• 96 Citations
  • 5 h-Index
20112019
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Research Output 2011 2019

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