Centre intégratif de génomique

Equipe principale | CIG Services communs | Groupe Benton | Groupe Fajas | Groupe Fankhauser | Groupe Franken | Groupe Gambetta | Groupe Gatfield | Groupe Larsch | Groupe Michalik | Groupe Reymond | Groupe Roignant | Groupe van Leeuwen | Groupe Vastenhouw | Groupe Vjestica | Plateforme de biostatistique | Plateforme Genomics Technologies Facility (GTF) | Plateforme Protein Analysis Facility (PAF)
Publications | Mémoires et thèses

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118 publications

2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 |
2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Moore Jill E., Purcaro Michael J., Pratt Henry E., Epstein Charles B., Shoresh Noam, Adrian Jessika, Kawli Trupti, Davis Carrie A., Dobin Alexander, Kaul Rajinder et al., 2020/07/30. Nature, 583 (7818) pp. 699-710.
[URN][DOI][WoS][Pmid][serval:BIB_4061F4C51B0F]
Perspectives on ENCODE
Snyder Michael P., Gingeras Thomas R., Moore Jill E., Weng Zhiping, Gerstein Mark B., Ren Bing, Hardison Ross C., Stamatoyannopoulos John A., Graveley Brenton R., Feingold Elise A. et al., 2020/07/30. Nature, 583 (7818) pp. 693-698.
[URN][DOI][WoS][Pmid][serval:BIB_0CCC50FF7936]
2019
De novo splice site variant of ARID1B associated with pathogenesis of Coffin-Siris syndrome.
Pranckėnienė L., Siavrienė E., Gueneau L., Preikšaitienė E., Mikštienė V., Reymond A., Kučinskas V., 2019/12. Molecular genetics & genomic medicine, 7 (12) pp. e1006. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F17EED3A2B89]
 
Chromatin three-dimensional interactions mediate genetic effects on gene expression.
Delaneau O., Zazhytska M., Borel C., Giannuzzi G., Rey G., Howald C., Kumar S., Ongen H., Popadin K., Marbach D. et al., 2019/05/03. Science, 364 (6439). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_266A5EFF0381]
mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.
Kuzminkova A.A., Sokol A.D., Ushakova K.E., Popadin K.Y., Gunbin K.V., 2019/02/26. BMC evolutionary biology, 19 (Suppl 1) p. 47. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8A8C756E7D57]
GENCODE reference annotation for the human and mouse genomes.
Frankish A., Diekhans M., Ferreira A.M., Johnson R., Jungreis I., Loveland J., Mudge J.M., Sisu C., Wright J., Armstrong J. et al., 2019/01/08. Nucleic acids research, 47 (D1) pp. D766-D773. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FACD746C7F1B]
2018
 
Mutations in MAST1 Cause Mega-Corpus-Callosum Syndrome with Cerebellar Hypoplasia and Cortical Malformations.
Tripathy R., Leca I., van Dijk T., Weiss J., van Bon B.W., Sergaki M.C., Gstrein T., Breuss M., Tian G., Bahi-Buisson N. et al., 2018/12/19. Neuron, 100 (6) pp. 1354-1368.e5. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_769F69929167]
Quantifying the Effects of 16p11.2 Copy Number Variants on Brain Structure: A Multisite Genetic-First Study.
Martin-Brevet S., Rodríguez-Herreros B., Nielsen J.A., Moreau C., Modenato C., Maillard A.M., Pain A., Richetin S., Jønch A.E., Qureshi A.Y. et al., 2018/08/15. Biological psychiatry, 84 (4) pp. 253-264. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8964BF69CE74]
 
Inactivation of AMMECR1 is associated with growth, bone, and heart alterations.
Moysés-Oliveira M., Giannuzzi G., Fish R.J., Rosenfeld J.A., Petit F., Soares M.F., Kulikowski L.D., Di-Battista A., Zamariolli M., Xia F. et al., 2018/02. Human mutation, 39 (2) pp. 281-291. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_37F48FE8E1F9]
KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis.
Gueneau L., Fish R.J., Shamseldin H.E., Voisin N., Tran Mau-Them F., Preiksaitiene E., Monroe G.R., Lai A., Putoux A., Allias F. et al., 2018/01/04. American journal of human genetics, 102 (1) pp. 116-132. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D335250BB897]
Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection.
Popadin K., Peischl S., Garieri M., Sailani M.R., Letourneau A., Santoni F., Lukowski S.W., Bazykin G.A., Nikolaev S., Meyer D. et al., 2018. GenomeRresearch, 28 (1) pp. 1-10. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E72B848928F3]
2017
 
Low number of fixed somatic mutations in a long-lived oak tree.
Schmid-Siegert E., Sarkar N., Iseli C., Calderon S., Gouhier-Darimont C., Chrast J., Cattaneo P., Schütz F., Farinelli L., Pagni M. et al., 2017/12. Nature plants, 3 (12) pp. 926-929. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_66296D0251EE]
CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits.
Macé A., Tuke M.A., Deelen P., Kristiansson K., Mattsson H., Nõukas M., Sapkota Y., Schick U., Porcu E., Rüeger S. et al., 2017/09/29. Nature communications, 8 (1) p. 744. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_220FBAC01D96]
Bayesian association scan reveals loci associated with human lifespan and linked biomarkers.
McDaid A.F., Joshi P.K., Porcu E., Komljenovic A., Li H., Sorrentino V., Litovchenko M., Bevers RPJ, Rüeger S., Reymond A. et al., 2017/07/27. Nature communications, 8 p. 15842. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C06E0694F6CC]
Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis.
Gschwind A.R., Singh A., Certa U., Reymond A., Heckel T., 2017/02/10. BMC genomics, 18 (1) p. 144. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A87ECF2238E9]
 
A New Split Hand/Foot Malformation with Long Bone Deficiency Familial Case.
Fusco C., Nittis P., Alfaiz A.A., Pellico M.T., Augello B., Malerba N., Zelante L., Reymond A., Merla G., 2017. Journal of Pediatric Genetics, 6 (2) pp. 98-102. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1F039028AEE7]
 
Centromere Destiny in Dicentric Chromosomes: New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region.
Chiatante G., Giannuzzi G., Calabrese F.M., Eichler E.E., Ventura M., 2017. Molecular Biology and Evolution, 34 (7) pp. 1669-1681. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7CF2371C7D64]
Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes.
Loviglio M.N., Leleu M., Männik K., Passeggeri M., Giannuzzi G., van der Werf I., Waszak S.M., Zazhytska M., Roberts-Caldeira I., Gheldof N. et al., 2017. Molecular Psychiatry, 22 (6) pp. 836-849. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8773892CB036]
Data on the time of integration of the human mitochondrial pseudogenes (NUMTs) into the nuclear genome.
Gunbin K., Peshkin L., Popadin K., Annis S., Ackermann R.R., Khrapko K., 2017. Data in Brief, 13 pp. 536-544. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_60150EE17FE4]
 
Inflammatory myopathy in a patient with Aicardi-Goutières syndrome.
Tumienė B., Voisin N., Preikšaitienė E., Petroška D., Grikinienė J., Samaitienė R., Utkus A., Reymond A., Kučinskas V., 2017. European Journal of Medical Genetics, 60 (3) pp. 154-158. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0DE163527E7F]
 
Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis.
Gunbin K., Peshkin L., Popadin K., Annis S., Ackermann R.R., Khrapko K., 2017. Mitochondrion, 34 pp. 20-23. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_000458578A8F]
 
The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs.
Loviglio M.N., Arbogast T., Jønch A.E., Collins S.C., Popadin K., Bonnet C.S., Giannuzzi G., Maillard A.M., Jacquemont S., 16p11.2 Consortium et al., 2017. American Journal of Human Genetics, 101 (4) pp. 564-577. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_12249EC890B3]
2016
 
GNB5 Mutations Cause an Autosomal-Recessive Multisystem Syndrome with Sinus Bradycardia and Cognitive Disability.
Lodder E.M., De Nittis P., Koopman C.D., Wiszniewski W., Moura de Souza C.F., Lahrouchi N., Guex N., Napolioni V., Tessadori F., Beekman L. et al., 2016/09/01. American journal of human genetics, 99 (3) pp. 704-710. Peer-reviewed.
[DOI][Pmid][serval:BIB_764CB1E0F6D0]
 
Histomorphological Phenotyping of the Adult Mouse Brain.
Mikhaleva A., Kannan M., Wagner C., Yalcin B., 2016/09/01. Current protocols in mouse biology, 6 (3) pp. 307-332. Peer-reviewed.
[DOI][Pmid][serval:BIB_3410E4929B2B]
 
De novo PIK3R2 variant causes polymicrogyria, corpus callosum hyperplasia and focal cortical dysplasia.
Terrone G., Voisin N., Abdullah Alfaiz A., Cappuccio G., Vitiello G., Guex N., D'Amico A., James Barkovich A., Brunetti-Pierri N., Del Giudice E. et al., 2016/08. European journal of human genetics, 24 (9) pp. 1359-1362. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C9725B978C04]
The Number of Genomic Copies at the 16p11.2 Locus Modulates Language, Verbal Memory, and Inhibition.
Hippolyte L., Maillard A.M., Rodriguez-Herreros B., Pain A., Martin-Brevet S., Ferrari C., Conus P., Macé A., Hadjikhani N., Metspalu A. et al., 2016/07/15. Biological psychiatry, 80 (2) pp. 129-139. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9660DE6D30D1]
 
West syndrome caused by homozygous variant in the evolutionary conserved gene encoding the mitochondrial elongation factor GUF1.
Alfaiz A.A., Müller V., Boutry-Kryza N., Ville D., Guex N., de Bellescize J., Rivier C., Labalme A., des Portes V., Edery P. et al., 2016/07. European journal of human genetics, 24 (7) pp. 1001-1008. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_83BC90BB9FA1]
 
16p11.2 Locus modulates response to satiety before the onset of obesity.
Maillard A.M., Hippolyte L., Rodriguez-Herreros B., Chawner S.J., Dremmel D., Agüera Z., Fagundo A.B., Pain A., Martin-Brevet S., Hilbert A. et al., 2016/05. International journal of obesity, 40 (5) pp. 870-876. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_DF2B3B0B794D]
Defining the Effect of the 16p11.2 Duplication on Cognition, Behavior, and Medical Comorbidities.
D'Angelo D., Lebon S., Chen Q., Martin-Brevet S., Snyder L.G., Hippolyte L., Hanson E., Maillard A.M., Faucett W.A., Macé A. et al., 2016. Jama Psychiatry, 73 (1) pp. 20-30. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FA7E8A43283E]
Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.
Nuttle X., Giannuzzi G., Duyzend M.H., Schraiber J.G., Narvaiza I., Sudmant P.H., Penn O., Chiatante G., Malig M., Huddleston J. et al., 2016. Nature, 536 (7615) pp. 205-209. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_CFCA0FE3B0E4]
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).
Lagarde J., Uszczynska-Ratajczak B., Santoyo-Lopez J., Gonzalez J.M., Tapanari E., Mudge J.M., Steward C.A., Wilming L., Tanzer A., Howald C. et al., 2016. Nature Communications, 7 p. 12339. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C29EE3009EC0]
Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics.
Loviglio M.N., Beck C.R., White J.J., Leleu M., Harel T., Guex N., Niknejad A., Bi W., Chen E.S., Crespo I. et al., 2016. Genome medicine, 8 (1) p. 105. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_1820D72F7FFD]
 
Inter-varietal structural variation in grapevine genomes.
Cardone M.F., D'Addabbo P., Alkan C., Bergamini C., Catacchio C.R., Anaclerio F., Chiatante G., Marra A., Giannuzzi G., Perniola R. et al., 2016. Plant Journal, 88 (4) pp. 648-661. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_ECA973143A83]
Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes.
Arbogast T., Ouagazzal A.M., Chevalier C., Kopanitsa M., Afinowi N., Migliavacca E., Cowling B.S., Birling M.C., Champy M.F., Reymond A. et al., 2016. PLoS Genetics, 12 (2) pp. e1005709. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_58A2FB3CAFC8]
 
Reporting incidental findings of genomic disorder-associated copy number variants to unselected biobank participants
Leitsalu L., Alavere H., Jacquemont S., Kolk A., Maillard A.M., Reigo A., Noukas M., Reymond A., Mannik K., Ng P.C. et al., 2016. Personalized Medicine, 13 (4) pp. 303-314.
[DOI][WoS][serval:BIB_3FBCEB3A9F4A]
2015
The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity.
Maillard A.M., Ruef A., Pizzagalli F., Migliavacca E., Hippolyte L., Adaszewski S., Dukart J., Ferrari C., Conus P., Männik K. et al., 2015/02. Molecular psychiatry, 20 (1) pp. 140-147. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_02ADC1E92D32]
 
A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology.
Migliavacca E., Golzio C., Männik K., Blumenthal I., Oh E.C., Harewood L., Kosmicki J.A., Loviglio M.N., Giannuzzi G., Hippolyte L. et al., 2015. American Journal of Human Genetics, 96 (5) pp. 784-796.
[DOI][WoS][Pmid][serval:BIB_9689D2C97A3A]
BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies.
Borck G., Hög F., Dentici M.L., Tan P.L., Sowada N., Medeira A., Gueneau L., Thiele H., Kousi M., Lepri F. et al., 2015. Genome Research, 25 (2) pp. 155-166.
[URN][DOI][WoS][Pmid][serval:BIB_BFE1C03EAD4D]
Copy number variations and cognitive phenotypes in unselected populations
Männik K., Mägi R., Macé A., Cole B., Guyatt A.L., Shihab H.A., Maillard A.M., Alavere H., Kolk A., Reigo A. et al., 2015. Journal of the American Medical Association, 313 (20) pp. 2044-2054. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C20E4A2E4D67]
 
Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome.
Dikoglu E., Alfaiz A., Gorna M., Bertola D., Chae J.H., Cho T.J., Derbent M., Alanay Y., Guran T., Kim O.H. et al., 2015. American Journal of Medical Genetics. Part A, 167 (7) pp. 1501-1509. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5FC5887518A1]
 
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.
Waszak S.M., Delaneau O., Gschwind A.R., Kilpinen H., Raghav S.K., Witwicki R.M., Orioli A., Wiederkehr M., Panousis N.I., Yurovsky A. et al., 2015. Cell, 162 (5) pp. 1039-1050. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_563E43FC3C7F]
2014
16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy.
Reinthaler E.M., Lal D., Lebon S., Hildebrand M.S., Dahl H.H., Regan B.M., Feucht M., Steinböck H., Neophytou B., Ronen G.M. et al., 2014. Human Molecular Genetics, 23 (22) pp. 6069-6080. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_30D0F629E19F]
A genome-wide association study of anorexia nervosa.
Boraska V., Franklin C.S., Floyd J.A., Thornton L.M., Huckins L.M., Southam L., Rayner N.W., Tachmazidou I., Klump K.L., Treasure J. et al., 2014. Molecular Psychiatry, 19 (10) pp. 1085-1094. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EBE853EF2EB7]
Comparative analysis of the transcriptome across distant species.
Gerstein M.B., Rozowsky J., Yan K.K., Wang D., Cheng C., Brown J.B., Davis C.A., Hillier L., Sisu C., Li J.J. et al., 2014. Nature, 512 (7515) pp. 445-448. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FB6B68CC71D1]
Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals.
Gilardi F., Migliavacca E., Naldi A., Baruchet M., Canella D., Le Martelot G., Guex N., Desvergne B., CycliX Consortium, 2014. PLoS Genetics, 10 (3) pp. e1004155. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3BEC48D77E63]
Identification of Novel Craniofacial Regulatory Domains Located far Upstream of SOX9 and Disrupted in Pierre Robin Sequence.
Gordon C.T., Attanasio C., Bhatia S., Benko S., Ansari M., Tan T.Y., Munnich A., Pennacchio L.A., Abadie V., Temple I.K. et al., 2014. Human Mutation, 35 (8) pp. 1011-1020. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9CED07B2960E]
Identification of structural variation in mouse genomes.
Keane T.M., Wong K., Adams D.J., Flint J., Reymond A., Yalcin B., 2014. Frontiers in Genetics, 5 p. 192.
[URN][DOI][Pmid][serval:BIB_46C695F7B599]
Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures.
Giannuzzi G., Migliavacca E., Reymond A., 2014. Genome Research, 24 (9) pp. 1455-1468.
[URN][DOI][WoS][Pmid][serval:BIB_20CA18A8E573]
 
TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease.
Alfaiz A.A., Micale L., Mandriani B., Augello B., Pellico M.T., Chrast J., Xenarios I., Zelante L., Merla G., Reymond A., 2014. Human Mutation, 35 (4) pp. 447-451.
[DOI][WoS][Pmid][serval:BIB_4A2DD35BA4D5]
The effect of homozygous deletion of the BBOX1 and Fibin genes on carnitine level and acyl carnitine profile.
Rashidi-Nezhad A., Talebi S., Saebnouri H., Akrami S.M., Reymond A., 2014. BMC Medical Genetics, 15 p. 75.
[URN][DOI][WoS][Pmid][serval:BIB_4370352767FD]
2013
 
MLL2 mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study.
Makrythanasis P., van Bon B.W., Steehouwer M., Rodríguez-Santiago B., Simpson M., Dias P., Anderlid B.M., Arts P., Bhat M., Augello B. et al., 2013/12. Clinical genetics, 84 (6) pp. 539-545. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F7CFC1017987]
A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains.
Simon M.M., Greenaway S., White J.K., Fuchs H., Gailus-Durner V., Wells S., Sorg T., Wong K., Bedu E., Cartwright E.J. et al., 2013. Genome Biology, 14 (7) pp. R82. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_90419D2019AD]
Assessment of transcript reconstruction methods for RNA-seq.
Steijger T., Abril J.F., Engström P.G., Kokocinski F., RGASP Consortium, Abril J.F., Abril J.F., Akerman M., Alioto T., Ambrosini G. et al., 2013. Nature Methods, 10 (12) pp. 1177-1184.
[URN][DOI][WoS][Pmid][serval:BIB_63C268AABFEF]
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
Kilpinen H., Waszak S.M., Gschwind A.R., Raghav S.K., Witwicki R.M., Orioli A., Migliavacca E., Wiederkehr M., Gutierrez-Arcelus M., Panousis N.I. et al., 2013. Science, 342 (6159) pp. 744-747.
[URN][DOI][WoS][Pmid][serval:BIB_3B38B04B8D47]
Hominoid fission of chromosome 14/15 and the role of segmental duplications.
Giannuzzi G., Pazienza M., Huddleston J., Antonacci F., Malig M., Vives L., Eichler E.E., Ventura M., 2013. Genome Research, 23 (11) pp. 1763-1773.
[URN][DOI][WoS][Pmid][serval:BIB_4C035F54B0D4]
Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity.
Walters R.G., Coin L.J., Ruokonen A., de Smith A.J., El-Sayed Moustafa J.S., Jacquemont S., Elliott P., Esko T., Hartikainen A.L., Laitinen J. et al., 2013. Plos One, 8 (3) pp. e58048.
[URN][DOI][WoS][Pmid][serval:BIB_0257103FC0D5]
Structural variation-associated expression changes are paralleled by chromatin architecture modifications.
Gheldof N., Witwicki R.M., Migliavacca E., Leleu M., Didelot G., Harewood L., Rougemont J., Reymond A., 2013. PLoS One, 8 (11) pp. e79973.
[URN][DOI][WoS][Pmid][serval:BIB_71521CB25C1A]
2012
 
2q34-qter duplication and 4q34.2-qter deletion in a patient with developmental delay.
Rashidi-Nezhad A., Parvaneh N., Farzanfar F., Azimi C., Harewood L., Akrami S.M., Reymond A., 2012. European Journal of Medical Genetics, 55 (3) pp. 203-210.
[DOI][WoS][Pmid][serval:BIB_55DE5303DB73]
A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders.
Zufferey F., Sherr E.H., Beckmann N.D., Hanson E., Maillard A.M., Hippolyte L., Macé A., Ferrari C., Kutalik Z., Andrieux J. et al., 2012. Journal of Medical Genetics, 49 (10) pp. 660-668. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_26004E3F396F]
A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish.
Micale L., Loviglio M.N., Manzoni M., Fusco C., Augello B., Migliavacca E., Cotugno G., Monti E., Borsani G., Reymond A. et al., 2012. PLoS One, 7 (10) pp. e46642.
[URN][DOI][WoS][Pmid][serval:BIB_74278C65208B]
 
An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium, Dunham I., Dunham I., Kundaje A., Aldred S.F., Collins P.J., Davis C.A., Doyle F., Epstein C.B., Frietze S. et al., 2012. Nature, 489 (7414) pp. 57-74.
[DOI][WoS][Pmid][serval:BIB_BDE6E4FA454B]
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
Howald C., Tanzer A., Chrast J., Kokocinski F., Derrien T., Walters N., Gonzalez J.M., Frankish A., Aken B.L., Hourlier T. et al., 2012. Genome Research, 22 (9) pp. 1698-1710.
[URN][DOI][WoS][Pmid][serval:BIB_E1581D2AC4AD]
 
Detecting long-range chromatin interactions using the chromosome conformation capture sequencing (4C-seq) method.
Gheldof N., Leleu M., Noordermeer D., Rougemont J., Reymond A., 2012. Methods in Molecular Biology, 786 pp. 211-225.
[DOI][WoS][Pmid][serval:BIB_9482D7177BA4]
Evidence for transcript networks composed of chimeric RNAs in human cells.
Djebali S., Lagarde J., Kapranov P., Lacroix V., Borel C., Mudge J.M., Howald C., Foissac S., Ucla C., Chrast J. et al., 2012. PLoS One, 7 (1) pp. e28213.
[URN][DOI][WoS][Pmid][serval:BIB_09687AEE4DF5]
GENCODE: the reference human genome annotation for The ENCODE Project.
Harrow J., Frankish A., Gonzalez J.M., Tapanari E., Diekhans M., Kokocinski F., Aken B.L., Barrell D., Zadissa A., Searle S. et al., 2012. Genome Research, 22 (9) pp. 1760-1774.
[URN][DOI][WoS][Pmid][serval:BIB_60ACD7FC0F0C]
KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant.
Golzio C., Willer J., Talkowski M.E., Oh E.C., Taniguchi Y., Jacquemont S., Reymond A., Sun M., Sawa A., Gusella J.F. et al., 2012. Nature, 485 (7398) pp. 363-367.
[URN][DOI][WoS][Pmid][serval:BIB_FE45367483B8]
Landscape of transcription in human cells.
Djebali S., Davis C.A., Merkel A., Dobin A., Lassmann T., Mortazavi A., Tanzer A., Lagarde J., Lin W., Schlesinger F. et al., 2012. Nature, 489 (7414) pp. 101-108.
[URN][DOI][WoS][Pmid][serval:BIB_7207A3318E3D]
Multifocal epithelial tumors and field cancerization from loss of mesenchymal CSL signaling.
Hu B., Castillo E., Harewood L., Ostano P., Reymond A., Dummer R., Raffoul W., Hoetzenecker W., Hofbauer G.F., Dotto G.P., 2012. Cell, 149 (6) pp. 1207-1220. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C13437B7972C]
Next-generation sequencing of experimental mouse strains.
Yalcin B., Adams D.J., Flint J., Keane T.M., 2012. Mammalian Genome, 23 (9-10) pp. 490-498.
[URN][DOI][WoS][Pmid][serval:BIB_44BEB847113F]
 
Structural variation and its effect on expression.
Harewood L., Chaignat E., Reymond A., 2012. Methods in Molecular Biology, 838 pp. 173-186.
[DOI][WoS][Pmid][serval:BIB_D6EAA1BF22E4]
The E3-Ubiquitin Ligase TRIM50 Interacts with HDAC6 and p62, and Promotes the Sequestration and Clearance of Ubiquitinated Proteins into the Aggresome.
Fusco C., Micale L., Egorov M., Monti M., D'Addetta E.V., Augello B., Cozzolino F., Calcagnì A., Fontana A., Polishchuk R.S. et al., 2012. PLoS One, 7 (7) pp. e40440.
[URN][DOI][WoS][Pmid][serval:BIB_6BC9845695E4]
The fine-scale architecture of structural variants in 17 mouse genomes.
Yalcin B., Wong K., Bhomra A., Goodson M., Keane T.M., Adams D.J., Flint J., 2012. Genome Biology, 13 (3) pp. R18.
[URN][DOI][WoS][Pmid][serval:BIB_2D73F306FA68]
The GENCODE pseudogene resource.
Pei B., Sisu C., Frankish A., Howald C., Habegger L., Mu X.J., Harte R., Balasubramanian S., Tanzer A., Diekhans M. et al., 2012. Genome Biology, 13 (9) pp. R51.
[URN][DOI][WoS][Pmid][serval:BIB_C74B18C4594F]
2011
A high-resolution anatomical atlas of the transcriptome in the mouse embryo.
Diez-Roux G., Banfi S., Sultan M., Geffers L., Anand S., Rozado D., Magen A., Canidio E., Pagani M., Peluso I. et al., 2011. PLoS Biology, 9 (1) pp. e1000582.
[URN][DOI][WoS][Pmid][serval:BIB_F3EE1FDA19D6]
 
A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium, 2011. Plos Biology, 9 (4) pp. e1001046.
[DOI][WoS][Pmid][serval:BIB_7651C0505F00]
 
Copy number variation modifies expression time courses.
Chaignat E., Yahya-Graison E.A., Henrichsen C.N., Chrast J., Schütz F., Pradervand S., Reymond A., 2011. Genome Research, 21 (1) pp. 106-113.
[DOI][WoS][Pmid][serval:BIB_F86987ABB7C7]
Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus.
Jacquemont S., Reymond A., Zufferey F., Harewood L., Walters R.G., Kutalik Z., Martinet D., Shen Y., Valsesia A., Beckmann N.D. et al., 2011. Nature, 478 (7367) pp. 97-102.
[URN][DOI][WoS][Pmid][serval:BIB_9700E363D9A2]
Mutation spectrum of MLL2 in a cohort of Kabuki syndrome patients.
Micale L., Augello B., Fusco C., Selicorni A., Loviglio M.N., Silengo M.C., Reymond A., Gumiero B., Zucchetti F., D'Addetta E.V. et al., 2011. Orphanet Journal of Rare Diseases, 6 (1) p. 38.
[URN][DOI][WoS][Pmid][serval:BIB_819A054F1309]
The origins, evolution, and functional potential of alternative splicing in vertebrates.
Mudge J.M., Frankish A., Fernandez-Banet J., Alioto T., Derrien T., Howald C., Reymond A., Guigó R., Hubbard T., Harrow J., 2011. Molecular Biology and Evolution, 28 (10) pp. 2949-2959.
[URN][DOI][WoS][Pmid][serval:BIB_F668C73CF97F]
Using transcription modules to identify expression clusters perturbed in Williams-Beuren syndrome.
Henrichsen C.N., Csárdi G., Zabot M.T., Fusco C., Bergmann S., Merla G., Reymond A., 2011. PLoS Computational Biology, 7 (1) pp. e1001054. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BAF4351682CD]
2010
A new highly penetrant form of obesity due to deletions on chromosome 16p11.2.
Walters R.G., Jacquemont S., Valsesia A., de Smith A.J., Martinet D., Andersson J., Falchi M., Chen F., Andrieux J., Lobbens S. et al., 2010/02/04. Nature, 463 (7281) pp. 671-675. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_779A2B29ACBA]
 
A t(7;12) balanced translocation with breakpoints overlapping those of the Williams-Beuren and 12q14 microdeletion syndromes.
Gimelli S., Chrast J., Baban A., Henrichsen C.N., Lerone M., Zuffardi O., Gimelli G., Reymond A., 2010. American Journal of Medical Genetics. Part A, 152A (5) pp. 1285-1294. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_078F653B401C]
 
An atypical 7q11.23 deletion in a normal IQ Williams-Beuren syndrome patient.
Ferrero G.B., Howald C., Micale L., Biamino E., Augello B., Fusco C., Turturo M.G., Forzano S., Reymond A., Merla G., 2010. European Journal of Human Genetics, 18 (1) pp. 33-38. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0141A423D0A6]
Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models.
Ricard G., Molina J., Chrast J., Gu W., Gheldof N., Pradervand S., Schütz F., Young J.I., Lupski J.R., Reymond A. et al., 2010. PLoS Biology, 8 (11) pp. e1000543. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_034A965C3133]
 
The effect of translocation-induced nuclear reorganization on gene expression.
Harewood L., Schütz F., Boyle S., Perry P., Delorenzi M., Bickmore W.A., Reymond A., 2010. Genome Research, 20 (5) pp. 554-564. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_38609FB2657D]
2009
Copy number variants, diseases and gene expression.
Henrichsen C.N., Chaignat E., Reymond A., 2009. Human Molecular Genetics, 18 (R1) pp. R1-R8. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DA076768B7BD]
Identifying protein-coding genes in genomic sequences.
Harrow J., Nagy A., Reymond A., Alioto T., Patthy L., Antonarakis S.E., Guigó R., 2009. Genome biology, 10 (1) p. 201. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_69A902D4D75D]
 
Segmental copy number variation shapes tissue transcriptomes.
Henrichsen C.N., Vinckenbosch N., Zöllner S., Chaignat E., Pradervand S., Schütz F., Ruedi M., Kaessmann H., Reymond A., 2009. Nature Genetics, 41 (4) pp. 424-429. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6CF6E18F8771]
 
The genome sequence of taurine cattle: a window to ruminant biology and evolution.
Bovine Genome Sequencing, Analysis Consortium, Elsik C.G., Tellam R.L., Worley K.C., Gibbs R.A., Muzny D.M., Weinstock G.M., Adelson D.L., Eichler E.E. et al., 2009. Science, 324 (5926) pp. 522-528. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EE8C1C9D9ECA]
Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls.
Makrythanasis P., Kapranov P., Bartoloni L., Reymond A., Deutsch S., Guigó R., Denoeud F., Drenkow J., Rossier C., Ariani F. et al., 2009. Human Mutation, 30 (9) pp. E866-E879. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_18732BEDBC91]
2008
Efficient targeted transcript discovery via array-based normalization of RACE libraries.
Djebali S., Kapranov P., Foissac S., Lagarde J., Reymond A., Ucla C., Wyss C., Drenkow J., Dumais E., Murray R.R. et al., 2008/07. Nature methods, 5 (7) pp. 629-635. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E3CD1DDFA801]
Abnormal social behaviors and altered gene expression rates in a mouse model for Potocki-Lupski syndrome.
Molina J., Carmona-Mora P., Chrast J., Krall P.M., Canales C.P., Lupski J.R., Reymond A., Walz K., 2008. Human Molecular Genetics, 17 (16) pp. 2486-2495. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FA3FDDAE1B36]
Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.
Attanasio C., Reymond A., Humbert R., Lyle R., Kuehn M.S., Neph S., Sabo P.J., Goldy J., Weaver M., Haydock A. et al., 2008. Genome biology, 9 (12) pp. R168. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6836FD75BA2C]
 
Infantile spasms is associated with deletion of the MAGI2 gene on chromosome 7q11.23-q21.11.
Marshall C.R., Young E.J., Pani A.M., Freckmann M.L., Lacassie Y., Howald C., Fitzgerald K.K., Peippo M., Morris C.A., Shane K. et al., 2008. American Journal of Human Genetics, 83 (1) pp. 106-111. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_74562E3FC31E]
Williams-Beuren syndrome TRIM50 encodes an E3 ubiquitin ligase.
Micale L., Fusco C., Augello B., Napolitano L.M., Dermitzakis E.T., Meroni G., Merla G., Reymond A., 2008. European Journal of Human Genetics, 16 (9) pp. 1038-1049. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C1B799B255F6]
2007
 
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Birney E., Stamatoyannopoulos J.A., Dutta A., Guigó R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., Thurman R.E. et al., 2007. Nature, 447 (7146) pp. 799-816. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1573FA50DE7C]
 
Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.
Lyle R., Prandini P., Osoegawa K., ten Hallers B., Humphray S., Zhu B., Eyras E., Castelo R., Bird C.P., Gagos S. et al., 2007. Genome Research, 17 (11) pp. 1690-1696. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C82AA61E8100]
 
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
Denoeud F., Kapranov P., Ucla C., Frankish A., Castelo R., Drenkow J., Lagarde J., Alioto T., Manzano C., Chrast J. et al., 2007. Genome Research, 17 (6) pp. 746-759. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_9E222586D534]
 
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Zheng D., Frankish A., Baertsch R., Kapranov P., Reymond A., Choo S.W., Lu Y., Denoeud F., Antonarakis S.E., Snyder M. et al., 2007. Genome Research, 17 (6) pp. 839-851. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C4C798041F92]
 
Side effects of genome structural changes.
Reymond A., Henrichsen C.N., Harewood L., Merla G., 2007. Current Opinion in Genetics and Development, 17 (5) pp. 381-386. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_014762682E1E]
 
Structured RNAs in the ENCODE selected regions of the human genome.
Washietl S., Pedersen J.S., Korbel J.O., Stocsits C., Gruber A.R., Hackermüller J., Hertel J., Lindemeyer M., Reiche K., Tanzer A. et al., 2007. Genome Research, 17 (6) pp. 852-864. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0AC27ED2CF2C]
 
The implications of alternative splicing in the ENCODE protein complement.
Tress M.L., Martelli P.L., Frankish A., Reeves G.A., Wesselink J.J., Yeats C., Olason P.I., Albrecht M., Hegyi H., Giorgetti A. et al., 2007. Proceedings of the National Academy of Sciences of the United States of America, 104 (13) pp. 5495-5500. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_8C90D5BA1A30]
2006
 
Chromosome 21, Disorders
Deutsch S., Antonarakis S., Reymond A., 2006. pp. 280-287 dans Ganten D., Ruckpaul K. (eds.) Encyclopedic reference of genomics and proteomics in molecular medicine, Springer.
[DOI][serval:BIB_0F3347D3ABCA]
EGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó R., Flicek P., Abril J.F., Reymond A., Lagarde J., Denoeud F., Antonarakis S., Ashburner M., Bajic V.B., Birney E. et al., 2006. Genome Biology, 7 Suppl 1 pp. S2.1-S231. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9B8BEDF24C37]
GENCODE: producing a reference annotation for ENCODE.
Harrow J., Denoeud F., Frankish A., Reymond A., Chen C.K., Chrast J., Lagarde J., Gilbert J.G., Storey R., Swarbreck D. et al., 2006. Genome Biology, 7 Suppl 1 pp. S4.1-S4.9. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F594806247A7]
 
Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes.
Merla G., Howald C., Henrichsen C.N., Lyle R., Wyss C., Zabot M.T., Antonarakis S.E., Reymond A., 2006. American Journal of Human Genetics, 79 (2) pp. 332-341. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_A78B3DE949B3]
 
Tandem chimerism as a means to increase protein complexity in the human genome.
Parra G., Reymond A., Dabbouseh N., Dermitzakis E.T., Castelo R., Thomson T.M., Antonarakis S.E., Guigó R., 2006. Genome Research, 16 (1) pp. 37-44.
[DOI][WoS][Pmid][serval:BIB_E801FA5E75F1]
The future is genome-wide.
Deutsch S., Reymond A., 2006. Genome Biology, 7 (8) p. 324.
[URN][DOI][WoS][Pmid][serval:BIB_4689B3FAB725]
 
Two high throughput technologies to detect segmental aneuploidies identify new Williams-Beuren syndrome patients with atypical deletions.
Howald C., Merla G., Digilio M.C., Amenta S., Lyle R., Deutsch S., Choudhury U., Bottani A., Antonarakis S.E., Fryssira H. et al., 2006. Journal of Medical Genetics, 43 (3) pp. 266-273. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AE9A3A0EBEFA]
2005
 
A novel TMPRSS3 missense mutation in a DFNB8/10 family prevents proteolytic activation of the protein.
Wattenhofer M., Sahin-Calapoglu N., Andreasen D., Kalay E., Caylan R., Braillard B., Fowler-Jaeger N., Reymond A., Rossier B.C., Karaguzel A. et al., 2005. Human Genetics, 117 (6) pp. 528-535. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FFEE7EE86CAA]
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.
Castelo R., Reymond A., Wyss C., Câmara F., Parra G., Antonarakis S.E., Guigó R., Eyras E., 2005. Nucleic Acids Research, 33 (6) pp. 1935-1939.
[URN][DOI][WoS][Pmid][serval:BIB_969A35C25E60]
 
Conserved non-genic sequences - an unexpected feature of mammalian genomes.
Dermitzakis E.T., Reymond A., Antonarakis S.E., 2005. Nature Reviews. Genetics, 6 (2) pp. 151-157. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_25C9FD53BD1D]
Emergence of young human genes after a burst of retroposition in primates.
Marques A.C., Dupanloup I., Vinckenbosch N., Reymond A., Kaessmann H., 2005. Plos Biology, 3 (11) pp. e357. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_42F38774BBD8]
Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.
Bonafé L., Dermitzakis E.T., Unger S., Greenberg C.R., Campos-Xavier B.A., Zankl A., Ucla C., Antonarakis S.E., Superti-Furga A., Reymond A., 2005. Plos Genetics, 1 (4) pp. e47. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_CC6ABC66BB92]
Gene finding in the chicken genome.
Eyras E., Reymond A., Castelo R., Bye J.M., Camara F., Flicek P., Huckle E.J., Parra G., Shteynberg D.D., Wyss C. et al., 2005. BMC Bioinformatics, 6 p. 131. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_35142]
 
How pathogenic is the p.D104N/endostatin polymorphic allele of COL18A1 in Knobloch syndrome? Reply
Antonarakis SE, Reymond A, Menzel O, Bekkeheien RC, Fukai N, Boye E, Kosztolanyi G, Aftimos S, Deutsch S, Scott HS et al., 2005. Human Mutation, 25 (3) pp. 316-316.
[DOI][WoS][serval:BIB_35138]
2004
 
Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.
Dermitzakis E.T., Kirkness E., Schwarz S., Birney E., Reymond A., Antonarakis S.E., 2004. Genome Research, 14 (5) pp. 852-859. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_7C2FEB973B83]
 
The ENCODE (ENCyclopedia Of DNA Elements) Project.
ENCODE Project Consortium, Reymond Alexandre, 2004. Science, 306 (5696) pp. 636-640.
[DOI][WoS][Pmid][serval:BIB_33406]
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