Computational Biologist, PhD

José Luis Villanueva-Cañas, Eva Gonzalez-Roca, Aitor Gastaminza Unanue, Esther Titos, Miguel Julián Martínez Yoldi, Andrea Vergara Gómez, Joan Antón Puig Butillé(2020). {ROBOCOV}: An affordable open-source robotic platform for {SARS}-{CoV}-2 testing by {RT}-{qPCR} . Cold Spring Harbor Laboratory

Jorge Ruiz-Orera, José Luis Villanueva-Cañas, William Blevins, M.Mar Albà(2017). De novo gene evolution: How do we transition from non-coding to coding? . {PeerJ}

Jorge Ruiz-Orera, José Luis Villanueva-Cañas, William Blevins, M.Mar Albà(2017). De novo gene evolution: How do we transition from non-coding to coding? . {PeerJ}

Jorge Ruiz-Orera, José Luis Villanueva-Cañas, William Blevins, M.Mar Albà(2017). How do we transition from non-coding to coding? . {PeerJ}

Jose Luis Villanueva-Canas, Jorge Ruiz-Orera, Isabel Agea, Maria Gallo, David Andreu, Mar Alba (2016). New genes and functional innovation in mammals .

(2020). Evolution of new proteins from translated sORFs in long non-coding RNAs . Experimental Cell Research.

Katherine E. Pickup, Felicitas Pardow, José Carbonell-Caballero, Antonios Lioutas, José Luis Villanueva-Cañas, Roni H. G. Wright, Miguel Beato (2019). Expression of Oncogenic Drivers in 3D Cell Culture Depends on Nuclear ATP Synthesis by NUDT5 . Cancers.

Katherine Pickup, Felicitas Pardow, José Carbonell-Caballero, Antonios Lioutas, José Luis Villanueva-Cañas, Roni Wright, Miguel Beato (2019). Expression of Oncogenic Drivers in 3D Cell Culture Depends on Nuclear ATP Synthesis by NUDT5 . Cancers.

(2019). Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster . Nucleic Acids Research.

Rech, G.E., Bogaerts-Márquez, M., Barrón, M.G., Merenciano, M., Villanueva-Cañas, J.L., Horváth, V., Fiston-Lavier, A.-S., Luyten, I., Venkataram, S., Quesneville, H., et al.(2019). Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila . PLoS Genetics. 15. (2).

Le Dily, F., Vidal, E., Cuartero, Y., Quilez, J., Nacht, A.S., Vicent, G.P., Carbonell-Caballero, J., Sharma, P., Le Dily, F., Vidal, E., et al.(2019). Hormone-control regions mediate steroid receptor–dependent genome organization . Genome Research. 29. (1). p. 29-39.

Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer, M. Mar Albà(2018). Translation of neutrally evolving peptides provides a basis for de novo gene evolution . Nature Ecology {\&} Evolution. 2. (5). p. 890--896. Springer Nature

Sheena L. Faherty, José Luis Villanueva-Cañas, Marina B. Blanco, M. Mar Albà, Anne D. Yoder(2018). Transcriptomics in the wild: Hibernation physiology in free-ranging dwarf lemurs . Molecular Ecology. 27. (3). p. 709--722. Wiley

François Le Dily, Enrique Vidal, Yasmina Cuartero, Javier Quilez, A. Silvina Nacht, Guillermo P. Vicent, José Carbonell-Caballero, Priyanka Sharma, José Luis Villanueva-Cañas, Roberto Ferrari, et al.(2018). Hormone-control regions mediate steroid receptor{\textendash}dependent genome organization . Genome Research. Cold Spring Harbor Laboratory

Ruiz-Orera, J., Verdaguer-Grau, P., Villanueva-Cañas, J.L., Messeguer, X., Albà, M.M.(2018). Translation of neutrally evolving peptides provides a basis for de novo gene evolution . Nature Ecology and Evolution. 2. (5). p. 890-896.

Faherty, S.L., Villanueva-Cañas, J.L., Blanco, M.B., Albà, M.M., Yoder, A.D.(2018). Transcriptomics in the wild: Hibernation physiology in free-ranging dwarf lemurs . Molecular Ecology. 27. (3). p. 709-722.

José Luis Villanueva-Cañas, Jorge Ruiz-Orera, M. Isabel Agea, Maria Gallo, David Andreu, M. Mar Albà(2017). New Genes and Functional Innovation in Mammals . Genome Biology and Evolution. 9. (7). p. 1886--1900. Oxford University Press ({OUP})

Villanueva-Cañas, J.L., Rech, G.E., de Cara, M.A.R., González, J.(2017). Beyond SNPs: how to detect selection on transposable element insertions . Methods in Ecology and Evolution. 8. (6). p. 728-737.

Villanueva-Ca{\~{n}}as, Jos{\'{e}} Luis and Rech, Gabriel E. and de Cara, Maria Angeles Rodriguez and Gonz{\'{a}}lez, Josefa(2017). Beyond SNPs: how to detect selection on transposable element insertions . Methods in Ecology and Evolution. 8. (6). p. 728--737.

Villanueva-Cañas, J.L., Ruiz-Orera, J., Agea, M.I., Gallo, M., Andreu, D., Albà, M.M.(2017). New genes and functional innovation in mammals . Genome Biology and Evolution. 9. (7). p. 1886-1900.

Abascal, Federico and Corvelo, Andr{\'{e}} and Cruz, Fernando and Villanueva-Ca{\~{n}}as, Jos{\'{e}} L. and Vlasova, Anna and Marcet-Houben, Marina and Mart{\'{i}}nez-Cruz, Bego{\~{n}}a and Cheng, Jade Yu and Prieto, Pablo and Quesada, V{\'{i}}ctor and Quilez, Javier and Li, Gang and Garc{\'{i}}a, Francisca and Rubio-Camarillo, Miriam and Frias, Leonor and Ribeca, Paolo and Capella-Guti{\'{e}}rrez, Salvador and Rodr{\'{i}}guez, Jos{\'{e}} M. and C{\^{a}}mara, Francisco and Lowy, Ernesto and Cozzuto, Luca and Erb, Ionas and Tress, Michael L. and Rodriguez-Ales, Jose L. and Ruiz-Orera, Jorge and Reverter, Ferran and Casas-Marce, Mireia and Soriano, Laura and Arango, Javier R. and Derdak, Sophia and Gal{\'{a}}n, Beatriz and Blanc, Julie and Gut, Marta and Lorente-Galdos, Belen and Andr{\'{e}}s-Nieto, Marta and L{\'{o}}pez-Ot{\'{i}}n, Carlos and Valencia, Alfonso and Gut, Ivo and Garc{\'{i}}a, Jos{\'{e}} L. and Guig{\'{o}}, Roderic and Murphy, William J. and Ruiz-Herrera, Aurora and Marques-Bonet, Tomas and Roma, Guglielmo and Notredame, Cedric and Mailund, Thomas and Alb{\`{a}}, M. Mar and Gabald{\'{o}}n, Toni and Alioto, Tyler and Godoy, Jos{\'{e}} A. and Pimm, SL and Jenkins, CN and Abell, R and Brooks, TM and Gittleman, JL and Joppa, LN and Raven, PH and Roberts, CM and Sexton, JO and Thomas, CD and Williamson, M and Frankham, R and Ballou, JD and Briscoe, DA and Shafer, ABA and Wolf, JBW and Alves, PC and Bergstrom, L and Bruford, MW and Brannstrom, I and Colling, G and Dalen, L and Meester, L and Ekblom, R and Li, G and Davis, BW and Eizirik, E and Murphy, WJ and Johnson, WE and Eizirik, E and Pecon-Slattery, J and Murphy, WJ and Antunes, A and Teeling, E and O'Brien, SJ and Nowell, K and Jackson, P and Casas-Marce, M and Soriano, L and L{\'{o}}pez-Bao, JV and Godoy, JA and Ruiz-L{\'{o}}pez, MJ and Ga{\~{n}}{\'{a}}n, N and Godoy, JA and Olmo, A and Garde, J and Espeso, G and Vargas, A and Mart{\'{i}}nez, F and Rold{\'{a}}n, ERS and Gomendio, M and Palomares, F and Godoy, JA and L{\'{o}}pez-Bao, JV and Rodr{\'{i}}guez, A and Roques, S and Casas-Marce, M and Revilla, E and Delibes, M and Pe{\~{n}}a, L and Garc{\'{i}}a, P and Jim{\'{e}}nez, MA and Benito, A and Alenza, MDP and S{\'{a}}nchez, B and Jim{\'{e}}nez, MA and S{\'{a}}nchez, B and Alenza, MDP and Garc{\'{i}}a, P and L{\'{o}}pez, JV and Rodr{\'{i}}guez, A and Mu{\~{n}}oz, A and Mart{\'{i}}nez, F and Vargas, A and Pe{\~{n}}a, L and Mart{\'{i}}nez, F and Manteca, X and Pastor, J and Steiner, CC and Putnam, AS and Hoeck, PEA and Ryder, OA and Kitzman, JO and MacKenzie, AP and Adey, A and Hiatt, JB and Patwardhan, RP and Sudmant, PH and Ng, SB and Alkan, C and Qiu, RL and Eichler, EE and Shendure, J and Parra, G and Bradnam, K and Ning, Z and Keane, T and Korf, I and Mailund, T and Dutheil, JY and Hobolth, A and Lunter, G and Schierup, MH and Mailund, T and Halager, AE and Westergaard, M and Dutheil, JY and Munch, K and Andersen, LN and Lunter, G and Prufer, K and Scally, A and Hobolth, A and Schierup, MH and Li, H and Durbin, R and Gutenkunst, RN and Hernandez, RD and Williamson, SH and Bustamante, CD and Clavero, M and Delibes, M and Rodr{\'{i}}guez-Varela, R and Tagliacozzo, A and Ure{\~{n}}a, I and Garc{\'{i}}a, N and Cr{\'{e}}gut-Bonnoure, E and Mannino, MA and Arsuaga, JL and Valdiosera, C and Koen, EL and Bowman, J and Lalor, JL and Wilson, PJ and Schmidt, K and Ratkiewicz, M and Konopinski, MK and Ellis, EC and Goldewijk, KK and Siebert, S and Lightman, D and Ramankutty, N and Nie, W and Wang, J and Su, W and Wang, D and Tanomtong, A and Perelman, PL and Graphodatsky, AS and Yang, F and Huerta-Cepas, J and Gabald{\'{o}}n, T and Lombardi, G and Burzyn, D and Mundinano, J and Berguer, P and Bekinschtein, P and Costa, H and Castillo, LF and Goldman, A and Meiss, R and Piazzon, I and Nepomnaschy, I and Schurigt, U and Eilenstein, R and Gajda, M and Leipner, C and Sevenich, L and Reinheckel, T and Peters, C and Wiederanders, B and Brauer, R and Yang, ZH and Heffner, HE and Heffner, RS and Hunt, DM and Buch, P and Michaelides, M and Boutin, TS and Rouzic, A and Capy, P and Lynch, M and Conery, JS and Morgan, MT and Gherman, A and Chen, PE and Teslovich, TM and Stankiewicz, P and Withers, M and Kashuk, CS and Chakravarti, A and Lupski, JR and Cutler, DJ and Katsanis, N and Lockton, S and Ross-Ibarra, J and Gaut, BS and Zhang, Y and Romanish, MT and Mager, DL and Glemin, S and Arndt, PF and Messer, PW and Petrov, D and Galtier, N and Duret, L and Katzman, S and Kern, AD and Pollard, KS and Salama, SR and Haussler, D and Cho, YS and Hu, L and Hou, H and Lee, H and Xu, J and Kwon, S and Oh, S and Kim, H-M and Jho, S and Kim, S and Li, S and Li, B and Cheng, C and Xiong, Z and Liu, Q and Lai, J and Carey, H and Zhang, Q and Zheng, H and Wei, S and Zhao, S and Zheng, P and Dong, S and Zhan, X and Wu, Q and Guo, X and Hu, Y and He, W and Zhang, S and Fan, W and Xue, Y and Prado-Mart{\'{i}}nez, J and Sudmant, PH and Narasimhan, V and Ayub, Q and Szpak, M and Frandsen, P and Chen, Y and Yngvadottir, B and Cooper, DN and Sarkissian, C and Ermini, L and Schubert, M and Melinda, A Yang and Librado, P and Fumagalli, M and J{\'{o}}nsson, H and Gila, K Bar-Gal and Albrechtsen, A and Filipe, G Vieira and Alhaddad, H and Khan, R and Grahn, RA and Gandolfi, B and Mullikin, JC and Cole, SA and Gruffydd-Jones, TJ and Haggstrom, J and Lohi, H and Longeri, M and Lyons, LA and Hill, WG and Robertson, A and Leffler, EM and Bullaughey, K and Matute, DR and Meyer, WK and Segurel, L and Venkat, A and Andolfatto, P and Przeworski, M and Bustamante, CD and Fledel-Alon, A and Williamson, S and Nielsen, R and Hubisz, MT and Glanowski, S and Tanenbaum, DM and White, TJ and Sninsky, JJ and Hernandez, RD and Loire, E and Chiari, Y and Bernard, A and Cahais, V and Romiguier, J and Nabholz, B and Lourenco, JM and Galtier, N and Pool, JE and Nielsen, R and Otto, SP and Barton, NH and Alonso, S and L{\'{o}}pez, S and Izagirre, N and Rua, C and Hamilton, JA and Miller, JM and Thomas, MA and Roemer, GW and Donlan, CJ and Dickson, BG and Matocq, M and Malaney, J and Kovach, RP and Luikart, G and Lowe, WH and Boyer, MC and Muhlfeld, CC and Reed, DH and Palomares, F and Rodr{\'{i}}guez, A and Revilla, E and L{\'{o}}pez-Bao, JV and Calzada, J and Griebel, T and Zacher, B and Ribeca, P and Raineri, E and Lacroix, V and Guigo, R and Sammeth, M and Ramskold, D and Wang, ET and Burge, CB and Sandberg, R and Robinson, MD and McCarthy, DJ and Smyth, GK and Brawand, D and Soumillon, M and Necsulea, A and Julien, P and Csardi, G and Harrigan, P and Weier, M and Liechti, A and Aximu-Petri, A and Kircher, M and Tarazona, S and Garcia-Alcalde, F and Dopazo, J and Ferrer, A and Conesa, A and Morgulis, A and Gertz, EM and Sch{\"{a}}ffer, AA and Agarwala, R and Haas, BJ and Salzberg, SL and Zhu, W and Pertea, M and Allen, JE and Orvis, J and White, O and Buell, CR and Wortman, JR and Nawrocki, EP and Kolbe, DL and Eddy, SR and Griffiths-Jones, S and Moxon, S and Marshall, M and Khanna, A and Eddy, SR and Bateman, A and Derrien, T and Johnson, R and Bussotti, G and Tanzer, A and Djebali, S and Tilgner, H and Guernec, G and Martin, D and Merkel, A and Knowles, DG and Zdobnov, EM and Apweiler, R and Kanehisa, M and Goto, S and Sato, Y and Furumichi, M and Tanabe, M and Matthews, L and Gopinath, G and Gillespie, M and Caudy, M and Croft, D and Bono, B and Garapati, P and Hemish, J and Hermjakob, H and Jassal, B and Gotz, S and Garcia-G{\'{o}}mez, JM and Terol, J and Williams, TD and Nagaraj, SH and Nueda, MJ and Robles, M and Talon, M and Dopazo, J and Conesa, A and Petersen, TN and Brunak, S and Heijne, G and Nielsen, H and Ordo{\~{n}}ez, GR and Puente, XS and Quesada, V and L{\'{o}}pez-Ot{\'{i}}n, C and Altschul, SF and Gish, W and Miller, W and Myers, EW and Lipman, DJ and Toll-Riera, M and Bosch, N and Bellora, N and Castelo, R and Armengol, L and Estivill, X and Alb{\`{a}}, MM and Trapnell, C and Williams, BA and Pertea, G and Mortazavi, A and Kwan, G and Baren, MJ and Salzberg, SL and Wold, BJ and Pachter, L and Seabright, M and Wursterhill, DH and Centerwall, WR and O'Brien, JT and Menninger, JC and Nash, WG and Kie{\l}basa, SM and Wan, R and Sato, K and Horton, P and Frith, MC and Quinlan, AR and Hall, IM and Huerta-Cepas, J and Capella-Guti{\'{e}}rrez, S and Pryszcz, LP and Denisov, I and Kormes, D and Marcet-Houben, M and Gabald{\'{o}}n, T and Gil, M and Zanetti, MS and Zoller, S and Anisimova, M and Huerta-Cepas, J and Dopazo, J and Gabald{\'{o}}n, T and Huerta-Cepas, J and Dopazo, H and Dopazo, J and Gabald{\'{o}}n, T and Huerta-Cepas, J and Capella-Guti{\'{e}}rrez, S and Pryszcz, LP and Marcet-Houben, M and Gabald{\'{o}}n, T and Slater, GS and Birney, E and Stamatakis, A and Loytynoja, A and Goldman, N and Villanueva-Ca{\~{n}}as, JL and Laurie, S and Alb{\`{a}}, MM and P{\'{e}}rez-Llamas, C and L{\'{o}}pez-Bigas, N and Flicek, P and Ahmed, I and Amode, MR and Barrell, D and Beal, K and Brent, S and Carvalho-Silva, D and Clapham, P and Coates, G and Fairley, S and Gascuel, O and Rubio-Camarillo, M and G{\'{o}}mez-L{\'{o}}pez, G and Fern{\'{a}}ndez, JM and Valencia, A and Pisano, DG and Cingolani, P and Platts, A and Wang, LL and Coon, M and Nguyen, T and Wang, L and Land, SJ and Lu, XY and Ruden, DM and Rodr{\'{i}}guez, JM and Maietta, P and Ezkurdia, I and Pietrelli, A and Wesselink, J-J and L{\'{o}}pez, G and Valencia, A and Tress, ML and Li, H and Durbin, R and Li, H and Handsaker, B and Wysoker, A and Fennell, T and Ruan, J and Homer, N and Marth, G and Abecasis, G and Durbin, R and Proc, GPD and Hach, F and Sarrafi, I and Hormozdiari, F and Alkan, C and Eichler, EE and Sahinalp, SC and Alkan, C and Kidd, JM and Marques-Bonet, T and Aksay, G and Antonacci, F and Hormozdiari, F and Kitzman, JO and Baker, C and Malig, M and Mutlu, O and Iqbal, Z and Caccamo, M and Turner, I and Flicek, P and McVean, G and Danecek, P and Auton, A and Abecasis, G and Albers, CA and Banks, E and DePristo, MA and Handsaker, RE and Lunter, G and Marth, GT and Sherry, ST and Davinson, AC and Hinkley, DV and Canty, A and Ripley, B and Al-Shahrour, F and D{\'{i}}az-Uriarte, R and Dopazo, J and Medina, I and Carbonell, J and Pulido, L and Madeira, SC and Goetz, S and Conesa, A and Tarraga, J and Pascual-Montano, A and Nogales-Cadenas, R and Santoyo, J and Prufer, K and Racimo, F and Patterson, N and Jay, F and Sankararaman, S and Sawyer, S and Heinze, A and Renaud, G and Sudmant, PH and Filippo, C and Dobrynin, P and Liu, S and Tamazian, G and Xiong, Z and Yurchenko, A and Krasheninnikova, K and Kliver, S and Schmidt-Kuntzel, A and Koepfli, K-P and Johnson, W and Carbone, L and Harris, R Alan and Gnerre, S and Veeramah, KR and Lorente-Galdos, B and Huddleston, J and Meyer, TJ and Herrero, J and Roos, C and Aken, B and Yim, HS and Cho, YS and Guang, XM and Kang, SG and Jeong, JY and Cha, SS and Oh, HM and Lee, JH and Yang, EC and Kwon, KK and Palkopoulou, E and Mallick, S and Skoglund, P and Enk, J and Rohland, N and Li, H and Omrak, A and Vartanyan, S and Poinar, H and G{\"{o}}therstr{\"{o}}m, A(2016). Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx . Genome Biology. 17. (1). p. 251. BioMed Central

Sheena L. Faherty, José Luis Villanueva-Cañas, Peter H. Klopfer, M. Mar Albà, Anne D. Yoder(2016). Gene expression profiling in the hibernating primate,Cheirogaleus medius . Genome Biol Evol. p. evw163. Oxford University Press ({OUP})

Vartia, Salla and Villanueva-Ca{\~{n}}as, Jos{\'{e}} L. and Finarelli, John and Farrell, Edward D. and Collins, Patrick C. and Hughes, Graham M. and Carlsson, Jeanette E. L. and Gauthier, David T. and McGinnity, Philip and Cross, Thomas F. and FitzGerald, Richard D. and Mirimin, Luca and Crispie, Fiona and Cotter, Paul D. and Carlsson, Jens(2016). A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding . Royal Society Open Science. 3. (1). p. 150565. The Royal Society

Faherty, S.L., Luis Villanueva-Cañas, J., Klopfer, P.H., Albà, M.M., Yoder, A.D.(2016). Gene expression profiling in the hibernating primate, Cheirogaleus medius . Genome Biology and Evolution. 8. (8).

Abascal, F., Corvelo, A., Cruz, F., Villanueva-Cañas, J.L., Vlasova, A., Marcet-Houben, M., Martínez-Cruz, B., Cheng, J.Y., Prieto, P., Quesada, V., et al.(2016). Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx . Genome Biology. 17. (1).

Vartia, S., Villanueva-Cañas, J.L., Finarelli, J., Farrell, E.D., Collins, P.C., Hughes, G.M., Carlsson, J.E.L., Gauthier, D.T., McGinnity, P., Vartia, S., et al.(2016). A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding . Royal Society Open Science. 3. (1).

Villanueva-Cañas JL, Faherty SL, Yoder AD, Albà MM, Integrative and comparative biology, 2014, vol. 54, no. 3, pp. 452-462 .

Villanueva-Cañas, J.L., Faherty, S.L., Yoder, A.D., Albà, M.M.(2014). Comparative genomics of mammalian hibernators using gene networks . Integrative and Comparative Biology. 54. (3). p. 452-462.

Villanueva-Cañas, J.L., Laurie, S., Albà, M.M.(2013). Improving genome-wide scans of positive selection by using protein isoforms of similar length . Genome Biology and Evolution. 5. (2). p. 457-467.

Villanueva-Cañas JL, Laurie S, Albà MM, Genome biology and evolution, 2013, vol. 5, no. 2, pp. 457-467 .

Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer, M Mar Albà(2016). Functional and non-functional classes of peptides produced by long non-coding {RNAs} . Cold Spring Harbor Laboratory Press