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20112023

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  • 2023

    Locality-sensitive bucketing functions for the edit distance

    Chen, K. & Shao, M., Dec 2023, In: Algorithms for Molecular Biology. 18, 1, 7.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1 Scopus citations
  • Seeding with minimized subsequence

    Li, X., Shi, Q., Chen, K. & Shao, M., Jun 1 2023, In: Bioinformatics. 39, p. I232-I241

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1 Scopus citations
  • Transcript assembly and annotations: Bias and adjustment

    Zhang, Q. & Shao, M., Dec 2023, In: PLoS computational biology. 19, 12, e1011734.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 2022

    Accurate assembly of multi-end RNA-seq data with Scallop2

    Zhang, Q., Shi, Q. & Shao, M., Mar 2022, In: Nature Computational Science. 2, 3, p. 148-152 5 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    8 Scopus citations
  • 2020

    Context-aware seeds for read mapping

    Xin, H., Shao, M. & Kingsford, C., May 23 2020, In: Algorithms for Molecular Biology. 15, 1, 10.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    3 Scopus citations
  • 2019

    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 journalArticlepeer-review

    Open Access
    11 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 journalArticlepeer-review

    Open Access
    22 Scopus citations
  • 2018

    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 journalArticlepeer-review

    Open Access
    21 Scopus citations
  • 2017

    accurate assembly of transcripts through phase-preserving graph decomposition

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

    Research output: Contribution to journalArticlepeer-review

    Open Access
    110 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 journalArticlepeer-review

    Open Access
    8 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 journalArticlepeer-review

    Open Access
    3 Scopus citations
  • 2016

    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 journalArticlepeer-review

    5 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 journalArticlepeer-review

    Open Access
    4 Scopus citations
  • 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., 2016, In: Nucleic acids research. 44, D1, p. D27-D37

    Research output: Contribution to journalArticlepeer-review

    Open Access
    44 Scopus citations
  • 2015

    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 journalArticlepeer-review

    38 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 journalArticlepeer-review

    Open Access
    11 Scopus citations
  • 2013

    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 S9.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    13 Scopus citations
  • 2011

    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 journalArticlepeer-review

    Open Access
    5 Scopus citations