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1. Environmental drivers of increased ecosystem respiration in a warming tundra

Author

Maes, S. L., primary, Dietrich, J., additional, Midolo, G., additional, Schwieger, S., additional, Kummu, M., additional, Vandvik, V., additional, Aerts, R., additional, Althuizen, I. H. J., additional, Biasi, C., additional, Björk, R. G., additional, Böhner, H., additional, Carbognani, M., additional, Chiari, G., additional, Christiansen, C. T., additional, Clemmensen, K. E., additional, Cooper, E. J., additional, Cornelissen, J. H. C., additional, Elberling, B., additional, Faubert, P., additional, Fetcher, N., additional, Forte, T. G. W., additional, Gaudard, J., additional, Gavazov, K., additional, Guan, Z., additional, Guðmundsson, J., additional, Gya, R., additional, Hallin, S., additional, Hansen, B. B., additional, Haugum, S. V., additional, He, J.-S., additional, Hicks Pries, C., additional, Hovenden, M. J., additional, Jalava, M., additional, Jónsdóttir, I. S., additional, Juhanson, J., additional, Jung, J. Y., additional, Kaarlejärvi, E., additional, Kwon, M. J., additional, Lamprecht, R. E., additional, Le Moullec, M., additional, Lee, H., additional, Marushchak, M. E., additional, Michelsen, A., additional, Munir, T. M., additional, Myrsky, E. M., additional, Nielsen, C. S., additional, Nyberg, M., additional, Olofsson, J., additional, Óskarsson, H., additional, Parker, T. C., additional, Pedersen, E. P., additional, Petit Bon, M., additional, Petraglia, A., additional, Raundrup, K., additional, Ravn, N. M. R., additional, Rinnan, R., additional, Rodenhizer, H., additional, Ryde, I., additional, Schmidt, N. M., additional, Schuur, E. A. G., additional, Sjögersten, S., additional, Stark, S., additional, Strack, M., additional, Tang, J., additional, Tolvanen, A., additional, Töpper, J. P., additional, Väisänen, M. K., additional, van Logtestijn, R. S. P., additional, Voigt, C., additional, Walz, J., additional, Weedon, J. T., additional, Yang, Y., additional, Ylänne, H., additional, Björkman, M. P., additional, Sarneel, J. M., additional, and Dorrepaal, E., additional

Published
2024
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2. Cell-type-directed design of synthetic enhancers

Author

Taskiran, Ibrahim I., primary, Spanier, Katina I., additional, Dickmänken, Hannah, additional, Kempynck, Niklas, additional, Pančíková, Alexandra, additional, Ekşi, Eren Can, additional, Hulselmans, Gert, additional, Ismail, Joy N., additional, Theunis, Koen, additional, Vandepoel, Roel, additional, Christiaens, Valerie, additional, Mauduit, David, additional, and Aerts, Stein, additional

Published
2023
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3. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, Nikolaus, Almouzni, Geneviève, Gorski, Stanislaw A., Aerts, Stein, Amit, Ido, Bertero, Michela G., and Bock, Christoph

Subjects
Medical research, Medicine, Experimental, Cellular therapy -- Usage, Longevity -- Research, Public health law, International -- Management, Company business management, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade. The LifeTime initiative is an ambitious, multidisciplinary programme that aims to improve healthcare by tracking individual human cells during disease processes and responses to treatment in order to develop and implement cell-based interceptive medicine in Europe., Author(s): Nikolaus Rajewsky [sup.1] [sup.2] [sup.3] [sup.4] , Geneviève Almouzni [sup.5] , Stanislaw A. Gorski [sup.1] , Stein Aerts [sup.6] [sup.7] , Ido Amit [sup.8] , Michela G. Bertero [sup.9] [...]

Published
2020
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4. Predicting crystal form stability under real-world conditions

Author

Firaha, Dzmitry, primary, Liu, Yifei Michelle, additional, van de Streek, Jacco, additional, Sasikumar, Kiran, additional, Dietrich, Hanno, additional, Helfferich, Julian, additional, Aerts, Luc, additional, Braun, Doris E., additional, Broo, Anders, additional, DiPasquale, Antonio G., additional, Lee, Alfred Y., additional, Le Meur, Sarah, additional, Nilsson Lill, Sten O., additional, Lunsmann, Walter J., additional, Mattei, Alessandra, additional, Muglia, Pierandrea, additional, Putra, Okky Dwichandra, additional, Raoui, Mohamed, additional, Reutzel-Edens, Susan M., additional, Rome, Sandrine, additional, Sheikh, Ahmad Y., additional, Tkatchenko, Alexandre, additional, Woollam, Grahame R., additional, and Neumann, Marcus A., additional

Published
2023
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5. Cell-type-directed design of synthetic enhancers.

Author

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

Abstract

Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes1. It has been a long-standing goal in the field to decode the regulatory logic of an enhancer and to understand the details of how spatiotemporal gene expression is encoded in an enhancer sequence. Here we show that deep learning models2–6, can be used to efficiently design synthetic, cell-type-specific enhancers, starting from random sequences, and that this optimization process allows detailed tracing of enhancer features at single-nucleotide resolution. We evaluate the function of fully synthetic enhancers to specifically target Kenyon cells or glial cells in the fruit fly brain using transgenic animals. We further exploit enhancer design to create ‘dual-code’ enhancers that target two cell types and minimal enhancers smaller than 50 base pairs that are fully functional. By examining the state space searches towards local optima, we characterize enhancer codes through the strength, combination and arrangement of transcription factor activator and transcription factor repressor motifs. Finally, we apply the same strategies to successfully design human enhancers, which adhere to enhancer rules similar to those of Drosophila enhancers. Enhancer design guided by deep learning leads to better understanding of how enhancers work and shows that their code can be exploited to manipulate cell states.Deep learning models were used to design synthetic cell-type-specific enhancers that work in fruit fly brains and human cell lines, an approach that also provides insights into these gene regulatory elements. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Author

Abbosh, Christopher, Birkbak, Nicolai J., Wilson, Gareth A., Jamal-Hanjani, Mariam, Constantin, Tudor, Salari, Raheleh, Le Quesne, John, Moore, David A., Veeriah, Selvaraju, Rosenthal, Rachel, Marafioti, Teresa, Kirkizlar, Eser, Watkins, Thomas B. K., McGranahan, Nicholas, Ward, Sophia, Martinson, Luke, Riley, Joan, Fraioli, Francesco, Al Bakir, Maise, Grnroos, Eva, Zambrana, Francisco, Endozo, Raymondo, Bi, Wenya Linda, Fennessy, Fiona M., Sponer, Nicole, Johnson, Diana, Laycock, Joanne, Shafi, Seema, Czyzewska-Khan, Justyna, Rowan, Andrew, Chambers, Tim, Matthews, Nik, Turajlic, Samra, Hiley, Crispin, Lee, Siow Ming, Forster, Martin D., Ahmad, Tanya, Falzon, Mary, Borg, Elaine, Lawrence, David, Hayward, Martin, Kolvekar, Shyam, Panagiotopoulos, Nikolaos, Janes, Sam M., Thakrar, Ricky, Ahmed, Asia, Blackhall, Fiona, Summers, Yvonne, Hafez, Dina, Naik, Ashwini, Ganguly, Apratim, Kareht, Stephanie, Shah, Rajesh, Joseph, Leena, Marie Quinn, Anne, Crosbie, Phil A., Naidu, Babu, Middleton, Gary, Langman, Gerald, Trotter, Simon, Nicolson, Marianne, Remmen, Hardy, Kerr, Keith, Chetty, Mahendran, Gomersall, Lesley, Fennell, Dean A., Nakas, Apostolos, Rathinam, Sridhar, Anand, Girija, Khan, Sajid, Russell, Peter, Ezhil, Veni, Ismail, Babikir, Irvin-Sellers, Melanie, Prakash, Vineet, Lester, Jason F., Kornaszewska, Malgorzata, Attanoos, Richard, Adams, Haydn, Davies, Helen, Oukrif, Dahmane, Akarca, Ayse U., Hartley, John A., Lowe, Helen L., Lock, Sara, Iles, Natasha, Bell, Harriet, Ngai, Yenting, Elgar, Greg, Szallasi, Zoltan, Schwarz, Roland F., Herrero, Javier, Stewart, Aengus, Quezada, Sergio A., Peggs, Karl S., Van Loo, Peter, Dive, Caroline, Lin, C. Jimmy, Rabinowitz, Matthew, Aerts, Hugo J. W. L., Hackshaw, Allan, Shaw, Jacqui A., Zimmermann, Bernhard G., Swanton, Charles, Bosshard-Carter, Leticia, Goh, Gerald, Gorman, Pat, Murugaesu, Nirupa, Hynds, Robert E., Horswell, Stuart, Bakir, Maise Al, Mitter, Richard, Escudero, Mickael, Xu, Hang, Goldman, Jacki, Stone, Richard Kevin, Denner, Tamara, Biggs, Jennifer, Costa, Marta, Begum, Sharmin, Phillimore, Ben, Nye, Emma, Graca, Sofia, Joshi, Kroopa, Furness, Andrew, Ben Aissa, Assma, Wong, Yien Ning Sophia, Georgiou, Andy, Simeon, Celia, Hector, Gemma, Smith, Amy, Aranda, Marie, Novelli, Marco, Papadatos-Pastos, Dionysis, Carnell, Dawn, Mendes, Ruheena, George, Jeremy, Navani, Neal, Taylor, Magali, Choudhary, Junaid, Califano, Raffaele, Taylor, Paul, Krysiak, Piotr, Rammohan, Kendadai, Fontaine, Eustace, Booton, Richard, Evison, Matthew, Moss, Stuart, Idries, Faiza, Bishop, Paul, Chaturvedi, Anshuman, Quinn, Anne Marie, Doran, Helen, Leek, Angela, Harrison, Phil, Moore, Katrina, Waddington, Rachael, Novasio, Juliette, Rogan, Jane, Smith, Elaine, Tugwood, Jonathan, Brady, Ged, Rothwell, Dominic G., Chemi, Francesca, Pierce, Jackie, Gulati, Sakshi, Bellamy, Mary, Bancroft, Hollie, Kerr, Amy, Kadiri, Salma, Webb, Joanne, Djearaman, Madava, Quesne, John Le, Thomas, Anne, Walter, Harriet, Monteiro, William, Marshall, Hilary, Nelson, Louise, Bennett, Jonathan, Primrose, Lindsay, Amadi, Anita, Palmer, Shirley, Miller, Joy, Buchan, Keith, Edwards, Alison, Morgan, Fiona, Verjee, Azmina, MacKenzie, Mairead, Wilcox, Maggie, Smith, Sean, Gower, Nicole, Ottensmeier, Christian, Chee, Serena, Johnson, Benjamin, Alzetani, Aiman, Shaw, Emily, Lim, Eric, De Sousa, Paulo, Barbosa, Monica Tavares, Bowman, Alex, Jordan, Simon, Rice, Alexandra, Raubenheimer, Hilgardt, Proli, Chiara, Cufari, Maria Elena, Ronquillo, John Carlo, Kwayie, Angela, Bhayani, Harshil, Hamilton, Morag, Bakar, Yusura, Mensah, Natalie, Ambrose, Lyn, Devaraj, Anand, Buderi, Silviu, Finch, Jonathan, Azcarate, Leire, Chavan, Hema, Green, Sophie, Mashinga, Hillaria, Nicholson, Andrew G., Lau, Kelvin, Sheaff, Michael, Schmid, Peter, Conibear, John, Light, Teresa, Horey, Tracey, Danson, Sarah, Bury, Jonathan, Edwards, John, Hill, Jennifer, Matthews, Sue, Kitsanta, Yota, Suvarna, Kim, Fisher, Patricia, Keerio, Allah Dino, Shackcloth, Michael, Gosney, John, Postmus, Pieter, Feeney, Sarah, Asante-Siaw, Julius, Dentro, Stefan, and Dessimoz, Christophe

Subjects
Lung cancer -- Genetic aspects -- Development and progression, DNA sequencing -- Methods, Phylogeny -- Observations, Cancer metastasis -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies., Author(s): Christopher Abbosh [1]; Nicolai J. Birkbak [1, 2]; Gareth A. Wilson [1, 2]; Mariam Jamal-Hanjani [1]; Tudor Constantin [3]; Raheleh Salari [3]; John Le Quesne [4]; David A. Moore [...]

Published
2017
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7. Using DNA sequencing data to quantify T cell fraction and therapy response

Author

Javier Herrero, Gary Middleton, Charles Swanton, John Edwards, Ricky Thakrar, David Pearce, Domenic Marrone, Mickael Escudero, Christian Ottensmeier, Francisco Gimeno Valiente, Jonas Demeulemeester, James Black, Kevin Litchfield, Claire Wilson, Neal Navani, Helen Lowe, JAMES READING, Nicholas McGranahan, Diana Johnson, Hugo Aerts, Benny Chain, Miljana Tanic, and Robert Hynds

Subjects
Multidisciplinary, Tumor-infiltrating lymphocytes, Somatic cell, T-cell receptor excision circles, medicine.medical_treatment, T cell, Ipilimumab, Immunotherapy, Biology, medicine.anatomical_structure, Immune system, medicine, Cancer research, Exome, medicine.drug
Abstract

The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31–32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes. A robust, cost-effective technique based on whole-exome sequencing data can be used to characterize immune infiltrates, relate the extent of these infiltrates to somatic changes in tumours, and enables prediction of tumour responses to immune checkpoint inhibition therapy.

Published
2021

8. Melanoma addiction to the long non-coding RNA SAMMSON

Author

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, and Marine, Jean-Christophe

Subjects
RNA -- Health aspects, Melanoma -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Focal amplifications of chromosome 3p13-3p14 occur in about 10% of melanomas and are associated with a poor prognosis. The melanoma-specific oncogene MITF resides at the epicentre of this amplicon (1). However, whether other loci present in this amplicon also contribute to melanomagenesis is unknown. Here we show that the recently annotated long non-coding RNA (lncRNA) gene SAMMSON is consistently co-gained with MITF. In addition, SAMMSON is a target of the lineage-specific transcription factor SOX10 and its expression is detectable in more than 90% of human melanomas. Whereas exogenous SAMMSON increases the clonogenic potential in trans, SAMMSON knockdown drastically decreases the viability of melanoma cells irrespective of their transcriptional cell state and BRAF, NRAS or TP53 mutational status. Moreover, SAMMSON targeting sensitizes melanoma to MAPK-targeting therapeutics both in vitro and in patient-derived xenograft models. Mechanistically, SAMMSON interacts with p32, a master regulator of mitochondrial homeostasis and metabolism, to increase its mitochondrial targeting and pro-oncogenic function. Our results indicate that silencing of the lineage addiction oncogene SAMMSON disrupts vital mitochondrial functions in a cancer-cell-specific manner; this silencing is therefore expected to deliver highly effective and tissue-restricted antimelanoma therapeutic responses., In silico analysis of single nucleotide polymorphism (SNP) array data from >300 human clinical samples from The Cancer Genome Atlas (TCGA) revealed that the chromosome 3p melanoma-specific focal amplifications invariably [...]

Published
2016

9. Decoding gene regulation in the fly brain

Author

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

Published
2022
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10. Consequences of biodiversity loss for litter decomposition across biomes

Author

Handa, I. Tanya, Aerts, Rien, Berendse, Frank, Berg, Matty P., Bruder, Andreas, Butenschoen, Olaf, Chauvet, Eric, Gessner, Mark O., Jabiol, Jeremy, Makkonen, Marika, McKie, Brendan G., Malmqvist, Bjorn, Peeters, Edwin T.H.M., Scheu, Stefan, Schmid, Bernhard, van Ruijven, Jasper, Vos, Veronique C.A., and Hattenschwiler, Stephan

Subjects
Biological diversity -- Research, Botanical research, Plant populations -- Environmental aspects, Biomass -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The decomposition of dead organic matter is a major determinant of carbon and nutrient cycling in ecosystems, and of carbon fluxes between the biosphere and the atmosphere (1-3). Decomposition is driven by a vast diversity of organisms that are structured in complex food webs (2,4). Identifying the mechanisms underlying the effects of biodiversity on decomposition is critical (4-6) given the rapid loss of species worldwide and the effects of this loss on human well-being (7-9). Yet despite comprehensive syntheses of studies on how biodiversity affects litter decomposition (4-6,10), key questions remain, including when, where and how biodiversity has a role and whether general patterns and mechanisms occur across ecosystems and different functional types of organism (4,9-12). Here, in field experiments across five terrestrial and aquatic locations, ranging from the subarctic to the tropics, we show that reducing the functional diversity of decomposer organisms and plant litter types slowed the cycling of litter carbon and nitrogen. Moreover, we found evidence of nitrogen transfer from the litter of nitrogen-fixing plants to that of rapidly decomposing plants, but not between other plant functional types, highlighting that specific interactions in litter mixtures control carbon and nitrogen cycling during decomposition. The emergence of this general mechanism and the coherence of patterns across contrasting terrestrial and aquatic ecosystems suggest that biodiversity loss has consistent consequences for litter decomposition and the cycling of major elements on broad spatial scales., Biological diversity that directly influences litter decomposition exists at multiple trophic levels (4). This diversity includes plants that produce litter mixtures of varying quality, microbial decomposers and invertebrate consumers of [...]

Published
2014

11. Inconsistency in large pharmacogenomic studies

Author

Haibe-Kains, Benjamin, El-Hachem, Nehme, Birkbak, Nicolai Juul, Jin, Andrew C., Beck, Andrew H., Aerts, Hugo J. W. L., and Quackenbush, John

Subjects
Gene expression -- Research, Pharmacology, Experimental -- Research, Pharmacogenetics -- Research, Dose-response relationship (Biochemistry) -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

This Analysis compares two large-scale pharmacogenomic data sets that catalogued the sensitivity of a large number of cancer cell lines to approved and potential drugs, and finds that whereas the gene expression data are largely concordant between the two studies, the reported drug sensitivity measures and subsequently their association with genomic features are highly discordant. Time to set a standard for drug responses Two large-scale data sets recently catalogued the sensitivity of a large number of cancer cell lines to pharmacological drugs, and integrated the drug-response data with genomic features, such as mutations and gene expression profiles. This Analysis by John Quackenbush and colleagues compares the two studies and finds that although the gene expression data are largely concordant between them, the reported drug-sensitivity measures and subsequently their association with genomic features are highly discordant. The authors call for standardization of drug-response measurements, to aid the discovery of robust biomarkers and mechanisms of drug response and hence progress in personalized cancer medicine. Two large-scale pharmacogenomic studies were published recently in this journal. Genomic data are well correlated between studies; however, the measured drug response data are highly discordant. Although the source of inconsistencies remains uncertain, it has potential implications for using these outcome measures to assess gene-drug associations or select potential anticancer drugs on the basis of their reported results., Author(s): Benjamin Haibe-Kains [sup.1] [sup.2] , Nehme El-Hachem [sup.1] , Nicolai Juul Birkbak [sup.3] , Andrew C. Jin [sup.4] , Andrew H. Beck [sup.4] , Hugo J. W. L. Aerts [...]

Published
2013
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12. Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Author

Abbosh, Christopher, Birkbak, Nicolai J., Wilson, Gareth A., Jamal-Hanjani, Mariam, Constantin, Tudor, Salari, Raheleh, Le Quesne, John, Moore, David A., Veeriah, Selvaraju, Rosenthal, Rachel, Marafioti, Teresa, Kirkizlar, Eser, Watkins, Thomas B. K., McGranahan, Nicholas, Ward, Sophia, Martinson, Luke, Riley, Joan, Fraioli, Francesco, Al Bakir, Maise, Grnroos, Eva, Zambrana, Francisco, Endozo, Raymondo, Bi, Wenya Linda, Fennessy, Fiona M., Sponer, Nicole, Johnson, Diana, Laycock, Joanne, Shafi, Seema, Czyzewska-Khan, Justyna, Rowan, Andrew, Chambers, Tim, Matthews, Nik, Turajlic, Samra, Hiley, Crispin, Lee, Siow Ming, Forster, Martin D., Ahmad, Tanya, Falzon, Mary, Borg, Elaine, Lawrence, David, Hayward, Martin, Kolvekar, Shyam, Panagiotopoulos, Nikolaos, Janes, Sam M., Thakrar, Ricky, Ahmed, Asia, Blackhall, Fiona, Summers, Yvonne, Hafez, Dina, Naik, Ashwini, Ganguly, Apratim, Kareht, Stephanie, Shah, Rajesh, Joseph, Leena, Quinn, Anne Marie, Crosbie, Phil A., Naidu, Babu, Middleton, Gary, Langman, Gerald, Trotter, Simon, Nicolson, Marianne, Remmen, Hardy, Kerr, Keith, Chetty, Mahendran, Gomersall, Lesley, Fennell, Dean A., Nakas, Apostolos, Rathinam, Sridhar, Anand, Girija, Khan, Sajid, Russell, Peter, Ezhil, Veni, Ismail, Babikir, Irvin-Sellers, Melanie, Prakash, Vineet, Lester, Jason F., Kornaszewska, Malgorzata, Attanoos, Richard, Adams, Haydn, Davies, Helen, Oukrif, Dahmane, Akarca, Ayse U., Hartley, John A., Lowe, Helen L., Lock, Sara, Iles, Natasha, Bell, Harriet, Ngai, Yenting, Elgar, Greg, Szallasi, Zoltan, Schwarz, Roland F., Herrero, Javier, Stewart, Aengus, Quezada, Sergio A., Peggs, Karl S., Van Loo, Peter, Dive, Caroline, Lin, C. Jimmy, Rabinowitz, Matthew, Aerts, Hugo J. W. L., Hackshaw, Allan, Shaw, Jacqui A., Zimmermann, Bernhard G., and Swanton, Charles

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Christopher Abbosh; Nicolai J. Birkbak; Gareth A. Wilson; Mariam Jamal-Hanjani; Tudor Constantin; Raheleh Salari; John Le Quesne; David A. Moore; Selvaraju Veeriah; Rachel Rosenthal; Teresa Marafioti; Eser Kirkizlar; Thomas [...]

Published
2018
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13. Transparency and reproducibility in artificial intelligence

Author

Haibe-Kains, Benjamin, Adam, George Alexandru, Hosny, Ahmed, Khodakarami, Farnoosh, Shraddha, Thakkar, Kusko, Rebecca, Sansone, Susanna-Assunta, Tong, Weida, Wolfinger, Russ D., Mason, Christopher E., Jones, Wendell, Dopazo, Joaquin, Furlanello, Cesare, Waldron, Levi, Wang, Bo, McIntosh, Chris, Goldenberg, Anna, Kundaje, Anshul, Greene, Casey S., Broderick, Tamara, Hoffman, Michael M., Leek, Jeffrey T., Korthauer, Keegan, Huber, Wolfgang, Brazma, Alvis, Pineau, Joelle, Tibshirani, Robert, Hastie, Trevor, Ioannidis, John P. A., Quackenbush, John, Aerts, Hugo J. W. L., RS: Carim - B06 Imaging, Beeldvorming, and MUMC+: DA BV Research (9)

Subjects
Reproducibility, Multidisciplinary, Computer science, Reproducibility of Results, Breast Neoplasms, Transparency (behavior), Data science, Article, United Kingdom, United States, Artificial Intelligence, AI, Humans, Female, Early Detection of Cancer, Algorithms, Mammography
Abstract

Breakthroughs in artificial intelligence (AI) hold enormous potential as it can automate complex tasks and go even beyond human performance. In their study, McKinney et al. showed the high potential of AI for breast cancer screening. However, the lack of methods’ details and algorithm code undermines its scientific value. Here, we identify obstacles hindering transparent and reproducible AI research as faced by McKinney et al., and provide solutions to these obstacles with implications for the broader field.

Published
2020

14. Insights into bilaterian evolution from three spiralian genomes

Author

Simakov, Oleg, Marletaz, Ferdinand, Cho, Sung-Jin, Edsinger-Gonzales, Eric, Havlak, Paul, Hellsten, Uffe, Kuo, Dian-Han, Larsson, Tomas, Lv, Jie, Arendt, Detlev, Savage, Robert, Osoegawa, Kazutoyo, de Jong, Pieter, Grimwood, Jane, Chapman, Jarrod A., Shapiro, Harris, Aerts, Andrea, Otillar, Robert P., Terry, Astrid Y., Boore, Jeffrey L., Grigoriev, Igor V., Lindberg, David R., Seaver, Elaine C., Weisblat, David A., Putnam, Nicholas H., and Rokhsar, Daniel S.

Subjects
Bilateria -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and [...]

Published
2013
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15. Do not discard Staphylococcus aureus WTA as a vaccine antigen

Author

van Dalen, Rob, Molendijk, Michèle M., Ali, Sara, van Kessel, Kok P. M., Aerts, Piet, van Strijp, Jos A. G., and de Haas, Carla J. C.

Subjects
Staphylococcus aureus -- Analysis, Plant cell walls -- Chemical properties, Bacterial vaccines -- Analysis, Antigens -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Rob van Dalen [sup.1] , Michèle M. Molendijk [sup.1] , Sara Ali [sup.2] , Kok P. M. van Kessel [sup.1] , Piet Aerts [sup.1] , Jos A. G. van [...]

Published
2019
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16. Origins and functional impact of copy number variation in the human genome

Author

Conrad, Donald F., Pinto, Dalila, Redon, Richard, Feuk, Lars, Gokcumen, Omer, Zhang, Yujun, Aerts, Jan, Andrews, T. Daniel, Barnes, Chris, Campbell, Peter, Fitzgerald, Tomas, Hu, Min, Ihm, Chun Hwa, Kristiansson, Kati, MacArthur, Daniel G., MacDonald, Jeffrey R., Onyiah, Ifejinelo, Pang, Andy Wing Chun, Robson, Sam, Stirrups, Kathy, Valsesia, Armand, Walter, Klaudia, Wei, John, Tyler-Smith, Chris, Carter, Nigel P., Lee, Charles, Scherer, Stephen W., and Hurles, Matthew E.

Subjects
Genetic variation -- Research, Human genome -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs., Genomes vary from one another in multifarious ways, and the totality of this genetic variation underpins the heritability of human traits. Over the past two years, the human reference sequence [...]

Published
2010
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17. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA

Author

Abbosh, Christopher, Frankell, Alexander M., Harrison, Thomas, Kisistok, Judit, Garnett, Aaron, Johnson, Laura, Veeriah, Selvaraju, Moreau, Mike, Chesh, Adrian, Chaunzwa, Tafadzwa L., Weiss, Jakob, Schroeder, Morgan R., Ward, Sophia, Grigoriadis, Kristiana, Shahpurwalla, Aamir, Litchfield, Kevin, Puttick, Clare, Biswas, Dhruva, Karasaki, Takahiro, Black, James R. M., Martínez-Ruiz, Carlos, Bakir, Maise Al, Pich, Oriol, Watkins, Thomas B. K., Lim, Emilia L., Huebner, Ariana, Moore, David A., Godin-Heymann, Nadia, L’Hernault, Anne, Bye, Hannah, Odell, Aaron, Roberts, Paula, Gomes, Fabio, Patel, Akshay J., Manzano, Elizabeth, Hiley, Crispin T., Carey, Nicolas, Riley, Joan, Cook, Daniel E., Hodgson, Darren, Stetson, Daniel, Barrett, J. Carl, Kortlever, Roderik M., Evan, Gerard I., Hackshaw, Allan, Daber, Robert D., Shaw, Jacqui A., Aerts, Hugo J. W. L., Licon, Abel, Stahl, Josh, Jamal-Hanjani, Mariam, Birkbak, Nicolai J., McGranahan, Nicholas, and Swanton, Charles

Abstract

Circulating tumour DNA (ctDNA) can be used to detect and profile residual tumour cells persisting after curative intent therapy1. The study of large patient cohorts incorporating longitudinal plasma sampling and extended follow-up is required to determine the role of ctDNA as a phylogenetic biomarker of relapse in early-stage non-small-cell lung cancer (NSCLC). Here we developed ctDNA methods tracking a median of 200 mutations identified in resected NSCLC tissue across 1,069 plasma samples collected from 197 patients enrolled in the TRACERx study2. A lack of preoperative ctDNA detection distinguished biologically indolent lung adenocarcinoma with good clinical outcome. Postoperative plasma analyses were interpreted within the context of standard-of-care radiological surveillance and administration of cytotoxic adjuvant therapy. Landmark analyses of plasma samples collected within 120 days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome. By measuring subclone cancer cell fractions in preoperative plasma, we found that subclones seeding future metastases were significantly more expanded compared with non-metastatic subclones. Our findings will support (neo)adjuvant trial advances and provide insights into the process of metastatic dissemination using low-ctDNA-level liquid biopsy.

Published
2023
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18. Carbon respiration from subsurface peat accelerated by climate warming in the subarctic

Author

Dorrepaal, Ellen, Toet, Sylvia, van Logtestijn, Richard S.P., Swart, Elferra, van de Weg, Martine J., Callaghan, Terry V., and Aerts, Rien

Subjects
Carbon cycle (Biogeochemistry) -- Research -- Environmental aspects, Soils -- Carbon content, Global warming -- Influence -- Research -- Environmental aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Influence, Research, Environmental aspects
Abstract

Among the largest uncertainties in current projections of future climate is the feedback between the terrestrial carbon cycle and climate (1). Northern peatlands contain one-third of the world's soil organic carbon, equivalent to more than half the amount of carbon in the atmosphere (2). Climate-warming-induced acceleration of carbon dioxide ([CO.sub.2]) emissions through enhanced respiration of thick peat deposits, centuries to millennia old, may form a strong positive carbon cycle-climate feedback. The long-term temperature sensitivity of carbon in peatlands, especially at depth, remains uncertain, however, because of the short duration or correlative nature of field studies (3-5) and the disturbance associated with respiration measurements below the surface in situ or during laboratory incubations (6,7). Here we combine non-disturbing in situ measurements of [CO.sub.2] respiration rates and isotopic ([[sup.13]C) composition of respired [CO.sub.2] in two whole-ecosystem climate-manipulation experiments in a subarctic peatland. We show that approximately 1°C warming accelerated total ecosystem respiration rates on average by 60% in spring and by 52% in summer and that this effect was sustained for at least eight years. While warming stimulated both short-term (plant-related) and longer-term (peat soil-related) carbon respiration processes, we find that at least 69% of the increase in respiration rate originated from carbon in peat towards the bottom (25-50 cm) of the active layer above the permafrost. Climate warming therefore accelerates respiration of the extensive, subsurface carbon reservoirs in peatlands to a much larger extent than was previously thought (6,7). Assuming that our data from a single site are indicative of the direct response to warming of northern peatland soils on a global scale, we estimate that climate warming of about 1°C over the next few decades could induce a global increase in heterotrophic respiration of 38-100 megatonnes of C per year. Our findings suggest a large, long-lasting, positive feedback of carbon stored in northern peatlands to the global climate system., The long-term effect of climate warming on soil carbon in terrestrial ecosystems has been debated for more than a decade (8-13). This controversy has focused primarily on upland mineral soils [...]

Published
2009

19. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Author

Stark, Alexander, Lin, Michael F., Kheradpour, Pouya, Pedersen, Jakob S., Parts, Leopold, Carlson, Joseph W., Crosby, Madeline A., Rasmussen, Matthew D., Roy, Sushmita, Deoras, Ameya N., Ruby, J. Graham, Brennecke, Julius, Matthews, Beverley B., Schroeder, Andrew J., Sian Gramates, L., St Pierre, Susan E., Roark, Margaret, Wiley Jr, Kenneth L., Kulathinal, Rob J., Zhang, Peili, Myrick, Kyl V., Antone, Jerry V., Gelbart, William M., Yu, Charles, Park, Soo, Wan, Kenneth H., Celniker, Susan E., Hodges, Emily, Hinrichs, Angie S., Caspi, Anat, Paten, Benedict, Park, Seung-Won, Han, Mira V., Maeder, Morgan L., Polansky, Benjamin J., Robson, Bryanne E., Aerts, Stein, van Helden, Jacques, Hassan, Bassem, Gilbert, Donald G., Eastman, Deborah A., Rice, Michael, Weir, Michael, Hahn, Matthew W., Park, Yongkyu, Dewey, Colin N., Pachter, Lior, Kent, W. James, Haussler, David, Lai, Eric C., Bartel, David P., Hannon, Gregory J., Kaufman, Thomas C., Eisen, Michael B., Clark, Andrew G., Smith, Douglas, and Kellis, Manolis

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Alexander Stark [1, 2, 35]; Michael F. Lin [1, 2, 35]; Pouya Kheradpour [2, 35]; Jakob S. Pedersen [3, 4, 35]; Leopold Parts [5, 6]; Joseph W. Carlson [7]; [...]

Published
2007
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20. The sequence and analysis of duplication-rich human chromosome 16

Author

Martin, Joel, Han, Cliff, Gordon, Laurie A., Terry, Astrid, Prabhakar, Shyam, She, Xinwei, Xie, Gary, Hellsten, Uffe, Chan, Yee Man, Altherr, Michael, Couronne, Olivier, Aerts, Andrea, Bajorek, Eva, Black, Stacey, Blumer, Heather, Branscomb, Elbert, Brown, Nancy C., Bruno, William J., Buckingham, Judith M., Callen, David F., Campbell, Connie S., Campbell, Mary L., Campbell, Evelyn W., Caoile, Chenier, Challacombe, Jean F., Chasteen, Leslie A., Chertkov, Olga, Chi, Han C., Christensen, Mari, Clark, Lynn M., Cohn, Judith D., Denys, Mirian, Detter, John C., Dickson, Mark, Dimitrijevic-Bussod, Mira, Escobar, Julio, Fawcett, Joseph J., Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstein, David, Goodwin, Lynne A., Grady, Deborah L., Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Hildebrand, Carl E., Huang, Wayne, Israni, Sanjay, Jett, Jamie, Jewett, Phillip B., Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Krawczyk, Marie-Claude, Leyba, Tina, Longmire, Jonathan L., Lopez, Frederick, Lou, Yunian, Lowry, Steve, Ludeman, Thom, Manohar, Chitra F., Mark, Graham A., McMurray, Kimberly L., Meincke, Linda J., Morgan, Jenna, Moyzis, Robert K., Mundt, Mark O., Munk, A. Christine, Nandkeshwar, Richard D., Pitluck, Sam, Pollard, Martin, Predki, Paul, Parson-Quintana, Beverly, Ramirez, Lucia, Rash, Sam, Retterer, James, Ricke, Darryl O., Robinson, Donna L., Rodriguez, Alex, Salamov, Asaf, Saunders, Elizabeth H., Scott, Duncan, Shough, Timothy, Stallings, Raymond L., Stalvey, Malinda, Sutherland, Robert D., Tapia, Roxanne, Tesmer, Judith G., Thayer, Nina, Thompson, Linda S., Tice, Hope, Torney, David C., Tran-Gyamfi, Mary, Tsai, Ming, Ulanovsky, Levy E., Ustaszewska, Anna, Vo, Nu, Scott White, P., Williams, Albert L., Wills, Patricia L., Wu, Jung-Rung, Wu, Kevin, Yang, Joan, DeJong, Pieter, Bruce, David, Doggett, Norman A., Deaven, Larry, Schmutz, Jeremy, Grimwood, Jane, Richardson, Paul, Rokhsar, Daniel S., Eichler, Evan E., Gilna, Paul, Lucas, Susan M., Myers, Richard M., Rubin, Edward M., and Pennacchio, Len A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Joel Martin [1]; Cliff Han [2]; Laurie A. Gordon [1]; Astrid Terry [1]; Shyam Prabhakar [4]; Xinwei She [5]; Gary Xie [1, 2]; Uffe Hellsten [1]; Yee Man Chan [...]

Published
2004
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21. A physical map of the chicken genome

Author

Wallis, John W., Aerts, Jan, Groenen, Martien A. M., Crooijmans, Richard P. M. A., Layman, Dan, Graves, Tina A., Scheer, Debra E., Kremitzki, Colin, Fedele, Mary J., Mudd, Nancy K., Cardenas, Marco, Higginbotham, Jamey, Carter, Jason, McGrane, Rebecca, Gaige, Tony, Mead, Kelly, Walker, Jason, Albracht, Derek, Davito, Jonathan, Yang, Shiaw-Pyng, Leong, Shin, Chinwalla, Asif, Sekhon, Mandeep, Wylie, Kristine, Dodgson, Jerry, Romanov, Michael N., Cheng, Hans, de Jong, Pieter J., Osoegawa, Kazutoyo, Nefedov, Mikhail, Zhang, Hongbin, McPherson, John D., Krzywinski, Martin, Schein, Jacquie, Hillier, LaDeana, Mardis, Elaine R., Wilson, Richard K., and Warren, Wesley C.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): John W. Wallis [1]; Jan Aerts [2]; Martien A. M. Groenen [2]; Richard P. M. A. Crooijmans [2]; Dan Layman [1]; Tina A. Graves [1]; Debra E. Scheer [1]; [...]

Published
2004
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22. The DNA sequence and comparative analysis of human chromosome 5

Author

Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, Steve, Gordon, Laurie A., Scott, Duncan, Xie, Gary, Huang, Wayne, Hellsten, Uffe, Tran-Gyamfi, Mary, She, Xinwei, Prabhakar, Shyam, Aerts, Andrea, Altherr, Michael, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caoile, Chenier, Challacombe, Jean F., Man Chan, Yee, Denys, Mirian, Detter, John C., Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstein, David, Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Lopez, Frederick, Lou, Yunian, Martinez, Diego, Medina, Catherine, Morgan, Jenna, Nandkeshwar, Richard, Noonan, James P., Pitluck, Sam, Pollard, Martin, Predki, Paul, Priest, James, Ramirez, Lucia, Retterer, James, Rodriguez, Alex, Rogers, Stephanie, Salamov, Asaf, Salazar, Angelica, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wheeler, Jeremy, Wu, Kevin, Yang, Joan, Dickson, Mark, Cheng, Jan-Fang, Eichler, Evan E., Olsen, Anne, Pennacchio, Len A., Rokhsar, Daniel S., Richardson, Paul, Lucas, Susan M., Myers, Richard M., and Rubin, Edward M.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Jeremy Schmutz (corresponding author) [1]; Joel Martin [2]; Astrid Terry [2]; Olivier Couronne [3]; Jane Grimwood [1]; Steve Lowry [2]; Laurie A. Gordon [2, 4]; Duncan Scott [2]; Gary [...]

Published
2004
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23. The DNA sequence and biology of human chromosome 19

Author

Grimwood, Jane, Gordon, Laurie A., Olsen, Anne, Terry, Astrid, Schmutz, Jeremy, Lamerdin, Jane, Hellsten, Uffe, Goodstein, David, Couronne, Olivier, Tran-Gyamfi, Mary, Aerts, Andrea, Altherr, Michael, Ashworth, Linda, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caenepeel, Sean, Carrano, Anthony, Caoile, Chenier, Man Chan, Yee, Christensen, Mari, Cleland, Catherine A., Copeland, Alex, Dalin, Eileen, Dehal, Paramvir, Denys, Mirian, Detter, John C., Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Garcia, Carmen, Georgescu, Anca M., Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Ho, Isaac, Huang, Wayne, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Larionov, Vladimer, Leem, Sun-Hee, Lopez, Frederick, Lou, Yunian, Lowry, Steve, Malfatti, Stephanie, Martinez, Diego, McCready, Paula, Medina, Catherine, Morgan, Jenna, Nelson, Kathryn, Nolan, Matt, Ovcharenko, Ivan, Pitluck, Sam, Pollard, Martin, Popkie, Anthony P., Predki, Paul, Quan, Glenda, Ramirez, Lucia, Rash, Sam, Retterer, James, Rodriguez, Alex, Rogers, Stephanine, Salamov, Asaf, Salazar, Angelica, She, Xinwei, Smith, Doug, Slezak, Tom, Solovyev, Victor, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wagner, Mark, Wheeler, Jeremy, Wu, Kevin, Xie, Gary, Yang, Joan, Dubchak, Inna, Furey, Terrence S., DeJong, Pieter, Dickson, Mark, Gordon, David, Eichler, Evan E., Pennacchio, Len A., Richardson, Paul, Stubbs, Lisa, Rokhsar, Daniel S., Myers, Richard M., Rubin, Edward M., and Lucas, Susan M.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Jane Grimwood (corresponding author) [1]; Laurie A. Gordon [2, 3]; Anne Olsen [2, 3]; Astrid Terry [2]; Jeremy Schmutz [1]; Jane Lamerdin [2, 3]; Uffe Hellsten [2]; David Goodstein [...]

Published
2004
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25. Fast core rotation in red-giant stars as revealed by gravity-dominated mixed modes

Author

Beck, Paul G., Montalban, Josefina, Kallinger, Thomas, De Ridder, Joris, Aerts, Conny, García, Rafael A., Hekker, Saskia, Dupret, Marc-Antoine, Mosser, Benoit, Eggenberger, Patrick, Stello, Dennis, Elsworth, Yvonne, Frandsen, Søren, Carrier, Fabien, Hillen, Michel, Gruberbauer, Michael, Christensen-Dalsgaard, Jørgen, Miglio, Andrea, Valentini, Marica, Bedding, Timothy R., Kjeldsen, Hans, Girouard, Forrest R., Hall, Jennifer R., and Ibrahim, Khadeejah A.

Published
2012
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26. Gravity modes as a way to distinguish between hydrogen- and helium-burning red giant stars

Author

Bedding, Timothy R., Mosser, Benoit, Huber, Daniel, Montalbán, Josefina, Beck, Paul, Christensen-Dalsgaard, Jørgen, Elsworth, Yvonne P., García, Rafael A., Miglio, Andrea, Stello, Dennis, White, Timothy R., De Ridder, Joris, Hekker, Saskia, Aerts, Conny, Barban, Caroline, Belkacem, Kevin, Broomhall, Anne-Marie, Brown, Timothy M., Buzasi, Derek L., Carrier, Fabien, Chaplin, William J., Di Mauro, Maria Pia, Dupret, Marc-Antoine, Frandsen, Søren, Gilliland, Ronald L., Goupil, Marie-Jo, Jenkins, Jon M., Kallinger, Thomas, Kawaler, Steven, Kjeldsen, Hans, Mathur, Savita, Noels, Arlette, Aguirre, Victor Silva, and Ventura, Paolo

Published
2011
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27. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

Author

Craddock, Nick, Hurles, Matthew E., Cardin, Niall, Pearson, Richard D., Plagnol, Vincent, Robson, Samuel, Vukcevic, Damjan, Barnes, Chris, Conrad, Donald F., Giannoulatou, Eleni, Holmes, Chris, Marchini, Jonathan L., Stirrups, Kathy, Tobin, Martin D., Wain, Louise V., Yau, Chris, Aerts, Jan, Ahmad, Tariq, Daniel Andrews, T., Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barrett, Jeffrey C., Barroso, Inês, Barton, Anne, Bennett, Amanda J., Bhaskar, Sanjeev, Blaszczyk, Katarzyna, Bowes, John, Brand, Oliver J., Braund, Peter S., Bredin, Francesca, Breen, Gerome, Brown, Morris J., Bruce, Ian N., Bull, Jaswinder, Burren, Oliver S., Burton, John, Byrnes, Jake, Caesar, Sian, Clee, Chris M., Coffey, Alison J., Connell, John M. C., Cooper, Jason D., Dominiczak, Anna F., Downes, Kate, Drummond, Hazel E., Dudakia, Darshna, Dunham, Andrew, Ebbs, Bernadette, Eccles, Diana, Edkins, Sarah, Edwards, Cathryn, Elliot, Anna, Emery, Paul, Evans, David M., Evans, Gareth, Eyre, Steve, Farmer, Anne, Nicol Ferrier, I., Feuk, Lars, Fitzgerald, Tomas, Flynn, Edward, Forbes, Alistair, Forty, Liz, Franklyn, Jayne A., Freathy, Rachel M., Gibbs, Polly, Gilbert, Paul, Gokumen, Omer, Gordon-Smith, Katherine, Gray, Emma, Green, Elaine, Groves, Chris J., Grozeva, Detelina, Gwilliam, Rhian, Hall, Anita, Hammond, Naomi, Hardy, Matt, Harrison, Pile, Hassanali, Neelam, Hebaishi, Husam, Hines, Sarah, Hinks, Anne, Hitman, Graham A, Hocking, Lynne, Howard, Eleanor, Howard, Philip, Howson, Joanna M. M., Hughes, Debbie, Hunt, Sarah, Isaacs, John D., Jain, Mahim, Jewell, Derek P., Johnson, Toby, Jolley, Jennifer D., Jones, Ian R., Jones, Lisa A., Kirov, George, Langford, Cordelia F., Lango-Allen, Hana, Mark Lathrop, G., Lee, James, Lee, Kate L., Lees, Charlie, Lewis, Kevin, Lindgren, Cecilia M., Maisuria-Armer, Meeta, Maller, Julian, Mansfield, John, Martin, Paul, Massey, Dunecan C. O., McArdle, Wendy L., McGuffin, Peter, McLay, Kirsten E., Mentzer, Alex, Mimmack, Michael L., Morgan, Ann E., Morris, Andrew P., Mowat, Craig, Myers, Simon, Newman, William, Nimmo, Elaine R., O’Donovan, Michael C., Onipinla, Abiodun, Onyiah, Ifejinelo, Ovington, Nigel R., Owen, Michael J., Palin, Kimmo, Parnell, Kirstie, Pernet, David, Perry, John R. B., Phillips, Anne, Pinto, Dalila, Prescott, Natalie J., Prokopenko, Inga, Quail, Michael A., Rafelt, Suzanne, Rayner, Nigel W., Redon, Richard, Reid, David M., Renwick, Anthony, Ring, Susan M., Robertson, Neil, Russell, Ellie, St Clair, David, Sambrook, Jennifer G., Sanderson, Jeremy D., Schuilenburg, Helen, Scott, Carol E., Scott, Richard, Seal, Sheila, Shaw-Hawkins, Sue, Shields, Beverley M., Simmonds, Matthew J., Smyth, Debbie J., Somaskantharajah, Elilan, Spanova, Katarina, Steer, Sophia, Stephens, Jonathan, Stevens, Helen E., Stone, Millicent A., Su, Zhan, Symmons, Deborah P. M., Thompson, John R., Thomson, Wendy, Travers, Mary E., Turnbull, Clare, Valsesia, Armand, Walker, Mark, Walker, Neil M., Wallace, Chris, Warren-Perry, Margaret, Watkins, Nicholas A., Webster, John, Weedon, Michael N., Wilson, Anthony G., Woodburn, Matthew, Wordsworth, Paul B., Young, Allan H., Zeggini, Eleftheria, Carter, Nigel P., Frayling, Timothy M., Lee, Charles, McVean, Gil, Munroe, Patricia B., Palotie, Aarno, Sawcer, Stephen J., Scherer, Stephen W., Strachan, David P., Tyler-Smith, Chris, Brown, Matthew A., Burton, Paul R., Caulfield, Mark J., Compston, Alastair, Farrall, Martin, Gough, Stephen C. L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V. S., Mathew, Christopher G., Pembrey, Marcus, Satsangi, Jack, Stratton, Michael R., Worthington, Jane, Deloukas, Panos, Duncanson, Audrey, Kwiatkowski, Dominic P., McCarthy, Mark I., Ouwehand, Willem H., Parkes, Miles, Rahman, Nazneen, Todd, John A., Samani, Nilesh J., and Donnelly, Peter

Published
2010
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32. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

Author

Martin, F., Aerts, A., Ahrén, D., Brun, A., Danchin, E. G. J., Duchaussoy, F., Gibon, J., Kohler, A., Lindquist, E., Pereda, V., Salamov, A., Shapiro, H. J., Wuyts, J., Blaudez, D., Buée, M., Brokstein, P., Canbäck, B., Cohen, D., Courty, P. E., Coutinho, P. M., Delaruelle, C., Detter, J. C., Deveau, A., DiFazio, S., Duplessis, S., Fraissinet-Tachet, L., Lucic, E., Frey-Klett, P., Fourrey, C., Feussner, I., Gay, G., Grimwood, J., Hoegger, P. J., Jain, P., Kilaru, S., Labbé, J., Lin, Y. C., Legué, V., Le Tacon, F., Marmeisse, R., Melayah, D., Montanini, B., Muratet, M., Nehls, U., Niculita-Hirzel, H., Oudot-Le Secq, M. P., Peter, M., Quesneville, H., Rajashekar, B., Reich, M., Rouhier, N., Schmutz, J., Yin, T., Chalot, M., Henrissat, B., Kües, U., Lucas, S., Van de Peer, Y., Podila, G. K., Polle, A., Pukkila, P. J., Richardson, P. M., Rouzé, P., Sanders, I. R., Stajich, J. E., Tunlid, A., Tuskan, G., and Grigoriev, I. V.

Published
2008
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33. Do not discard Staphylococcus aureus WTA as a vaccine antigen

Author

Rob, van Dalen, Michèle M, Molendijk, Sara, Ali, Kok P M, van Kessel, Piet, Aerts, Jos A G, van Strijp, Carla J C, de Haas, Jeroen, Codée, and Nina M, van Sorge

Subjects
Methicillin-Resistant Staphylococcus aureus, Methicillin, Staphylococcus aureus, Vaccines, Glycosylation, Cell Wall, Humans, Staphylococcal Infections
Published
2018

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

Author

Rajewsky, Nikolaus, Almouzni, Geneviève, Clevers, Hans, Heutink, Peter, Heymans, Stephane R B, Heyn, Holger, Huch, Meritxell, Huitinga, Inge, Jackowiak, Paulina, Jongsma, Karin R, Journot, Laurent, Junker, Jan Philipp, Katz, Shauna, De Strooper, Bart, Kehren, Jeanne, Kempa, Stefan, Kirchhof, Paulus, Klein, Christine, Koralewska, Natalia, Korbel, Jan O, Kühnemund, Malte, Lamond, Angus I, Lauwers, Elsa, Le Ber, Isabelle, Eggert, Angelika, Leinonen, Ville, López-Tobón, Alejandro, Lundberg, Emma, Lunkes, Astrid, Maatz, Henrike, Mann, Matthias, Marelli, Luca, Matser, Vera, Matthews, Paul M, Mechta-Grigoriou, Fatima, Ellenberg, Jan, Menon, Radhika, Nielsen, Anne F, Pagani, Massimiliano, Pasterkamp, R Jeroen, Pitkänen, Asla, Popescu, Valentin, Pottier, Cyril, Puisieux, Alain, Rademakers, Rosa, Reiling, Dory, Fernández, Xosé M, Reiner, Orly, Remondini, Daniel, Ritchie, Craig, Rohrer, Jonathan D, Saliba, Antoine-Emmanuel, Sanchez-Valle, Raquel, Santosuosso, Amedeo, Sauter, Arnold, Scheltema, Richard A, Scheltens, Philip, Figlerowicz, Marek, Schiller, Herbert B, Schneider, Anja, Seibler, Philip, Sheehan-Rooney, Kelly, Shields, David J, Sleegers, Kristel, Smit, August B, Smith, Kenneth G C, Smolders, Ilse, Synofzik, Matthis, Gasser, Susan M, Tam, Wai Long, Teichmann, Sarah A, Thom, Maria, Turco, Margherita Y, van Beusekom, Heleen M M, Vandenberghe, Rik, Van den Hoecke, Silvie, van de Poel, Ibo, van der Ven, Andre, van der Zee, Julie, Hubner, Norbert, van Lunzen, Jan, van Minnebruggen, Geert, van Oudenaarden, Alexander, Van Paesschen, Wim, van Swieten, John C, van Vught, Remko, Verhage, Matthijs, Verstreken, Patrik, Villa, Carlo Emanuele, Vogel, Jörg, Kjems, Jørgen, von Kalle, Christof, Walter, Jörn, Weckhuysen, Sarah, Weichert, Wilko, Wood, Louisa, Ziegler, Anette-Gabriele, Zipp, Frauke, Knoblich, Jürgen A, Gorski, Stanislaw 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, Aerts, Stein, Parkinson, Helen, Piccolo, Stefano, Pinheiro, Inês, Pombo, Ana, Popp, Christian, Reik, Wolf, Roman-Roman, Sergio, Rosenstiel, Philip, Schultze, Joachim L, Stegle, Oliver, Amit, Ido, Tanay, Amos, Testa, Giuseppe, Thanos, Dimitris, Theis, Fabian J, Torres-Padilla, Maria-Elena, Valencia, Alfonso, Vallot, Céline, Vidal, Marie, Voet, Thierry, Bertero, Michela G, Groups, LifeTime Community Working, Alberi, Lavinia, Alexander, Stephanie, Alexandrov, Theodore, Arenas, Ernest, Bagni, Claudia, Balderas, Robert, Bandelli, Andrea, Becher, Burkhard, Becker, Matthias, Bock, Christoph, Beerenwinkel, Niko, Benkirane, Monsef, Beyer, Marc, Bickmore, Wendy A, Biessen, Erik E A L, Blomberg, Niklas, Blumcke, Ingmar, Bodenmiller, Bernd, Borroni, Barbara, Boumpas, Dimitrios T, Bredenoord, Annelien L, Bourgeron, Thomas, Bowers, Sarion, Braeken, Dries, Brooksbank, Catherine, Brose, Nils, Bruining, Hilgo, Bury, Jo, Caporale, Nicolo, Cattoretti, Giorgio, Chabane, Nadia, Cavalli, Giacomo, Chneiweiss, Hervé, Cook, Stuart A, Curatolo, Paolo, de Jonge, Marien I, Deplancke, Bart, de Witte, Peter, Dimmeler, Stefanie, Draganski, Bogdan, Drews, Anna, Chiocca, Susanna, Dumbrava, Costica, Engelhardt, Stefan, Gasser, Thomas, Giamarellos-Bourboulis, Evangelos J, Graff, Caroline, Grün, Dominic, Gut, Ivo G, Hansson, Oskar, Henshall, David C, and Herland, Anna

Subjects
Male, medicine.medical_specialty, Legislation, Medical, Cell- and Tissue-Based Therapy, MEDLINE, Diseases, Artificial Intelligence, Health care, Pathology, medicine, Humans, Medical physics, Multidisciplinary, Education, Medical, business.industry, Published Erratum, Publisher Correction, Europe, Early Diagnosis, Health, Medicine, Female, ddc:500, Single-Cell Analysis, Systems biology, business, Delivery of Health Care, Biomarkers, Cell based
Abstract

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.

Published
2021

37. Functional neuroanatomy of human rapid-eye-movement sleep and dreaming

Author

Maquet, Pierre, Peters, Jean-Marie, Aerts, Joel, Delfiore, Guy, Degueldre, Christian, Luxen, Andre, and Franck, Georges

Subjects
Sleep -- Stages, Brain stimulation -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Functional interactions occur between the anterior cingulate cortex, amygdaloid complexes and various posterior areas of the brain during rapid-eye-movement (REM) sleep. These interactions may cause restimulation of affective components of memories and thus consolidate memory traces. The cerebral microcirculation is positively correlated with REM sleep in the left thalamus, both amygdaloid complexes, pontine tegmentum, anterior cingulate cortex and right parietal operculum.

Published
1996

39. Leprosy: the world's oldest human-rights issue

Author

Aerts, Ann

Subjects
No Matter Where the Journey Takes Me: One Man's Quest for a Leprosy-Free World (Nonfiction work) -- Sasakawa, Yohei -- Book reviews, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Ann Aerts lauds a taut account of a battle against an ancient disease. Ann Aerts lauds a taut account of a battle against an ancient disease., Author(s): Ann Aerts Author Affiliations: Leprosy: the world's oldest human-rights issue Leprosy survivor Nguyen Van Phuc at the Van Mon Leprosy hospice compound in Thai Binh, Vietnam. [see PDF for [...]

Published
2019
Full Text
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40. Do not discard Staphylococcus aureus WTA as a vaccine antigen

Author

Rob van Dalen, Jos A. G. van Strijp, Nina M. van Sorge, Kok P. M. van Kessel, Sara Ali, Michèle M. Molendijk, Jeroen D. C. Codée, Piet C. Aerts, and Carla J. C. de Haas

Subjects
Multidisciplinary, Chemistry, Staphylococcus aureus, medicine, Vaccine antigen, medicine.disease_cause, Microbiology
Published
2019

41. Safikhani et al. reply

Author

Safikhani, Zhaleh, El-Hachem, Nehme, Smirnov, Petr, Freeman, Mark, Goldenberg, Anna, Birkbak, Nicolai J., Beck, Andrew H., Aerts, Hugo J. W. L., Quackenbush, John, and Haibe-Kains, Benjamin

Subjects
Pharmaceutical research -- Methods, Pharmacogenomics -- Genetic aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Zhaleh Safikhani [1, 2]; Nehme El-Hachem [3]; Petr Smirnov [1]; Mark Freeman [1]; Anna Goldenberg [4, 5]; Nicolai J. Birkbak [6, 7]; Andrew H. Beck [8, 9]; Hugo J. [...]

Published
2016
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42. Safikhani et al. reply

Author

John Quackenbush, Petr Smirnov, Nehme El-Hachem, Benjamin Haibe-Kains, Anna Goldenberg, Mark Freeman, Nicolai Juul Birkbak, Zhaleh Safikhani, Andrew H. Beck, and Hugo J.W.L. Aerts

Subjects
0301 basic medicine, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Multidisciplinary, Systems biology, 030220 oncology & carcinogenesis, medicine, Cancer, Nanotechnology, Computational biology, Biology, medicine.disease
Published
2016

43. Consequences of biodiversity loss for litter decomposition across biomes

Author

Bernhard Schmid, Edwin T. H. M. Peeters, Brendan G. McKie, Stefan Scheu, Rien Aerts, Marika Makkonen, Veronique C. A. Vos, I. Tanya Handa, Jasper van Ruijven, Matty P. Berg, Mark O. Gessner, Eric Chauvet, Björn Malmqvist, Frank Berendse, Olaf Butenschoen, Andreas Bruder, Jérémy Jabiol, Stephan Hättenschwiler, University of Zurich, Hättenschwiler, Stephan, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Département des Sciences Biologiques, Université du Québec à Montréal = University of Québec in Montréal (UQAM), VU University Amsterdam, Nature Conservation and Plant Ecology Group, Wageningen University and Research [Wageningen] (WUR), Department of Aquatic Ecology, Swiss Federal institute of aquatic science and technology-IBZ, Institute of Integrative Biology IBZ, J. F. Blumenbach Institute of Zoology and Anthropology, Georg-August-University [Göttingen], Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin Institute of Technology, Finnish Environment Institute (SYKE), Department of Ecology and Environmental Science [Umeå], Umeå University, Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Wageningen University and Research Centre (WUR), Universität Zürich [Zürich] = University of Zurich (UZH), European Science Foundation (ESF) as part of the EUROCORES programme EuroDIVERSITY (BioCycle research project), Centre de Coopération Internationale en Recherche Agronomique - CIRAD (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Leibniz-Institut für Gewässerökologie und Binnenfischerei - IGB (GERMANY), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut de Recherche pour le Développement - IRD (FRANCE), Montpellier SupAgro (FRANCE), Finnish Environment Institute - SYKE (FINLAND), Technische Universität Berlin - TU Berlin (GERMANY), Umea University (SWEDEN), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université de Montpellier 1 (FRANCE), Université de Montpellier 2 (FRANCE), Université du Québec à Montréal - UQAM (CANADA), Wageningen University & Research - WUR (NETHERLANDS), Swiss Federal Institute of Aquatic Science and Technology - EAWAG (SWITZERLAND), Ecole Pratique des Hautes Etudes - EPHE (FRANCE), Georg-August-Universität Göttingen (GERMANY), Sveriges lantbruksuniversitet - SLU (SWEDEN), Eidgenössische Technische Hochschule Zürich - ETHZ (SWITZERLAND), Université de Montpellier 3 (FRANCE), Vrije University Amsterdam - VU (NETHERLANDS), Universität Zürich - UZH (SWITZERLAND), Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Systems Ecology, Animal Ecology, and Amsterdam Global Change Institute

Subjects
Nutrient cycle, Aquatic Ecology and Water Quality Management, services, species functional diversity, leaf-litter, Nitrogen, Biodiversité et Ecologie, Biodiversity, ta1171, Plant Ecology and Nature Conservation, Biology, Decomposer, Carbon Cycle, 10127 Institute of Evolutionary Biology and Environmental Studies, traits, Litter, Ecosystem, patterns, 14. Life underwater, Nitrogen cycle, climate, Ecologie, Environnement, Tropical Climate, 1000 Multidisciplinary, Multidisciplinary, WIMEK, Arctic Regions, Ecology, Aquatic ecosystem, Nitrogen Cycle, Plants, 15. Life on land, Plant litter, Aquatische Ecologie en Waterkwaliteitsbeheer, PE&RC, Carbon, 13. Climate action, Biodiversity loss, Plantenecologie en Natuurbeheer, 570 Life sciences, biology, 590 Animals (Zoology), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ecosystems
Abstract

The decomposition of dead organic matter is a major determinant of carbon and nutrient cycling in ecosystems, and of carbon fluxes between the biosphere and the atmosphere1, 2, 3. Decomposition is driven by a vast diversity of organisms that are structured in complex food webs2, 4. Identifying the mechanisms underlying the effects of biodiversity on decomposition is critical4, 5, 6 given the rapid loss of species worldwide and the effects of this loss on human well-being7, 8, 9. Yet despite comprehensive syntheses of studies on how biodiversity affects litter decomposition4, 5, 6, 10, key questions remain, including when, where and how biodiversity has a role and whether general patterns and mechanisms occur across ecosystems and different functional types of organism4, 9, 10, 11, 12. Here, in field experiments across five terrestrial and aquatic locations, ranging from the subarctic to the tropics, we show that reducing the functional diversity of decomposer organisms and plant litter types slowed the cycling of litter carbon and nitrogen. Moreover, we found evidence of nitrogen transfer from the litter of nitrogen-fixing plants to that of rapidly decomposing plants, but not between other plant functional types, highlighting that specific interactions in litter mixtures control carbon and nitrogen cycling during decomposition. The emergence of this general mechanism and the coherence of patterns across contrasting terrestrial and aquatic ecosystems suggest that biodiversity loss has consistent consequences for litter decomposition and the cycling of major elements on broad spatial scales.

Published
2014

44. Leprosy: the world’s oldest human-rights issue

Author

Ann Aerts

Subjects
0301 basic medicine, Multidisciplinary, History, Battle, Human rights, media_common.quotation_subject, Ancient history, medicine.disease, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, medicine, 030212 general & internal medicine, Leprosy, media_common
Abstract

Ann Aerts lauds a taut account of a battle against an ancient disease. Ann Aerts lauds a taut account of a battle against an ancient disease.

Published
2019

45. Erratum: Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Author

Abbosh, Christopher, primary, Birkbak, Nicolai J., additional, Wilson, Gareth A., additional, Jamal-Hanjani, Mariam, additional, Constantin, Tudor, additional, Salari, Raheleh, additional, Le Quesne, John, additional, Moore, David A., additional, Veeriah, Selvaraju, additional, Rosenthal, Rachel, additional, Marafioti, Teresa, additional, Kirkizlar, Eser, additional, Watkins, Thomas B. K., additional, McGranahan, Nicholas, additional, Ward, Sophia, additional, Martinson, Luke, additional, Riley, Joan, additional, Fraioli, Francesco, additional, Al Bakir, Maise, additional, Grönroos, Eva, additional, Zambrana, Francisco, additional, Endozo, Raymondo, additional, Bi, Wenya Linda, additional, Fennessy, Fiona M., additional, Sponer, Nicole, additional, Johnson, Diana, additional, Laycock, Joanne, additional, Shafi, Seema, additional, Czyzewska-Khan, Justyna, additional, Rowan, Andrew, additional, Chambers, Tim, additional, Matthews, Nik, additional, Turajlic, Samra, additional, Hiley, Crispin, additional, Lee, Siow Ming, additional, Forster, Martin D., additional, Ahmad, Tanya, additional, Falzon, Mary, additional, Borg, Elaine, additional, Lawrence, David, additional, Hayward, Martin, additional, Kolvekar, Shyam, additional, Panagiotopoulos, Nikolaos, additional, Janes, Sam M., additional, Thakrar, Ricky, additional, Ahmed, Asia, additional, Blackhall, Fiona, additional, Summers, Yvonne, additional, Hafez, Dina, additional, Naik, Ashwini, additional, Ganguly, Apratim, additional, Kareht, Stephanie, additional, Shah, Rajesh, additional, Joseph, Leena, additional, Quinn, Anne Marie, additional, Crosbie, Phil A., additional, Naidu, Babu, additional, Middleton, Gary, additional, Langman, Gerald, additional, Trotter, Simon, additional, Nicolson, Marianne, additional, Remmen, Hardy, additional, Kerr, Keith, additional, Chetty, Mahendran, additional, Gomersall, Lesley, additional, Fennell, Dean A., additional, Nakas, Apostolos, additional, Rathinam, Sridhar, additional, Anand, Girija, additional, Khan, Sajid, additional, Russell, Peter, additional, Ezhil, Veni, additional, Ismail, Babikir, additional, Irvin-Sellers, Melanie, additional, Prakash, Vineet, additional, Lester, Jason F., additional, Kornaszewska, Malgorzata, additional, Attanoos, Richard, additional, Adams, Haydn, additional, Davies, Helen, additional, Oukrif, Dahmane, additional, Akarca, Ayse U., additional, Hartley, John A., additional, Lowe, Helen L., additional, Lock, Sara, additional, Iles, Natasha, additional, Bell, Harriet, additional, Ngai, Yenting, additional, Elgar, Greg, additional, Szallasi, Zoltan, additional, Schwarz, Roland F., additional, Herrero, Javier, additional, Stewart, Aengus, additional, Quezada, Sergio A., additional, Peggs, Karl S., additional, Van Loo, Peter, additional, Dive, Caroline, additional, Lin, C. Jimmy, additional, Rabinowitz, Matthew, additional, Aerts, Hugo J. W. L., additional, Hackshaw, Allan, additional, Shaw, Jacqui A., additional, Zimmermann, Bernhard G., additional, and Swanton, Charles, additional

Published
2017
Full Text
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46. Erratum: Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Author

Martin Hayward, Jason F. Lester, Thomas B.K. Watkins, Selvaraju Veeriah, Joan K. Riley, Phil Crosbie, Tudor Constantin, Matthew Rabinowitz, Wenya Linda Bi, Karl S. Peggs, Nicholas McGranahan, Francisco Zambrana, Marianne Nicolson, Samra Turajlic, Gerald Langman, Raheleh Salari, Rajesh Shah, Simon Trotter, Malgorzata Kornaszewska, Bernhard Zimmermann, Hugo J.W.L. Aerts, Tanya Ahmad, Sridhar Rathinam, Siow Ming Lee, Ayse U. Akarca, Christopher Abbosh, Fiona H Blackhall, Dina Hafez, Nicolai Juul Birkbak, Peter Russell, David Moore, Lesley Gomersall, Nicole Sponer, Apostolos Nakas, Gareth A. Wilson, John A. Hartley, Melanie Irvin-Sellers, Sophia Ward, Veni Ezhil, Fiona M. Fennessy, Aengus Stewart, Anne Marie Quinn, Peter Van Loo, Eser Kirkizlar, Vineet Prakash, Tim Chambers, Zoltan Szallasi, Seema Shafi, Ricky Thakrar, Dahmane Oukrif, Sergio A. Quezada, Sajid A. Khan, Babu Naidu, Harriet Bell, Sam M. Janes, Mariam Jamal-Hanjani, Andrew N. Rowan, Mary Falzon, Asia Ahmed, Eva Grönroos, Justyna Czyzewska-Khan, Stephanie Kareht, Mahendran Chetty, Dean A. Fennell, Ashwini Naik, Helen Lowe, Roland F. Schwarz, Allan Hackshaw, Apratim Ganguly, Joanne Laycock, Crispin T. Hiley, Shyam Kolvekar, Elaine Borg, Yvonne Summers, Diana Johnson, Martin Forster, David Lawrence, Greg Elgar, Richard Attanoos, Keith M. Kerr, Charles Swanton, Rachel Rosenthal, Teresa Marafioti, Maise Al Bakir, Girija Anand, Hardy Remmen, Gary Middleton, Francesco Fraioli, Luke Martinson, Leena Dennis Joseph, C. Jimmy Lin, Natasha Iles, Yenting Ngai, Caroline Dive, Nikolaos Panagiotopoulos, Nik Matthews, Haydn Adams, John Le Quesne, Helen Davies, Jacqui Shaw, Sara Lock, Babikir Ismail, Javier Herrero, and Raymondo Endozo

Subjects
0301 basic medicine, Multidisciplinary, medicine.diagnostic_test, business.industry, Volumetric data, Computed tomography, medicine.disease, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Positron emission tomography, 030220 oncology & carcinogenesis, Medicine, Stage (cooking), business, Lung cancer, Nuclear medicine
Abstract

Nature 545, 446–451 (2017); doi:10.1038/nature22364 For 6 of the 96 patients included in this Article (patients CRUK0014, CRUK0030, CRUK0048, CRUK0059, CRUK0096 and CRUK0097) incorrect tumour volumetric data and positron emission tomography (PET) tumour background ratio (TBR) data were analysed. This error occurred because of the incorrect assignment of patient identifiers during the anonymization mandated by the independent review board of pre-operative computed tomography (CT) scans belonging to these patients.

Published
2017

47. The DNA sequence and comparative analysis of human chromosome 5

Author

Nancy Hammon, Arthur Kobayashi, Stacey Black, Uffe Hellsten, Daniel S. Rokhsar, Lauren Haydu, Frederick Lopez, Nina Thayer, Diego Martinez, Mirian Denys, Paul Predki, Laurie Gordon, Eva Bajorek, Eidelyn Gonzales, Catherine Medina, Richard D. Nandkeshwar, Sanjay Israni, Richard M. Myers, Hope Tice, Jean F. Challacombe, Anne O. Olsen, Chenier Caoile, State Lowry, Alex Rodriguez, Paul G. Richardson, Kevin Wu, D. Scott, Xinwei She, Matthew Groza, James P. Noonan, Anna Ustaszewska, María Laura Ríos Gómez, Jane Grimwood, Jeremy Wheeler, Len A. Pennacchio, Martin O. Pollard, Tijana Glavina, Dea Fotopulos, Joel Martin, Heather Kimbal, Kristen Kadner, Dave Flowers, Joan Yang, Astrid Terry, Lucía Ramírez, Ming Tsai, Yee Man Chan, Michael R. Altherr, Susan Lucas, Jan Fang Cheng, Sam Pitluck, Sam Rash, Igor V. Grigoriev, Wayne Huang, Yunian Lou, Chris Detter, Shyam Prabhakar, James Priest, Angelica Salazar, Gary Xie, Nu Vo, Elbert Branscomb, Jamie Jett, Stephanie Rogers, David Goodstenin, Olivier Couronne, Julio Escobar, James Retterer, Mary Bao Tran-Gyamfi, Trevor Hawkins, Jeremy Schmutz, Evan E. Eichler, Andrea Aerts, Mark Dickson, Jenna Morgan, Edward M. Rubin, and Asaf Salamov

Subjects
Pan troglodytes, Molecular Sequence Data, Biology, Synteny, Muscular Atrophy, Spinal, Complete sequence, Chromosome 15, Gene Duplication, Chromosome 19, Animals, Humans, Conserved Sequence, Chromosome 12, Genetics, Chromosome 7 (human), Base Composition, Multidisciplinary, Interleukins, Genetic Diseases, Inborn, Genomics, Sequence Analysis, DNA, Cadherins, Physical Chromosome Mapping, Chromosome 17 (human), Genes, Vertebrates, Chromosomes, Human, Pair 5, Chromosome 21, Pseudogenes
Abstract

Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

Published
2004

48. Mutations close in on gene regulation: a genome-wide analysis of DNA and RNA sequences, gene expression and DNA modifications in 200 samples of acute myeloid leukaemia sets the stage for data integration and verification that will enhance our understanding of this cancer

Author

Aerts, Stein and Cools, Jan

Subjects
Gene mutations -- Research, Nucleotide sequencing -- Research, RNA sequencing -- Research, DNA sequencing -- Research, Genetic regulation -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Acute myeloid leukaemia exhibits variable genetics, presentation and clinical outcome. Writing in the New England Journal of Medicine, Ley and colleagues (1) from the Cancer Genome Atlas Research Network present [...]

Published
2013

49. Melanoma addiction to the long non-coding RNA SAMMSON

Author

Marco Spinazzi, Stefan Van Aelst, Jo Vandesompele, Patrick Laurette, Jean-Christophe Marine, Irwin Davidson, Sven Eyckerman, Pieter Baatsen, Bart De Strooper, Jasper Wouters, Denis L. J. Lafontaine, Enrico Radaelli, Roberto Vendramin, Mark Fiers, Els Hermans, Katrien Vanderheyden, Carina Leonelli, Joost van den Oord, Eleonora Leucci, Stein Aerts, Aljosja Rogiers, Pieter Mestdagh, Kris Gevaert, Frédéric Amant, Other departments, Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), and Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Neuroblastoma RAS viral oncogene homolog, Carcinogenesis, Cell Survival, Mitochondrial translation, SOX10, Biology, Chromosomes, Mitochondrial Proteins, Mice, 03 medical and health sciences, melanoma, Gene Knockdown Techniques, Animals, Humans, Gene silencing, Cell Lineage, Molecular Targeted Therapy, Cell Proliferation, Microphthalmia-Associated Transcription Factor, Gene knockdown, Multidisciplinary, SOXE Transcription Factors, Gene Amplification, Oncogenes, Amplicon, Microphthalmia-associated transcription factor, Xenograft Model Antitumor Assays, Clone Cells, 3. Good health, mitochondria, 030104 developmental biology, Pair 3, Cancer research, RNA, Long Noncoding, Female, Mitogen-Activated Protein Kinases, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Human
Abstract

International audience; Focal amplifications of chromosome 3p13-3p14 occur in about 10% of melanomas and are associated with a poor prognosis. The melanoma-specific oncogene MITF resides at the epicentre of this amplicon. However, whether other loci present in this amplicon also contribute to melanomagenesis is unknown. Here we show that the recently annotated long non-coding RNA (lncRNA) gene SAMMSON is consistently co-gained with MITF. In addition, SAMMSON is a target of the lineage-specific transcription factor SOX10 and its expression is detectable in more than 90% of human melanomas. Whereas exogenous SAMMSON increases the clonogenic potential in trans, SAMMSON knockdown drastically decreases the viability of melanoma cells irrespective of their transcriptional cell state and BRAF, NRAS or TP53 mutational status. Moreover, SAMMSON targeting sensitizes melanoma to MAPK-targeting therapeutics both in vitro and in patient-derived xenograft models. Mechanistically, SAMMSON interacts with p32, a master regulator of mitochondrial homeostasis and metabolism, to increase its mitochondrial targeting and pro-oncogenic function. Our results indicate that silencing of the lineage addiction oncogene SAMMSON disrupts vital mitochondrial functions in a cancer-cell-specific manner; this silencing is therefore expected to deliver highly effective and tissue-restricted anti-melanoma therapeutic responses.

Published
2016

50. Origins and functional impact of copy number variation in the human genome

Author

Dalila Pinto, Daniel G. MacArthur, Yujun Zhang, Omer Gokcumen, Armand Valsesia, Ifejinelo Onyiah, Chris P. Barnes, Lars Feuk, Stephen W. Scherer, Andy Wing Chun Pang, Chun Hwa Ihm, K. Kristiansson, Chris Tyler-Smith, Donald F. Conrad, Samuel Robson, Jeffrey R. MacDonald, Matthew E. Hurles, Klaudia Walter, Min Hu, Peter J. Campbell, Nigel P. Carter, Kathy Stirrups, Tomas W Fitzgerald, T. Daniel Andrews, John Wei, Jan Aerts, Richard Redon, and Charles Lee

Subjects
Genetics, Linkage disequilibrium, Multidisciplinary, DNA Copy Number Variations, Genotype, Genome, Human, Racial Groups, Reproducibility of Results, Genomics, Single-nucleotide polymorphism, Biology, Genome, Polymorphism, Single Nucleotide, Article, Structural variation, Haplotypes, Mutagenesis, Gene Duplication, Humans, Human genome, Genetic Predisposition to Disease, Copy-number variation, Genetic association, Genome-Wide Association Study, Oligonucleotide Array Sequence Analysis
Abstract

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.

Published
2009

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