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247 results on '"Rougemont J"'

1. Feature extraction and signal processing for nylon DNA microarrays

Author

Bertucci F, Loï L, Bourgeois A, Loriod B, Rougemont J, Lopez F, Hingamp P, Houlgatte R, and Granjeaud S

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background High-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature location or in signal integration methodology may be a significant contribution to the observed variance in gene expression levels. Results We explore sources of variability in feature extraction from DNA microarrays on Nylon membrane with radioactive detection. We introduce a mathematical model of the signal emission and derive methods for correcting biases such as overshining, saturation or variation in probe amount. We also provide a quality metric which can be used qualitatively to flag weak or untrusted signals or quantitatively to modulate the weight of each experiment or gene in higher level analyses (clustering or discriminant analysis). Conclusions Our novel feature extraction methodology, based on a mathematical model of the radioactive emission, reduces variability due to saturation, neighbourhood effects and variable probe amount. Furthermore, we provide a fully automatic feature extraction software, BZScan, which implements the algorithms described in this paper.

Published
2004
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2. Dynamics of kinks in the Ginzburg-Landau equation: Approach to a metastable shape and collapse of embedded pairs of kinks

Author

Rougemont, J.

Subjects
Nonlinear Sciences - Pattern Formation and Solitons
Abstract

We consider initial data for the real Ginzburg-Landau equation having two widely separated zeros. We require these initial conditions to be locally close to a stationary solution (the ``kink'' solution) except for a perturbation supported in a small interval between the two kinks. We show that such a perturbation vanishes on a time scale much shorter than the time scale for the motion of the kinks. The consequences of this bound, in the context of earlier studies of the dynamics of kinks in the Ginzburg-Landau equation, [ER], are as follows: we consider initial conditions $v_0$ whose restriction to a bounded interval $I$ have several zeros, not too regularly spaced, and other zeros of $v_0$ are very far from $I$. We show that all these zeros eventually disappear by colliding with each other. This relaxation process is very slow: it takes a time of order exponential of the length of $I$.

Published
1998
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3. Coarsening by Ginzburg-Landau Dynamics

Author

Eckmann, J. -P. and Rougemont, J.

Subjects
Nonlinear Sciences - Chaotic Dynamics
Abstract

We study slowly moving solutions of the real Ginzburg-Landau equation on the line, by a method due to J. Carr and R.L. Pego. These are functions taking alternately positive or negative values on large intervals. A consequence of our approach is that we can propose a rigorous derivation of a stochastic model of coarsening by successive elimination of the smallest interval, which was described in earlier work by A.J. Bray, B. Derrida and C. Godr\`eche., Comment: 30 pages, TeX + postscript figures

Published
1997
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7. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Author

Loviglio MN, Leleu M, Männik K, Passeggeri M, Giannuzzi G, van der Werf I, Waszak SM, Zazhytska M, Roberts-Caldeira I, Gheldof N, Migliavacca E, Alfaiz AA, Hippolyte L, Maillard AM, 2p15 Consortium, 16p112 Consortium, Merla G, Van Dijck A, Kooy RF, Sanlaville D, Rosenfeld JA, Shaffer LG, Andrieux J, Marshall C, Scherer SW, Shen Y, Gusella JF, Thorsteinsdottir U, Thorleifsson G, Dermitzakis ET, Deplancke B, Beckmann JS, Rougemont J, Jacquemont S, Reymond A, Loviglio, Mn, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, van der Werf, I, Waszak, Sm, Zazhytska, M, Roberts-Caldeira, I, Gheldof, N, Migliavacca, E, Alfaiz, Aa, Hippolyte, L, Maillard, Am, 2p15, Consortium, 16p112, Consortium, Merla, G, Van Dijck, A, Kooy, Rf, Sanlaville, D, Rosenfeld, Ja, Shaffer, Lg, Andrieux, J, Marshall, C, Scherer, Sw, Shen, Y, Gusella, Jf, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, Et, Deplancke, B, Beckmann, J, Rougemont, J, Jacquemont, S, and Reymond, A

Abstract

Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.

Published
2017

8. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Author

Loviglio, M.N., Leleu, M., Mannik, K., Passeggeri, M., Giannuzzi, G., Werf, I. van der, Waszak, S.M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Hippolyte, L., Maillard, A.M., Dijck, A. Van, Kooy, R.F., Sanlaville, D., Rosenfeld, J.A., Shaffer, L.G., Andrieux, J., Marshall, C., Scherer, S.W., Shen, Y., Gusella, J.F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E.T., Deplancke, B., Beckmann, J.S., Rougemont, J., Jacquemont, S., Reymond, A., Vulto-van Silfhout, A.T., Schouten, M.I., Pfundt, R.P., Leeuw, N. de, et al., Loviglio, M.N., Leleu, M., Mannik, K., Passeggeri, M., Giannuzzi, G., Werf, I. van der, Waszak, S.M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Hippolyte, L., Maillard, A.M., Dijck, A. Van, Kooy, R.F., Sanlaville, D., Rosenfeld, J.A., Shaffer, L.G., Andrieux, J., Marshall, C., Scherer, S.W., Shen, Y., Gusella, J.F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E.T., Deplancke, B., Beckmann, J.S., Rougemont, J., Jacquemont, S., Reymond, A., Vulto-van Silfhout, A.T., Schouten, M.I., Pfundt, R.P., Leeuw, N. de, and et al.

Abstract

Contains fulltext : 174530.pdf (publisher's version ) (Open Access), Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.

Published
2017

9. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Author

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., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., Zollino, Marcella, Van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., Zollino, M. (ORCID:0000-0003-4871-9519), 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., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., Zollino, Marcella, Van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., and Zollino, M. (ORCID:0000-0003-4871-9519)

Abstract

Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.

Published
2017

10. Does the Pressure-Volume Relationship Exist?

Author

Benabid, A. L., de Rougemont, J., Chirossel, J. P., Barge, M., Shulman, Kenneth, editor, Marmarou, Anthony, editor, Miller, J. Douglas, editor, Becker, Donald P., editor, Hochwald, Gerald M., editor, and Brock, Mario, editor

Published
1980
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13. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Author

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., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., Collaborators: Loviglio MN, Männik, K, van der Werf, I, Giannuzzi, G, Zazhytska, M, Gheldof, N, Migliavacca, E, Alfaiz, Aa, Roberts Caldeira, I, Hippolyte, L, Maillard, Am, Ferrarini, A, Butschi, Fn, Conrad, B, Addor, Mc, Belfiore, M, Roetzer, K, Dijck, Av, Blaumeiser, B, Kooy, F, Roelens, F, Dheedene, A, Chiaie, Bd, Menten, B, Oostra, A, Caberg, Jh, Carter, M, Kellam, B, Stavropoulos, Dj, Marshall, C, Scherer, Sw, Weksberg, R, Cytrynbaum, C, Bassett, A, Lowther, C, Gillis, J, Mackay, S, Bache, I, Ousager, Lb, Smerdel, Mp, Graakjaer, J, Kjaergaard, S, Metspalu, A, Mathieu, M, Bonneau, D, Guichet, A, Parent, P, Férec, C, Gerard, M, Plessis, G, Lespinasse, J, Masurel, A, Marle, N, Faivre, L, Callier, P, Layet, V, Meur, Nl, Le Goff, C, Duban Bedu, B, Sukno, S, Boute, O, Andrieux, J, Blanchet, P, Geneviève, D, Puechberty, J, Schneider, A, Leheup, B, Jonveaux, P, Mercier, S, David, A, Le Caignec, C, de Pontual, L, Pipiras, E, Jacquette, A, Keren, B, Gilbert Dussardier, B, Bilan, F, Goldenberg, A, Chambon, P, Toutain, A, Till, M, Sanlaville, D, Leube, B, Royer Pokora, B, Grabe, Hj, Schmidt, Co, Schurmann, C, Homuth, G, Thorleifsson, G, Thorsteinsdottir, U, Bernardini, L, Novelli, A, Micale, L, Merla, G, Zollino, M, Mari, Francesca, Rizzo, Cl, Renieri, Alessandra, Silengo, M, Vulto van Silfhout AT, Schouten, M, Pfundt, R, de Leeuw, N, Vansenne, F, Maas, Sm, Barge Schaapveld DQ, Knegt, Ac, Stadheim, B, Rodningen, O, Houge, G, Price, S, Hawkes, L, Campbell, C, Kini, U, Vogt, J, Walters, R, Blakemore, A, Gusella, Jf, Shen, Y, Scott, D, Bacino, Ca, Tsuchiya, K, Ladda, R, Sell, S, Asamoah, A, Hamati, Ai, Rosenfeld, Ja, Shaffer, Lg, Mitchell, E, Hodge, Jc, Beckmann, Js, Jacquemont, S, Reymond, A, Ewans, Lj, Mowat, D, Walker, J, Amor, Dj, Esch, Hv, Leroy, P, Bamforth, Js, Babu, D, Isidor, B, Didonato, N, Hackmann, K, Passeggeri, M, Haeringen, Av, Smith, R, Ellingwood, S, Farber, Dm, Puri, V, Zadeh, N, Weaver, Dd, Miller, M, Wilks, T, Jorgez, Cj, Lafayette, D, Blaumeiser, Bettina, 2p15 Consortium, 16p11.2 Consortium, Loviglio, M.N., Männik, K., van der Werf, I., Giannuzzi, G., Zazhytska, M., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Roberts-Caldeira, I., Hippolyte, L., Maillard, A.M., Ferrarini, A., Butschi, F.N., Conrad, B., Addor, M.C., Belfiore, M., Roetzer, K., Dijck, A.V., Blaumeiser, B., Kooy, F., Roelens, F., Dheedene, A., Chiaie, B.D., Menten, B., Oostra, A., Caberg, J.H., Carter, M., Kellam, B., Stavropoulos, D.J., Marshall, C., Scherer, S.W., Weksberg, R., Cytrynbaum, C., Bassett, A., Lowther, C., Gillis, J., MacKay, S., Bache, I., Ousager, L.B., Smerdel, M.P., Graakjaer, J., Kjaergaard, S., Metspalu, A., Mathieu, M., Bonneau, D., Guichet, A., Parent, P., Férec, C., Gerard, M., Plessis, G., Lespinasse, J., Masurel, A., Marle, N., Faivre, L., Callier, P., Layet, V., Meur, N.L., Le Goff, C., Duban-Bedu, B., Sukno, S., Boute, O., Andrieux, J., Blanchet, P., Geneviève, D., Puechberty, J., Schneider, A., Leheup, B., Jonveaux, P., Mercier, S., David, A., Le Caignec, C., de Pontual, L., Pipiras, E., Jacquette, A., Keren, B., Gilbert-Dussardier, B., Bilan, F., Goldenberg, A., Chambon, P., Toutain, A., Till, M., Sanlaville, D., Leube, B., Royer-Pokora, B., Grabe, H.J., Schmidt, C.O., Schurmann, C., Homuth, G., Thorleifsson, G., Thorsteinsdottir, U., Bernardini, L., Novelli, A., Micale, L., Merla, G., Zollino, M., Mari, F., Rizzo, C.L., Renieri, A., Silengo, M., Vulto-van Silfhout, A.T., Schouten, M., Pfundt, R., de Leeuw, N., Vansenne, F., Maas, S.M., Barge-Schaapveld, D.Q., Knegt, A.C., Stadheim, B., Rodningen, O., Houge, G., Price, S., Hawkes, L., Campbell, C., Kini, U., Vogt, J., Walters, R., Blakemore, A., Gusella, J.F., Shen, Y., Scott, D., Bacino, C.A., Tsuchiya, K., Ladda, R., Sell, S., Asamoah, A., Hamati, A.I., Rosenfeld, J.A., Shaffer, L.G., Mitchell, E., Hodge, J.C., Beckmann, J.S., Jacquemont, S., Reymond, A., Ewans, L.J., Mowat, D., Walker, J., Amor, D.J., Esch, H.V., Leroy, P., Bamforth, J.S., Babu, D., Isidor, B., DiDonato, N., Hackmann, K., Passeggeri, M., Haeringen, A.V., Smith, R., Ellingwood, S., Farber, D.M., Puri, V., Zadeh, N., Weaver, D.D., Miller, M., Wilks, T., Jorgez, C.J., Lafayette, D., Other departments, and Human Genetics

Subjects
0301 basic medicine, Male, Microcephaly, Autism Spectrum Disorder, Obesity/genetics, Settore MED/03 - GENETICA MEDICA, Body Mass Index, Microcephaly/genetics, Gene duplication, Chromosome Duplication, ddc:576.5, Copy-number variation, Child, In Situ Hybridization, In Situ Hybridization, Fluorescence, Genetics, medicine.diagnostic_test, Chromosome Mapping, Middle Aged, Phenotype, Chromatin, Chemistry, Psychiatry and Mental Health, Child, Preschool, Female, Original Article, Chromosomes, Human, Pair 16/genetics, Megalencephaly/genetics, Chromosome Deletion, Autistic Disorder/genetics, Molecular Biology, Cellular and Molecular Neuroscience, Human, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Adult, Adolescent, DNA Copy Number Variations, Locus (genetics), DNA Copy Number Variations/genetics, Biology, Aged, Autistic Disorder, Chromosomes, Human, Pair 16, Humans, Infant, Intellectual Disability, Megalencephaly, Obesity, Chromosomes, Fluorescence, Chromatin/metabolism, 03 medical and health sciences, medicine, Preschool, Gene, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Pair 16, medicine.disease, Intellectual Disability/genetics, Autism Spectrum Disorder/genetics, 030104 developmental biology, Human medicine, Chromosome Mapping/methods, Fluorescence in situ hybridization
Abstract

Contains fulltext : 174530.pdf (Publisher’s version ) (Open Access) Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.

Published
2015

14. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

Author

Bultet, LA, Aguilar-Rodriguez, J, Ahrens, CH, Ahrne, EL, Ai, N, Aimo, L, Akalin, A, Aleksiev, T, Alocci, D, Altenhoff, A, Alves, I, Ambrosini, G, Pedone, PA, Angelina, P, Anisimova, M, Appel, R, Argoud-Puy, G, Arnold, K, Arpat, B, Artimo, P, Ascencao, K, Auchincloss, A, Axelsen, K, Gerritsen, VB, Bairoch, A, Barisal, P, Baratin, D, Barbato, A, Barbie, V, Barras, D, Barreiro, M, Barret, S, Bastian, F, Batista Neto, TM, Baudis, M, Beaudoing, E, Beckmann, JS, Bekkar, AK, Cammoun, LBH, Benmohammed, S, Bernard, M, Bertelli, C, Bertoni, M, Bienert, S, Bignucolo, O, Bilbao, A, Bilican, A, Blank, D, Blatter, M-C, Blum, L, Bocquet, J, Boeckmann, B, Bolleman, JT, Bordoli, L, Bosshard, L, Boucher, G, Bougueleret, L, Boutet, E, Bovigny, C, Bratulic, S, Breuza, L, Bridge, AJ, Britan, A, Brito, F, Frazao, JB, Bruggmann, R, Bucher, P, Burdet, F, Burger, L, Cabello, EM, Gomez, RMC, Calderon, S, Cannarozzi, G, Carl, S, Casas, CC, Catherinet, S, Perier, RC, Charpilloz, C, Chaskar, PD, Chen, W, Pepe, AC, Chopard, B, Chu, HY, Civic, N, Claassen, M, Clottu, S, Colombo, M, Cosandier, I, Coudert, E, Crespo, I, Creus, M, Cuche, B, Cuendet, MA, Cusin, I, Daga, N, Daina, A, Dauvillier, J, David, F, Davydov, I, Ferreira, MDSRM, de Beer, T, de Castro, E, de Santana, C, Delafontaine, J, Delorenzi, M, Delucinge-Vivier, C, Demirel, O, Derham, R, Dermitzakis, EM, Dib, L, Diene, S, Dilek, N, Dilmi, J, Domagalski, MJ, Dorier, J, Dornevil, D, Dousse, A, Dreos, R, Duchen, P, Roggli, PD, Duperret, ID, Durinx, C, Duvaud, S, Engler, R, Frkek, S, Lopez, PE, Fstreicher, A, Excoffier, L, Fabbretti, R, Falcone, J-L, Falquet, L, Famiglietti, ML, Ferreira, A-M, Feuermann, M, Filliettaz, M, Hegel, V, Foucal, A, Franceschini, A, Fucile, G, Gaidatzis, D, Garcia, V, Gasteiger, E, Gateau, A, Gatti, L, Gaudet, P, Gaudinat, A, Gehant, S, Gfeller, D, Gharib, WH, Ghraichy, M, Gidoin, C, Gil, M, Gleizes, A, Gobeill, J, Gonnet, G, Gos, A, Gotz, L, Gouy, A, Grbic, D, Groux, R, Gruaz-Gumowski, N, Grun, D, Gschwind, A, Guex, N, Gupta, S, Getaz, M, Haake, D, Haas, J, Hatzimanikatis, V, Heckel, G, Gardiol, DFH, Hinard, V, Hinz, U, Homicsko, K, Horlacher, O, Hosseini, S-R, Hotz, H-R, Hulo, C, Hundsrucker, C, Ibberson, M, Ilmjarv, S, Ioannidis, V, Ioannidis, P, Iseli, C, Ivanek, R, Iwaszkiewicz, J, Jacquet, P, Jacquot, M, Jagannathan, V, Jan, M, Jensen, J, Johansson, MU, Johner, N, Jungo, F, Junier, T, Kahraman, A, Katsantoni, M, Keller, G, Kerhornou, A, Khalid, F, Klingbiel, D, Kimljenovic, A, Kriventseva, E, Kryuchkova, N, Kumar, S, Kutalik, Z, Kuznetsov, D, Kuzyakiv, R, Lane, L, Lara, V, Ledesma, L, Leleu, M, Lemercier, P, Lew, D, Lieberherr, D, Liechti, R, Lisacek, F, Fischer, H, Litsios, G, Liu, J, Lombardot, T, Mace, A, Maffioletti, S, Mahi, M-A, Maiolo, M, Majjigapu, SR, Malmstrom, L, Mangold, V, Marek, D, Mariethoz, J, Marin, R, Martin, O, Martin, X, Martin-Campos, T, Mary, C, Masclaux, F, Masson, P, Meier, C, Messina, A, Lenoir, MM, Meyer, X, Michel, P-A, Michielin, O, Milanese, A, Missiaglia, E, Perez, JM, Caria, VM, Moret, P, Moretti, S, Morgat, A, Mottaz, A, Mottin, L, Mouscaz, Y, Mueller, M, Murri, R, Mylonas, R, Neuenschwander, S, Nikitin, F, Niknejad, A, Nouspikel, N, Nso, LN, Okoniewski, M, Omasits, U, Paccaud, B, Pachkov, M, Paesano, SG, Pagni, M, Palagi, PM, Pasche, E, Payne, JL, Pedruzzi, I, Peischl, S, Peitsch, M, Perlini, S, Pilbout, S, Podvinec, M, Pohlmann, R, Polizzi, D, Potter, D, Poux, S, Pozzato, M, Pradervand, S, Praz, V, Pruess, M, Pujadas, E, Racle, J, Raschi, M, Ratib, O, Rausell, A, de Laval, VR, Redaschi, N, Rempfer, C, Ren, G, Vandati, RAR, Rib, L, Grognuz, OR, Altimiras, ER, Rivoire, C, Robin, T, Robinson-Rechavi, M, Rodrigues, J, Roechert, B, Roelli, P, Romano, V, Rossier, G, Roth, A, Rougemont, J, Roux, J, Royo, H, Ruch, P, Ruinelli, M, Rustom, M, Sates, A, Roehrig, UF, Rueeger, S, Salamin, N, Sankar, M, Sarkar, N, Saxenhofer, M, Schaeffer, M, Schaerli, Y, Schaper, E, Schmid, A, Schmid, E, Schmid, C, Schmid, M, Schmidt, S, Schmocker, D, Schneider, M, Schuepbach, T, Schwede, T, Schuetz, F, Sengstag, T, Serrano, M, Sethi, A, Shahmirzadi, O, Sigrist, C, Silvestro, D, Simao Neto, FA, Simillion, C, Simonovic, M, Skunca, N, Sluzek, K, Soneson, C, Sprouffske, K, Stadler, M, Staehli, S, Stevenson, B, Stockinger, H, Straszewski, J, Stricker, T, Studer, G, Stutz, A, Suffiotti, M, Sundaram, S, Szklarczyk, D, Szovenyi, P, Tegenfeldt, F, Teixeira, D, Tellenbach, S, Smith, AAT, Tognolli, M, Topolsky, I, Thuong, VDT, Tsantoulis, P, Tzika, AC, Agote, AU, van Nimwegen, E, von Mering, C, Varadarajan, A, Veranneman, M, Verbregue, L, Veuthey, A-L, Vishnyakova, D, Vyas, R, Wagner, A, Walther, D, Wan, HW, Wang, M, Waterhouse, R, Waterhouse, A, Wicki, A, Wigger, L, Wirapati, P, Witschi, U, Wyder, S, Wyler, K, Wuethrich, D, Xenarios, I, Yamada, K, Yan, Z, Yasrebi, H, Zahn, M, Zangger, N, Zdobnov, E, Zerzion, D, Zoete, V, Zoller, S, Bultet, LA, Aguilar-Rodriguez, J, Ahrens, CH, Ahrne, EL, Ai, N, Aimo, L, Akalin, A, Aleksiev, T, Alocci, D, Altenhoff, A, Alves, I, Ambrosini, G, Pedone, PA, Angelina, P, Anisimova, M, Appel, R, Argoud-Puy, G, Arnold, K, Arpat, B, Artimo, P, Ascencao, K, Auchincloss, A, Axelsen, K, Gerritsen, VB, Bairoch, A, Barisal, P, Baratin, D, Barbato, A, Barbie, V, Barras, D, Barreiro, M, Barret, S, Bastian, F, Batista Neto, TM, Baudis, M, Beaudoing, E, Beckmann, JS, Bekkar, AK, Cammoun, LBH, Benmohammed, S, Bernard, M, Bertelli, C, Bertoni, M, Bienert, S, Bignucolo, O, Bilbao, A, Bilican, A, Blank, D, Blatter, M-C, Blum, L, Bocquet, J, Boeckmann, B, Bolleman, JT, Bordoli, L, Bosshard, L, Boucher, G, Bougueleret, L, Boutet, E, Bovigny, C, Bratulic, S, Breuza, L, Bridge, AJ, Britan, A, Brito, F, Frazao, JB, Bruggmann, R, Bucher, P, Burdet, F, Burger, L, Cabello, EM, Gomez, RMC, Calderon, S, Cannarozzi, G, Carl, S, Casas, CC, Catherinet, S, Perier, RC, Charpilloz, C, Chaskar, PD, Chen, W, Pepe, AC, Chopard, B, Chu, HY, Civic, N, Claassen, M, Clottu, S, Colombo, M, Cosandier, I, Coudert, E, Crespo, I, Creus, M, Cuche, B, Cuendet, MA, Cusin, I, Daga, N, Daina, A, Dauvillier, J, David, F, Davydov, I, Ferreira, MDSRM, de Beer, T, de Castro, E, de Santana, C, Delafontaine, J, Delorenzi, M, Delucinge-Vivier, C, Demirel, O, Derham, R, Dermitzakis, EM, Dib, L, Diene, S, Dilek, N, Dilmi, J, Domagalski, MJ, Dorier, J, Dornevil, D, Dousse, A, Dreos, R, Duchen, P, Roggli, PD, Duperret, ID, Durinx, C, Duvaud, S, Engler, R, Frkek, S, Lopez, PE, Fstreicher, A, Excoffier, L, Fabbretti, R, Falcone, J-L, Falquet, L, Famiglietti, ML, Ferreira, A-M, Feuermann, M, Filliettaz, M, Hegel, V, Foucal, A, Franceschini, A, Fucile, G, Gaidatzis, D, Garcia, V, Gasteiger, E, Gateau, A, Gatti, L, Gaudet, P, Gaudinat, A, Gehant, S, Gfeller, D, Gharib, WH, Ghraichy, M, Gidoin, C, Gil, M, Gleizes, A, Gobeill, J, Gonnet, G, Gos, A, Gotz, L, Gouy, A, Grbic, D, Groux, R, Gruaz-Gumowski, N, Grun, D, Gschwind, A, Guex, N, Gupta, S, Getaz, M, Haake, D, Haas, J, Hatzimanikatis, V, Heckel, G, Gardiol, DFH, Hinard, V, Hinz, U, Homicsko, K, Horlacher, O, Hosseini, S-R, Hotz, H-R, Hulo, C, Hundsrucker, C, Ibberson, M, Ilmjarv, S, Ioannidis, V, Ioannidis, P, Iseli, C, Ivanek, R, Iwaszkiewicz, J, Jacquet, P, Jacquot, M, Jagannathan, V, Jan, M, Jensen, J, Johansson, MU, Johner, N, Jungo, F, Junier, T, Kahraman, A, Katsantoni, M, Keller, G, Kerhornou, A, Khalid, F, Klingbiel, D, Kimljenovic, A, Kriventseva, E, Kryuchkova, N, Kumar, S, Kutalik, Z, Kuznetsov, D, Kuzyakiv, R, Lane, L, Lara, V, Ledesma, L, Leleu, M, Lemercier, P, Lew, D, Lieberherr, D, Liechti, R, Lisacek, F, Fischer, H, Litsios, G, Liu, J, Lombardot, T, Mace, A, Maffioletti, S, Mahi, M-A, Maiolo, M, Majjigapu, SR, Malmstrom, L, Mangold, V, Marek, D, Mariethoz, J, Marin, R, Martin, O, Martin, X, Martin-Campos, T, Mary, C, Masclaux, F, Masson, P, Meier, C, Messina, A, Lenoir, MM, Meyer, X, Michel, P-A, Michielin, O, Milanese, A, Missiaglia, E, Perez, JM, Caria, VM, Moret, P, Moretti, S, Morgat, A, Mottaz, A, Mottin, L, Mouscaz, Y, Mueller, M, Murri, R, Mylonas, R, Neuenschwander, S, Nikitin, F, Niknejad, A, Nouspikel, N, Nso, LN, Okoniewski, M, Omasits, U, Paccaud, B, Pachkov, M, Paesano, SG, Pagni, M, Palagi, PM, Pasche, E, Payne, JL, Pedruzzi, I, Peischl, S, Peitsch, M, Perlini, S, Pilbout, S, Podvinec, M, Pohlmann, R, Polizzi, D, Potter, D, Poux, S, Pozzato, M, Pradervand, S, Praz, V, Pruess, M, Pujadas, E, Racle, J, Raschi, M, Ratib, O, Rausell, A, de Laval, VR, Redaschi, N, Rempfer, C, Ren, G, Vandati, RAR, Rib, L, Grognuz, OR, Altimiras, ER, Rivoire, C, Robin, T, Robinson-Rechavi, M, Rodrigues, J, Roechert, B, Roelli, P, Romano, V, Rossier, G, Roth, A, Rougemont, J, Roux, J, Royo, H, Ruch, P, Ruinelli, M, Rustom, M, Sates, A, Roehrig, UF, Rueeger, S, Salamin, N, Sankar, M, Sarkar, N, Saxenhofer, M, Schaeffer, M, Schaerli, Y, Schaper, E, Schmid, A, Schmid, E, Schmid, C, Schmid, M, Schmidt, S, Schmocker, D, Schneider, M, Schuepbach, T, Schwede, T, Schuetz, F, Sengstag, T, Serrano, M, Sethi, A, Shahmirzadi, O, Sigrist, C, Silvestro, D, Simao Neto, FA, Simillion, C, Simonovic, M, Skunca, N, Sluzek, K, Soneson, C, Sprouffske, K, Stadler, M, Staehli, S, Stevenson, B, Stockinger, H, Straszewski, J, Stricker, T, Studer, G, Stutz, A, Suffiotti, M, Sundaram, S, Szklarczyk, D, Szovenyi, P, Tegenfeldt, F, Teixeira, D, Tellenbach, S, Smith, AAT, Tognolli, M, Topolsky, I, Thuong, VDT, Tsantoulis, P, Tzika, AC, Agote, AU, van Nimwegen, E, von Mering, C, Varadarajan, A, Veranneman, M, Verbregue, L, Veuthey, A-L, Vishnyakova, D, Vyas, R, Wagner, A, Walther, D, Wan, HW, Wang, M, Waterhouse, R, Waterhouse, A, Wicki, A, Wigger, L, Wirapati, P, Witschi, U, Wyder, S, Wyler, K, Wuethrich, D, Xenarios, I, Yamada, K, Yan, Z, Yasrebi, H, Zahn, M, Zangger, N, Zdobnov, E, Zerzion, D, Zoete, V, and Zoller, S

Abstract

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

Published
2016

17. Assessment of transcript reconstruction methods for RNA-seq

Author

Steijger, T., Abril, J.F., Engström, P.G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S.E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Gerstein, M., Gingeras, T.R., Gonzalez, D., Grimmond, S.M., Guigó, R., Habegger, L., Harrow, J., Hubbard, T.J., Iseli, C., Jean, G., Kahles, A., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M.H., Searle, S.M., Solorzano, N.D., Solovyev, V., Stanke, M., Stevenson, B.J., Stockinger, H., Valsesia, A., Weese, D., White, S., Wold, B.J., Wu, J., Wu, T.D., Zeller, G., Zerbino, D., Zhang, M.Q., RGASP Consortium, Head of Medical Sequencing, Institut de Génétique et Développement de Rennes (IGDR), Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Department of Statistics [Berkeley], University of California [Berkeley], University of California-University of California, Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Sanger Institute, Wellcome Trust, Laboratoire d'Informatique de Nantes Atlantique (LINA), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (CRICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Protéines de défense des réponses immune et inflammatoire : identification, régulation et rôles physiopathologiques, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lausanne (UNIL), Centre Georges Chevrier. Ordre et désordre dans l'histoire des sociétés (UMR5605) (CGC), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), School of Life Sciences [Lausanne], Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Department of Computer Science [Royal Holloway], Royal Holloway [University of London] (RHUL), University of California [Santa Cruz] (UCSC), University of California, Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Institut de Génétique et Développement de Rennes ( IGDR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -IFR140-Centre National de la Recherche Scientifique ( CNRS ), Centro de Regulación Genómica ( CRG ), Universitat Pompeu Fabra [Barcelona], Department of Statistics, Laboratoire d'Informatique de Nantes Atlantique ( LINA ), Mines Nantes ( Mines Nantes ) -Université de Nantes ( UN ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière ( CRICM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université de Lausanne ( UNIL ), Centre Georges Chevrier. Ordre et désordre dans l'histoire des sociétés (UMR5605) ( CGC ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Bourgogne ( UB ), Ecole Polytechnique Fédérale de Lausanne ( EPFL ), Swiss Institute of Bioinformatics ( SIB ), Swiss Institute of Bioinformatics, Centro Nacional de Análisi Genómico ( CNAG ), Royal Holloway [University of London] ( RHUL ), University of California [Santa Cruz] ( UCSC ), Swiss Institute of Bioinformatics - Lausanne ( SIB ), Stony Brook University [The State University of New York] ( SBU ), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL), University of California [Santa Cruz] (UC Santa Cruz), and University of California (UC)

Subjects
Technology, Messenger, RNA, Messenger/metabolism, RNA-Seq, RGASP Consortium, Sequence Analysis, RNA/methods, Biochemistry, Genome, Medical and Health Sciences, Exon, 0302 clinical medicine, Transcription (biology), 2.1 Biological and endogenous factors, ddc:576.5, Aetiology, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genetics, 0303 health sciences, Genome project, Exons, Biological Sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Drosophila melanogaster, RNA splicing, Sequence Analysis, Algorithms, Biotechnology, RNA Splicing, Computational biology, Biology, Biologia computacional, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Empalmament (Genètica), Animals, Humans, Caenorhabditis elegans, Molecular Biology, 030304 developmental biology, GENCODE, Gene Expression Profiling, Intron, Computational Biology, Cell Biology, Computational Biology/methods, Introns, RNA Splice Sites, Software, RNA, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery, Developmental Biology
Abstract

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data. This work was supported by grants BIO2011-26205 and CSD2007-00050 from the Ministerio de Educación y Ciencia

Published
2013

18. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

Author

Bonhoure, N, Bounova, G, Bernasconi, D, Praz, V, Lammers, F, Canella, D, Willis, I M, Herr, W, Hernandez, N, Delorenzi, M, Deplancke, B, Desvergne, B, Guex, N, Naef, F, Rougemont, J, Schibler, U, Andersin, T, Cousin, P, Gilardi, F, Gos, P, Raghav, S, Villeneuve, D, Fabbretti, R, Vlegel, V, Xenarios, I, Migliavacca, E, David, F, Jarosz, Y, Kuznetsov, D, Liechti, R, Martin, O, Delafontaine, J, Cajan, J, Gustafson, K, Krier, I, Leleu, M, Molina, N, Naldi, A, Rib, L, Symul, L, Bonhoure, N, Bounova, G, Bernasconi, D, Praz, V, Lammers, F, Canella, D, Willis, I M, Herr, W, Hernandez, N, Delorenzi, M, Deplancke, B, Desvergne, B, Guex, N, Naef, F, Rougemont, J, Schibler, U, Andersin, T, Cousin, P, Gilardi, F, Gos, P, Raghav, S, Villeneuve, D, Fabbretti, R, Vlegel, V, Xenarios, I, Migliavacca, E, David, F, Jarosz, Y, Kuznetsov, D, Liechti, R, Martin, O, Delafontaine, J, Cajan, J, Gustafson, K, Krier, I, Leleu, M, Molina, N, Naldi, A, Rib, L, and Symul, L

Published
2014

19. The Dynamic Architecture of Hox Gene Clusters

Author

Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., de Laat, W., Duboule, D., Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., de Laat, W., and Duboule, D.

Abstract

The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the colinear activation of these compact gene clusters., The spatial and temporal control of Hox gene transcription is essential for patterning the vertebrate body axis. Although this process involves changes in histone posttranslational modifications, the existence of particular three-dimensional (3D) architectures remained to be assessed in vivo. Using high-resolution chromatin conformation capture methodology, we examined the spatial configuration of Hox clusters in embryonic mouse tissues where different Hox genes are active. When the cluster is transcriptionally inactive, Hox genes associate into a single 3D structure delimited from flanking regions. Once transcription starts, Hox clusters switch to a bimodal 3D organization where newly activated genes progressively cluster into a transcriptionally active compartment. This transition in spatial configurations coincides with the dynamics of chromatin marks, which label the progression of the gene clusters from a negative to a positive transcription status. This spatial compartmentalization may be key to process the colinear activation of these compact gene clusters.

Published
2012

20. Stochastic phase oscillators and circadian bioluminescence recordings

Author

Rougemont, J., Naef, F., Rougemont, J., and Naef, F.

Abstract

Cultured circadian oscillators from peripheral tissues were recently shown to be both cell-autonomous and self-sustained. Therefore, the dominant cause for amplitude reduction observed in bioluminescence recordings of cultured fibroblasts is desynchronization, rather than the damping of individual oscillators. Here, we review a generic model for quantifying luminescence signals from biochemical oscillators, based on noisy-phase oscillators. Our model incorporates three essential features of circadian clocks: the stability of the limit cycle, fluctuations, and intercellular coupling. The model is then used to analyze bioluminescence recordings from immortalized and primary fibroblasts. Fits to population recordings allow simultaneous estimation of the stability of the limit cycle (or equivalently, the stiffness of individual frequencies), the period dispersion, and the interaction strength between cells. Consistent with other work, coupling is found to be weak and insufficient to synchronize cells. Interestingly, we find that frequency fluctuations remain correlated for longer periods than one clock cycle, which is confirmed from individual cell recordings. We discuss briefly how to link the generic model with more microscopic models, which suggests mechanisms by which circadian oscillators resist fluctuations and maintain accurate timing in the periphery.

Published
2010
Full Text
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21. The Microbe browser for comparative genomics

Author

Gattiker, A, Dessimoz, C, Schneider, A, Xenarios, I, Pagni, M, Rougemont, J, Gattiker, A, Dessimoz, C, Schneider, A, Xenarios, I, Pagni, M, and Rougemont, J

Abstract

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/api

Published
2009

22. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Author

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, Migliavacca, E, Alfaiz, A A, Hippolyte, L, Maillard, A M, Van Dijck, A, Kooy, R F, Sanlaville, D, Rosenfeld, J A, Shaffer, L G, Andrieux, J, Marshall, C, Scherer, S W, Shen, Y, Gusella, J F, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, E T, Deplancke, B, Beckmann, J S, Rougemont, J, Jacquemont, S, and Reymond, A

Abstract

Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.

Published
2017
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25. [Catheterization of the inferior petrosal sinus. Its role in the diagnosis of Cushing's syndrome. Experience with 23 explorations]

Author

Bessac L, Bachelot I, Vasdev A, Martinie M, Bonnier L, Olivier CHABRE, Jg, Passagia, and De Rougemont J

Subjects
Adenoma, Adult, Male, Lung Neoplasms, Adolescent, Carcinoid Tumor, Cranial Sinuses, Middle Aged, Catheterization, Adrenocorticotropic Hormone, Humans, Female, Pituitary Neoplasms, Cushing Syndrome, Aged
Abstract

Selective catheterization of the inferior petrosal sinus has been performed in 23 patients: 11 Cushing's disease, 5 lung carcinoid tumors whose diagnosis has been confirmed by surgery and 7 ACTH-dependent hypercortisolism whose final diagnosis has not yet been proved. The pituitary origin of hormone secretion is accepted if the central-to-peripheral ratio (C/PR) is equal or greater than 2 on basal values and/or during CRF test. On basal values, all subjects but one with confirmed pituitary lesions exhibited a C/PRor = 2; the carcinoid tumors never exceeded the value of 1.3. After CRF injection, all the pituitary tumors showed an increase in C/PR; one patient with a lung carcinoid tumor (CRF-negative) showed a pituitary ACTH secretion (C/PR = 3.7). The localization of pituitary adenoma by the lateralization of hormone secretion is disappointing, except, perhaps, for very small extremely lateral adenomas. No accident occurred in our series, nor in the literature. This investigation seems the most reliable approach to prove the pituitary origin of hormonal hypersecretion. We recommend it to be performed in ACTH-dependent Cushing's syndrome when the secretory pattern is not typical and/or pituitary imaging is normal.

Published
1992

36. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes

Author

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, Migliavacca, E, Alfaiz, A A, Hippolyte, L, Maillard, A M, Loviglio, Maria Nicla, Männik, Katrin, Van Der Werf, Ilse, Giannuzzi, Giuliana, Zazhytska, Marianna, Gheldof, Nele, Migliavacca, Eugenia, Alfaiz, Ali A, Roberts-Caldeira, Inês, Hippolyte, Loyse, Maillard, Anne M, Ferrarini, Alessandra, Butschi, Florence Niel, Conrad, Bernard, Addor, Marie-Claude, Belfiore, Marco, Roetzer, Katharina, Dijck, Anke Van, Blaumeiser, Bettina, Kooy, Frank, Roelens, Filip, Dheedene, Annelies, Chiaie, Barbara Delle, Menten, Björn, Oostra, Ann, Caberg, Jean-Hubert, Carter, Melissa, Kellam, Barbara, Stavropoulos, Dimitri J, Marshall, Christian, Scherer, Stephen W, Weksberg, Rosanna, Cytrynbaum, Cheryl, Bassett, Anne, Lowther, Chelsea, Gillis, Jane, Mackay, Sara, Bache, Iben, Ousager, Lilian B, Smerdel, Maja Patricia, Graakjaer, Jesper, Kjaergaard, Susanne, Metspalu, Andres, Mathieu, Michele, Bonneau, Dominique, Guichet, Agnes, Parent, Philippe, Férec, Claude, Gerard, Marion, Plessis, Ghislaine, Lespinasse, James, Masurel, Alice, Marle, Nathalie, Faivre, Laurence, Callier, Patrick, Layet, Valerie, Meur, Nathalie Le, Le Goff, Céline, Duban-Bedu, Bénédicte, Sukno, Sylvie, Boute, Odile, Andrieux, Joris, Blanchet, Patricia, Geneviève, David, Puechberty, Jacques, Schneider, Anouck, Leheup, Bruno, Jonveaux, Philippe, Mercier, Sandra, David, Albert, Le Caignec, Cédric, De Pontual, Loic, Pipiras, Eva, Jacquette, Aurelia, Keren, Boris, Gilbert-Dussardier, Brigitte, Bilan, Frederic, Goldenberg, Alice, Chambon, Pascal, Toutain, Annick, Till, Marianne, Sanlaville, Damien, Leube, Barbara, Royer-Pokora, Brigitte, Grabe, Hans Jörgen, Schmidt, Carsten Oliver, Schurmann, Claudia, Homuth, Georg, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Bernardini, Laura, Novelli, Antonio, Micale, Lucia, Merla, Giuseppe, Zollino, Marcella, Mari, Francesca, Rizzo, Caterina Lo, Renieri, Alessandra, Silengo, Margherita, Vulto-Van Silfhout, Anneke T, Schouten, Meyke, Pfundt, Rolph, De Leeuw, Nicole, Vansenne, Fleur, Maas, Saskia M, Barge-Schaapveld, Daniela Qcm, Knegt, Alida C, Stadheim, Barbro, Rodningen, Olaug, Houge, Gunnar, Price, Sue, Hawkes, Lara, Campbell, Carolyn, Kini, Usha, Vogt, Julie, Walters, Robin, Blakemore, Alexandra, Gusella, James F, Shen, Yiping, Scott, Daryl, Bacino, Carlos A, Tsuchiya, Karen, Ladda, Roger, Sell, Susan, Asamoah, Alexander, Hamati, Aline I, Rosenfeld, Jill A, Shaffer, Lisa G, Mitchell, Elyse, Hodge, Jennelle C, Beckmann, Jacques S, Jacquemont, Sébastien, Reymond, Alexandre, Ewans, Lisa J, Mowat, David, Walker, Jan, Amor, David J, Esch, Hilde Van, Leroy, Patricia, Bamforth, John-Steven, Babu, Deepti, Isidor, Bertrand, Didonato, Nataliya, Hackmann, Karl, Passeggeri, Marzia, Haeringen, Arie Van, Smith, Rosemarie, Ellingwood, Sara, Farber, Darren M, Puri, Vinay, Zadeh, Neda, Weaver, David D, Miller, Mandy, Wilks, Timothy, Jorgez, Carolina J, Lafayette, Deedee, Van Dijck, A, Kooy, R F, Sanlaville, D, Rosenfeld, J A, Shaffer, L G, Andrieux, J, Marshall, C, Scherer, S W, Shen, Y, Gusella, J F, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, E T, Deplancke, B, Beckmann, J S, Rougemont, J, Jacquemont, S, Reymond, A, 2p15 Consortium, and 16p11 2 Consortium

Abstract

Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.

37. Protein expression profiling identifies subclasses of breast cancer and predicts prognosis

Author

Jacquemier, J., Christophe Ginestier, Rougemont, J., Bardou, V. -J, Charafe-Jauffret, E., Geneix, J., Adélaïde, J., Koki, A., Houvenaeghel, G., Hassoun, J., Maraninchi, D., Viens, P., Birnbaum, D., and Bertucci, F.

Subjects
Adult, Aged, 80 and over, Proteomics, Cancer Research, Protein Array Analysis, Reproducibility of Results, Breast Neoplasms, Middle Aged, Prognosis, Immunohistochemistry, Oncology, Multivariate Analysis, Humans, Female, Aged
Abstract

Breast cancer is a heterogeneous disease whose evolution is difficult to predict by using classic histoclinical prognostic factors. Prognostic classification can benefit from molecular analyses such as large-scale expression profiling. Using immunohistochemistry on tissue microarrays, we have monitored the expression of 26 selected proteins in more than 1,600 cancer samples from 552 consecutive patients with early breast cancer. Both an unsupervised approach and a new supervised method were used to analyze these profiles. Hierarchical clustering identified relevant clusters of coexpressed proteins and clusters of tumors. We delineated protein clusters associated with the estrogen receptor and with proliferation. Tumor clusters correlated with several histoclinical features of samples, including 5-year metastasis-free survival (MFS), and with the recently proposed pathophysiologic taxonomy of disease. The supervised method identified a set of 21 proteins whose combined expression significantly correlated to MFS in a learning set of 368 patients (P < 0.0001) and in a validation set of 184 patients (P < 0.0001). Among the 552 patients, the 5-year MFS was 90% for patients classified in the “good-prognosis class” and 61% for those classified in the “poor-prognosis class” (P < 0.0001). This difference remained significant when the molecular grouping was applied according to lymph node or estrogen receptor status, as well as the type of adjuvant systemic therapy. In multivariate analysis, the 21-protein set was the strongest independent predictor of clinical outcome. These results show that protein expression profiling may be a clinically useful approach to assess breast cancer heterogeneity and prognosis in stage I, II, or III disease.

44. PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Author

Weissbrodt David G, Shani Noam, Sinclair Lucas, Lefebvre Grégory, Rossi Pierre, Maillard Julien, Rougemont Jacques, and Holliger Christof

Subjects
Microbial ecology, T-RFLP, Pyrosequencing, Digital T-RFLP, Bioinformatics methodology, Microbiology, QR1-502
Abstract

Abstract Background In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples. DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. Digital T-RFLP profiles were generated from the denoised full pyrosequencing datasets, and the sequences contributing to each digital T-RF were classified to taxonomic bins using the Greengenes reference database. The method was tested both on bacterial communities found in chloroethene-contaminated groundwater samples and in aerobic granular sludge biofilms originating from wastewater treatment systems. Results PyroTRF-ID was efficient for high-throughput mapping and digital T-RFLP profiling of pyrosequencing datasets. After denoising, a dataset comprising ca. 10′000 reads of 300 to 500 bp was typically processed within ca. 20 minutes on a high-performance computing cluster, running on a Linux-related CentOS 5.5 operating system, enabling parallel processing of multiple samples. Both digital and experimental T-RFLP profiles were aligned with maximum cross-correlation coefficients of 0.71 and 0.92 for high- and low-complexity environments, respectively. On average, 63±18% of all experimental T-RFs (30 to 93 peaks per sample) were affiliated to phylotypes. Conclusions PyroTRF-ID profits from complementary advantages of pyrosequencing and T-RFLP and is particularly adapted for optimizing laboratory and computational efforts to describe microbial communities and their dynamics in any biological system. The high resolution of the microbial community composition is provided by pyrosequencing, which can be performed on a restricted set of selected samples, whereas T-RFLP enables simultaneous fingerprinting of numerous samples at relatively low cost and is especially adapted for routine analysis and follow-up of microbial communities on the long run.

Published
2012
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45. A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing

Author

Zangger Nadine, Quenneville Simon, Malani Nirav, Ambrosini Giovanna, Groner Anna C, Meylan Sylvain, Kapopoulou Adamandia, Kauzlaric Annamaria, Rougemont Jacques, Ciuffi Angela, Bushman Frederic D, Bucher Philipp, and Trono Didier

Subjects
KAP1, KRAB-zinc finger proteins, transcriptional repression, chromatin, heterochromatin, histone modifications, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background KRAB-ZFPs (Krüppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors responsible for the formation of facultative heterochromatin. We have recently shown that KRAB/KAP1 can mediate long-range transcriptional repression through heterochromatin spreading, but also demonstrated that this process is at times countered by endogenous influences. Method To investigate this issue further we used an ectopic KRAB-based repressor. This system allowed us to tether KRAB/KAP1 to hundreds of euchromatic sites within genes, and to record its impact on gene expression. We then correlated this KRAB/KAP1-mediated transcriptional effect to pre-existing genomic and chromatin structures to identify specific characteristics making a gene susceptible to repression. Results We found that genes that were susceptible to KRAB/KAP1-mediated silencing carried higher levels of repressive histone marks both at the promoter and over the transcribed region than genes that were insensitive. In parallel, we found a high enrichment in euchromatic marks within both the close and more distant environment of these genes. Conclusion Together, these data indicate that high levels of gene activity in the genomic environment and the pre-deposition of repressive histone marks within a gene increase its susceptibility to KRAB/KAP1-mediated repression.

Published
2011
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46. MIMAS 3.0 is a Multiomics Information Management and Annotation System

Author

Rougemont Jacques, Collin Olivier, Xenarios Ioannis, Liechti Robin, Hermida Leandro, Gattiker Alexandre, and Primig Michael

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. Description MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. Conclusion We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.

Published
2009
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47. Probabilistic base calling of Solexa sequencing data

Author

Iseli Christian, Amzallag Arnaud, Rougemont Jacques, Farinelli Laurent, Xenarios Ioannis, and Naef Felix

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. Results We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. Conclusion We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.

Published
2008
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48. MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

Author

Beaudoing Emmanuel, Deraco Stéphane, Tagett Rebecca, Granjeaud Samuel, Honoré Paul, Rougemont Jacques, Debono Stéphane, and Hingamp Pascal

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusion MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.

Published
2006
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50. DNA microarray data and contextual analysis of correlation graphs

Author

Hingamp Pascal and Rougemont Jacques

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation. Results We study networks of co-expressed genes obtained from DNA microarray experiments. The mathematical concept of curvature on graphs is used to group genes or samples into clusters to which relevant gene or sample annotations are automatically assigned. Application to publicly available yeast and human lymphoma data demonstrates the reliability of the method in spite of its simplicity, especially with respect to the small number of parameters involved. Conclusions We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. The automatic annotations and the graphical interface improve the readability of the data. A C++ implementation, called Trixy, is available from http://tagc.univ-mrs.fr/bioinformatics/trixy.html.

Published
2003
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