• 95 Citations
  • 5 h-Index
20112019
If you made any changes in Pure, your changes will be visible here soon.

Research Output 2011 2019

  • 95 Citations
  • 5 h-Index
  • 13 Article
  • 5 Conference contribution
2019

Context-aware seeds for read mapping

Xin, H., Shao, M. & Kingsford, C., Sep 2019, 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Huber, K. T. & Gusfield, D. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 15. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 143).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Seed
Escherichia coli
Genes

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads

Tung, L. H., Shao, M. & Kingsford, C., Dec 18 2019, In : Genome biology. 20, 1, 287.

Research output: Contribution to journalArticle

Open Access
Pectinidae
scallops
Transcriptome
transcriptome
RNA Isoforms

Theory and A heuristic for the minimum path flow decomposition problem

Shao, M. & Kingsford, C., Mar 1 2019, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 2, p. 658-670 13 p., 8126870.

Research output: Contribution to journalArticle

Open Access
Problem Decomposition
Heuristics
Decomposition
Path
Catfishes
2018
4 Citations (Scopus)

SQUID: Transcriptomic structural variation detection from RNA-seq

Ma, C., Shao, M. & Kingsford, C., Apr 12 2018, In : Genome biology. 19, 1, 52.

Research output: Contribution to journalArticle

Open Access
transcriptomics
RNA
gene fusion
gene
Gene Fusion
2017
16 Citations (Scopus)

accurate assembly of transcripts through phase-preserving graph decomposition

Shao, M. & Kingsford, C., Jan 1 2017, In : Nature Biotechnology. 35, 12, p. 1167-1169 3 p.

Research output: Contribution to journalArticle

Pectinidae
RNA
Exons
Decomposition
1 Citation (Scopus)

DeepBound: Accurate identification of transcript boundaries via deep convolutional neural fields

Shao, M., Ma, J. & Wang, S., Jul 15 2017, In : Bioinformatics. 33, 14, p. i267-i273

Research output: Contribution to journalArticle

Open Access
RNA
Genes
Statistical Models
Alignment
Gene expression
1 Citation (Scopus)

On Computing Breakpoint Distances for Genomes with Duplicate Genes

Shao, M. & Moret, B. M. E., Jun 2017, In : Journal of Computational Biology. 24, 6, p. 571-580 10 p.

Research output: Contribution to journalArticle

Open Access
Duplicate Genes
Genome
Genes
Gene
Computing
2016
3 Citations (Scopus)

A fast and exact algorithm for the exemplar breakpoint distance

Shao, M. & Moret, B. M. E., May 2016, In : Journal of Computational Biology. 23, 5, p. 337-346 10 p.

Research output: Contribution to journalArticle

Exact Algorithms
Fast Algorithm
Genes
Duplicate Genes
Gene
3 Citations (Scopus)

A maximum-likelihood approach for building cell-type trees by lifting

Nair, N. U., Hunter, L., Shao, M., Grnarova, P., Lin, Y., Bucher, P. & Bernard, B. M., Jan 11 2016, In : BMC genomics. 17, 1, 14.

Research output: Contribution to journalArticle

Open Access
Cell Differentiation
Histone Code
Phylogeny
Epigenomics
Genome
2 Citations (Scopus)

On computing breakpoint distances for genomes with duplicate genes

Shao, M. & Moret, B. M. E., Jan 1 2016, Research in Computational Molecular Biology - 20th Annual Conference, RECOMB 2016, Proceedings. Singh, M. (ed.). Springer Verlag, p. 189-203 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9649).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genome
Genes
Gene
Computing
Distance Measure
16 Citations (Scopus)

The SIB Swiss Institute of bioinformatics' resources: Focus on curated databases

Bultet, L. A., Aguilar-Rodríguez, J., Ahrens, C. H., Ahrné, E. L., Ai, N., Aimo, L., Akalin, A., Aleksiev, T., Alocci, D., Altenhoff, A., Alves, I., Ambrosini, G., Pedone, P. A., Angelino, P., Anisimova, M., Appel, R., Argoud-Puy, G., Arnold, K., Arpat, B., Artimo, P. & 658 others, Ascencao, K., Auchincloss, A., Axelsen, K., Gerritsen, V. B., Bairoch, A., Bansal, P., Baratin, D., Barbato, A., Barbié, V., Barras, D., Barreiro, M., Barret, S., Bastian, F., Neto, T. B., Baudis, M., Beaudoing, E., Beckmann, J. S., Bekkar, A. K., Ben Hamida Cammoun, L., 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, J. T., Bordoli, L., Bosshard, L., Bouchet, G., Bougueleret, L., Boutet, E., Bovigny, C., Bratulic, S., Breuza, L., Bridge, A. J., Britan, A., Brito, F., Frazão, J. B., Bruggmann, R., Bucher, P., Burdet, F., Burger, L., Cabello, E. M., Gomez, R. M. C., Calderon, S., Cannarozzi, G., Carl, S., Casas, C. C., Catherinet, S., Périer, R. C., Charpilloz, C., Chaskar, P. D., Chen, W., Pepe, A. C., Chopard, B., Chu, H. Y., Civic, N., Claassen, M., Clottu, S., Colombo, M., Cosandier, I., Coudert, E., Crespo, I., Creus, M., Cuche, B., Cuendet, M. A., Cusin, I., Daga, N., Daina, A., Dauvillier, J. Ô., David, F., Davydov, I., De Sa Ricca Manadelo Ferreira, M., De Beer, T., De Castro, E., De Santana, C., Delafontaine, J., Delorenzi, M., Delucinge-Vivier, C., Demirel, Ö., Derham, R., Dermitzakis, E. M., Dib, L., Diene, S., Dilek, N., Dilmi, J., Domagalski, M. J., Dorier, J., Dornevil, D., Dousse, A., Dreos, R., Duchen, P., Roggli, P. D., Duperret, I. D., Durinx, C., Duvaud, S., Engler, R., Erkek, S., López, P. E., Estreicher, A., Excoffier, L., Fabbretti, R., Falcone, J. L., Falquet, L., Famiglietti, M. L., Ferreira, A. M., Feuermann, M., Filliettaz, M., Flegel, 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, W. H., 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., Gétaz, M., Haake, D., Haas, J., Hatzimanikatis, V., Heckel, G., Gardiol, D. F. H., Hinard, V., Hinz, U., Homicsko, K., Horlacher, O., Hosseini, S. R., Hotz, H. R., Hulo, C., Hundsrucker, C., Ibberson, M., Ilmjärv, S., Ioannidis, V., Ioannidis, P., Iseli, C., Ivanek, R., Iwaszkiewicz, J., Jacquet, P., Jacquot, M., Jagannathan, V., Jan, M., Jensen, J., Johansson, M. U., Johner, N., Jungo, F., Junier, T., Kahraman, A., Katsantoni, M., Keller, G., Kerhornou, A., Khalid, F., Klingbiel, D., Komljenovic, 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., Lischer, H., Litsios, G., Liu, J., Lombardot, T., Macé, A., Maffioletti, S., Mahi, M. A., Maiolo, M., Majjigapu, S. R., Malmström, L., Mangold, V., Marek, D., Mariethoz, J., Marin, R., Martin, O., Martin, X., Martín-Campos, T., Mary, C., Masclaux, F., Masson, P., Meier, C., Messina, A., Lenoir, M. M., Meyer, X., Michel, P. A., Michielin, O., Milanese, A., Missiaglia, E., Perez, J. M., Caria, V. M., 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, L. N., Okoniewski, M., Omasits, U., Paccaud, B., Pachkov, M., Paesano, S. G., Pagni, M., Palagi, P. M., Pasche, E., Payne, J. L., 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, V. R., Redaschi, N., Rempfer, C., Ren, G., Vahdati, R. A. R., Rib, L., Grognuz, O. R., Altimiras, E. R., 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., Sater, M. R. A., Röhrig, U. F., Rüeger, 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., Schütz, F., Sengstag, T., Serrano, M., Sethi, A., Shahmirzadi, O., Sigrist, C., Silvestro, D., Neto, F. A. S., 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., Övenyi, P. S., Tegenfeldt, F., Teixeira, D., Tellenbach, S., Smith, A. A. T., Tognolli, M., Topolsky, I., Van Du Tran, T., Tsantoulis, P., Tzika, A. C., Agote, A. U., Van Nimwegen, E., Von Mering, C., Varadarajan, A., Veranneman, M., Verbregue, L., Veuthey, A. L., Vishnyakova, D., Vyas, R., Wagner, A., Walther, D., Wan, H. W., Wang, M., Waterhouse, R., Waterhouse, A., Wicki, A., Wigger, L., Wirapati, P., Witschi, U., Wyder, S., Wyler, K., Wüthrich, D., Xenarios, I., Yamada, K., Yan, Z., Yasrebi, H., Zahn, M., Zangger, N., Zdobnov, E., Zerzion, D., Zoete, V., Zoller, S., Abriata, L., Aebischer, T., Akhmedov, M., Filho, A. A. M., Andreozzi, S., Appel, N., Armand, F., Arribas, A., Asgari, S., Ataman, M., Audagnotto, M., Aydin, D., Bady, P., Bank, C., Barac, D., Bargeton, B., Barido-Sottani, J., Barillari, C., Bartha, I., Bean, A., Becker, J., Beerenwinkel, N., Bellement, G., Benedetti, F., Bergmann, S., Berneche, S., Bevers, R., Biasse, D., Bichsel, M., Bieler, J., Piccini, A. P. B., Do Amaral, M. B., Bolliger, C., Boskova, V., Brown, A., Bryois, J., Buil, A., Cannavo, R., Cardner, M., Carelli, F. N., Carmona, S., Cascione, L., Chakrabarti, A., Chaturvedi, N., Choobdar, S., Clivaz, C., Constantinescu, S., Corre, T., Quezada, D. C. C., Croce, R., Cuendet, A., Cui, J., Dainese, R., Dal Peraro, M., Dallavilla, T., De Oliveira, L., Delaleu, N., Delaneau, O., Deplancke, B., Dharmarajan, L., Diekmann, M., Dimitrakopoulos, C., Dimitriades-Schmutz, B., Dimitrova, Y., Dirmeier, S., Dobay, M. P., Dougoud, M., Duc, J., Dumont, G., Du Plessis, L., Dörr, D., Elfstroem, K., Elmer, F. J., Ewing, G. B., Fanaswala, I., Fellay, J., Feller, C., Fengos, G., Ferrer, A., Fiaux, S., Field, C., Finci, I., Fofonjka, A., Fonti, G., Fried, P., Frochaux, M., Fuentes, J., Galbusera, L., Galimberti, M., Garcia-Albornoz, M., Garcia-Escudero, R., Garieri, M., Georgieva, L., Ghiurcuta, C. G., Ghosh, S., Gnann, A., Gnuegge, R., Golumbeanu, M., Gomez, H., Goudet, J. Ô., Gruber, A. J., Gruhl, F., Guethe, S., Guillot, E., Guimarães, J., Gumienny, R. W., Gunawan, R., Gustafson, K., Gypas, F., Hadadi, N., Hameri, T., Hammer, C., Heer, F., Heller, D. M., Hersch, M., Hofmann, A. L., Howald, C., Hutter, S., Iber, D., Irwin, K., Jahn, K., Jedlinski, D., Jethava, V., Jorjani, H., Julou, T., Kaessmann, H., Kalantzi, A., Kanitz, A., Kapopoulou, A., Karamasioti, E., Karimaddini, Z., Keller, I., Kiparissides, A., Kohler, M., Kousathanas, A., Kuipers, J., Kupczyk, P., Kwee, I., Kühnert, D., Lakshmanan, L. N., Lamparter, D., Lang, B., Laurent, S., Laurent, S., Leigh, D., Lin, Y., Lindsay, H., Link, V., Linnik, J., Liphardt, T., Liu, Y., Loetscher, A., Luomi, A. O., Lykov, K., Machlab, D., Magnus, C., Maillard-Wermelinger, A., Malafeev, A., Malaspinas, A. S., Parera, R. M., Manesso, E., Manukyan, L., Mapelli, S. N., Marbach, D., Lopez, M. J. M., Wynn, M. M., Martin, G., Martins, A. F., Matthes, K., Mazza, C., McDaid, A., Mermet, J. Ô., Michos, O., Milinkovitch, M. C., Misios, A., Miskovic, L., Mitov, V., Mitra, A., Mittal, N., Montazeri, H., Moret, B., Naef, F., Nair, N., Nicolas, D. L., Nicolet, S., Noh, H., Nowicka, M., Oeyaas, O., Omidi, S., Ongen, H., Ormond, L., Ottoz, D., Panousis, N., Gao, N. P., Modarres, H. P., Pečerska, J., Vieira, J. P., Pivkin, I., Planet, E., Céspedes, S. P., Pradhan, R., Prados, J., Racko, D., Radigois, M. F., Rasmussen, D., Riba, A., Rinn, B., Rivoal, M., Robinson, M., Rossi, S., Rudolf, F., Rueedi, R., Ruscheweyh, H. J., Rybinski, M., Rzepiela, A. J., Sakoparnig, T., San Román Rincón, M. M., Savoglidis, G., Scepanovic, P., Schaad, O., Schleiss, R., Schmich, F., Schmidt, R., Schulthess, S., Schwalie, P. C., Seifert, D., Seijo, M., Shao, M., Shim, H., Singer, J., Sobel, J., Soh, K. C., Flitman, R. S., Soto, S., Sousa, V., Stadler, T., Stasiak, A., Stefani, A., Steger, Y., Stelling, J., Stopka, A., Stévant, I., Sunnaker, M., Syed, A. P., Tamo, G., Tanaka, S., Theiler, G., Thorball, C. A. W., Thurnherr, T., Ccenhua, M. R. T., Tidin, O., Tokic, M., Riera, M. T., Tomasini, M., Tymoshenko, S., Ud-Dean, M., Urchueguia, A., Quintero, N. V., Vinckenbosch, L., Viñuela, A., Vollmer, J., Voordijk, S., Wang, J., Wang, Z., Warnefors, M., Weber, L. M., Wegmann, D., Whitehead, E., Wicky, A., Widmer, L., Ye, M., Yerly, F., Yeung, J., Yordanov, P., Zavolan, M., Zehnder, T., Zhang, C., Zhou, X., Zisaki, A., Zoller, B. & Zollinger, A., Jan 1 2016, In : Nucleic acids research. 44, D1, p. D27-D37

Research output: Contribution to journalArticle

Open Access
Computational Biology
Databases
Biological Science Disciplines
Mental Competency
Industry
2015
1 Citation (Scopus)

A fast and exact algorithm for the exemplar breakpoint distance

Shao, M. & Moret, B. M. E., Jan 1 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Przytycka, T. M. (ed.). Springer Verlag, p. 309-322 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9029).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Exact Algorithms
Fast Algorithm
Genes
Gene
Genome
9 Citations (Scopus)

An exact algorithm to compute the double-cut-and-join distance for genomes with duplicate genes

Shao, M., Lin, Y. & Moret, B. M. E., May 1 2015, In : Journal of Computational Biology. 22, 5, p. 425-435 11 p.

Research output: Contribution to journalArticle

Duplicate Genes
Exact Algorithms
Join
Genome
Genes
5 Citations (Scopus)

Comparing genomes with rearrangements and segmental duplications

Shao, M. & Moret, B. M. E., Jun 15 2015, In : Bioinformatics. 31, 12, p. i329-i338

Research output: Contribution to journalArticle

Open Access
Genomic Segmental Duplications
Duplication
Rearrangement
Genome
Genes
2014
18 Citations (Scopus)

An exact algorithm to compute the DCJ distance for genomes with duplicate genes

Shao, M., Lin, Y. & Moret, B., Jan 1 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer Verlag, p. 280-292 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Exact Algorithms
Join
Genome
Genes
Gene

On the DCJ median problem

Shao, M. & Moret, B. M. E., Jan 1 2014, Combinatorial Pattern Matching - 25th Annual Symposium, CPM 2014, Proceedings. Springer Verlag, p. 273-282 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8486 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Join
Genes
Genome
Seed
Subgraph
2013
10 Citations (Scopus)

Sorting genomes with rearrangements and segmental duplications through trajectory graphs.

Shao, M., Lin, Y. & Moret, B., 2013, In : BMC bioinformatics. 14 Suppl 15, p. S9

Research output: Contribution to journalArticle

Open Access
Genomic Segmental Duplications
Duplication
Rearrangement
Sorting
Genome
2011
5 Citations (Scopus)

Incorporating Ab Initio energy into threading approaches for protein structure prediction

Shao, M., Wang, S., Wang, C., Yuan, X., Li, S. C., Zheng, W. & Bu, D., Feb 15 2011, In : BMC bioinformatics. 12, SUPPL. 1, S54.

Research output: Contribution to journalArticle

Open Access
Protein Structure Prediction
Alignment
Proteins
Energy Function
Energy