• 100 Citations
  • 5 h-Index
20112019

Research output per year

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Research Output

  • 100 Citations
  • 5 h-Index
  • 13 Article
  • 5 Conference contribution
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Article

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

18 Scopus citations

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

3 Scopus citations

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
3 Scopus citations

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

9 Scopus citations

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
5 Scopus citations

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
2 Scopus citations

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
5 Scopus citations

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
1 Scopus citations

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

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
11 Scopus citations

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
4 Scopus citations

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

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
17 Scopus citations