMID 19165344 DOI: 10.1371/Journal.Pgen.1000351 |
0.765 |
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| 2008 |
Aerts S, Butland S. Sequencing the regulatory genome. Genome Biology. 9: 313. PMID 18598374 DOI: 10.1186/Gb-2008-9-6-313 |
0.407 |
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| 2008 |
Tranchevent LC, Barriot R, Yu S, Van Vooren S, Van Loo P, Coessens B, De Moor B, Aerts S, Moreau Y. ENDEAVOUR update: a web resource for gene prioritization in multiple species. Nucleic Acids Research. 36: W377-84. PMID 18508807 DOI: 10.1093/Nar/Gkn325 |
0.418 |
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| 2008 |
Van Loo P, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P. ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues? Genome Biology. 9: R66. PMID 18394174 DOI: 10.1186/Gb-2008-9-4-R66 |
0.423 |
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| 2008 |
Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM. Text-mining assisted regulatory annotation. Genome Biology. 9: R31. PMID 18271954 DOI: 10.1186/Gb-2008-9-2-R31 |
0.621 |
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| 2008 |
Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 36: D107-13. PMID 18006570 DOI: 10.1093/Nar/Gkm967 |
0.622 |
|
| 2007 |
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, ... ... Aerts S, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32. PMID 17994088 DOI: 10.1038/Nature06340 |
0.638 |
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| 2007 |
Aerts S, van Helden J, Sand O, Hassan BA. Fine-tuning enhancer models to predict transcriptional targets across multiple genomes. Plos One. 2: e1115. PMID 17973026 DOI: 10.1371/Journal.Pone.0001115 |
0.655 |
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| 2006 |
Dabrowski M, Aerts S, Kaminska B. Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus. Bmc Bioinformatics. 7: 367. PMID 16884529 DOI: 10.1186/1471-2105-7-367 |
0.458 |
|
| 2006 |
Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nature Biotechnology. 24: 537-44. PMID 16680138 DOI: 10.1038/Nbt1203 |
0.645 |
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| 2006 |
Dabrowski M, Adach A, Aerts S, Moreau Y, Kaminska B. Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro. Journal of Neurochemistry. 97: 87-91. PMID 16635255 DOI: 10.1111/J.1471-4159.2005.03537.X |
0.345 |
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| 2006 |
Aerts S, Lambrechts D, Maity S, Loo PV, Coessens B, Smet FD, Tranchevent L, Moor BD, Marynen P, Hassan B, Carmeliet P, Moreau Y. Erratum: Gene prioritization through genomic data fusion Nature Biotechnology. 24: 719-719. DOI: 10.1038/Nbt0606-719D |
0.565 |
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| 2005 |
Aerts S, Van Loo P, Thijs G, Mayer H, de Martin R, Moreau Y, De Moor B. TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Research. 33: W393-6. PMID 15980497 DOI: 10.1093/Nar/Gki354 |
0.413 |
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| 2004 |
Aerts S, Thijs G, Dabrowski M, Moreau Y, De Moor B. Comprehensive analysis of the base composition around the transcription start site in Metazoa. Bmc Genomics. 5: 34. PMID 15171795 DOI: 10.1186/1471-2164-5-34 |
0.42 |
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| 2004 |
Aerts S, Van Loo P, Moreau Y, De Moor B. A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. Bioinformatics (Oxford, England). 20: 1974-6. PMID 15044242 DOI: 10.1093/Bioinformatics/Bth179 |
0.323 |
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| 2004 |
Denys H, Jadidizadeh A, Amini Nik S, Van Dam K, Aerts S, Alman BA, Cassiman JJ, Tejpar S. Identification of IGFBP-6 as a significantly downregulated gene by beta-catenin in desmoid tumors. Oncogene. 23: 654-64. PMID 14737101 DOI: 10.1038/Sj.Onc.1207160 |
0.379 |
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| 2003 |
Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M. Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends in Genetics : Tig. 19: 570-7. PMID 14550631 DOI: 10.1016/J.Tig.2003.08.006 |
0.325 |
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| 2003 |
Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B. Computational detection of cis -regulatory modules. Bioinformatics (Oxford, England). 19: ii5-14. PMID 14534164 DOI: 10.1093/bioinformatics/btg1052 |
0.396 |
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| 2003 |
Dabrowski M, Aerts S, Van Hummelen P, Craessaerts K, De Moor B, Annaert W, Moreau Y, De Strooper B. Gene profiling of hippocampal neuronal culture. Journal of Neurochemistry. 85: 1279-88. PMID 12753086 DOI: 10.1046/J.1471-4159.2003.01753.X |
0.439 |
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| 2003 |
Aerts S, Thijs G, Coessens B, Staes M, Moreau Y, De Moor B. Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Research. 31: 1753-64. PMID 12626717 DOI: 10.1093/Nar/Gkg268 |
0.446 |
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