Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research

Por Erdemir, Ahmet, Hunter, Peter J., Holzapfel, Gerhard A., Loew, Leslie M., Middleton, John, Jacobs, Christopher R., Nithiarasu, Perumal, Löhner, Rainlad, Wei, Guowei, Winkelstein, Beth A., Barocas, Victor H., Guilak, Farshid, Ku, Joy P., Hicks, Jennifer L., Delp, Scott L., Sacks, Michael S., Weiss, Jeffrey A., Ateshian, Gerard A., Maas, Steve A., McCulloch, Andrew D., Peng, Grace C. Y.
Publicado no J Biomech Eng (2018)

Accelerating single molecule localization microscopy through parallel processing on a high‐performance computing cluster

Por MUNRO, I., GARCÍA, E., YAN, M., GULDBRAND, S., KUMAR, S., KWAKWA, K., DUNSBY, C., NEIL, M.A.A., FRENCH, P.M.W.
Publicado no J Microsc (2018)

A computational framework to explore large-scale biosynthetic diversity

Por Navarro-Muñoz, Jorge C., Selem-Mojica, Nelly, Mullowney, Michael W., Kautsar, Satria A., Tryon, James H., Parkinson, Elizabeth I., De Los Santos, Emmanuel L.C., Yeong, Marley, Cruz-Morales, Pablo, Abubucker, Sahar, Roeters, Arne, Lokhorst, Wouter, Fernandez-Guerra, Antonio, Cappelini, Luciana Teresa Dias, Goering, Anthony W., Thomson, Regan J., Metcalf, William W., Kelleher, Neil L., Barona-Gomez, Francisco, Medema, Marnix H.
Publicado no Nat Chem Biol (2019)

Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

Por Andrews, T. D., Whittle, B., Field, M. A., Balakishnan, B., Zhang, Y., Shao, Y., Cho, V., Kirk, M., Singh, M., Xia, Y., Hager, J., Winslade, S., Sjollema, G., Beutler, B., Enders, A., Goodnow, C. C.
Publicado em 2012

A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes

Por Fonseca, Vagner, Libin, Pieter J. K., Theys, Kristof, Faria, Nuno R., Nunes, Marcio R. T., Restovic, Maria I., Freire, Murilo, Giovanetti, Marta, Cuypers, Lize, Nowé, Ann, Abecasis, Ana, Deforche, Koen, Santiago, Gilberto A., de Siqueira, Isadora C., San, Emmanuel J., Machado, Kaliane C. B., Azevedo, Vasco, Filippis, Ana Maria Bispo-de, da Cunha, Rivaldo Venâncio, Pybus, Oliver G., Vandamme, Anne-Mieke, Alcantara, Luiz C. J., de Oliveira, Tulio
Publicado no PLoS Negl Trop Dis (2019)

Developing 3D SEM in a broad biological context

Por Kremer, A, Lippens, S, Bartunkova, S, Asselbergh, B, Blanpain, C, Fendrych, M, Goossens, A, Holt, M, Janssens, S, Krols, M, Larsimont, J-C, Mc Guire, C, Nowack, MK, Saelens, X, Schertel, A, Schepens, B, Slezak, M, Timmerman, V, Theunis, C, Van Brempt, R, Visser, Y, GuÉRin, CJ
Publicado no J Microsc (2015)

Chaste: An Open Source C++ Library for Computational Physiology and Biology

Por Mirams, Gary R., Arthurs, Christopher J., Bernabeu, Miguel O., Bordas, Rafel, Cooper, Jonathan, Corrias, Alberto, Davit, Yohan, Dunn, Sara-Jane, Fletcher, Alexander G., Harvey, Daniel G., Marsh, Megan E., Osborne, James M., Pathmanathan, Pras, Pitt-Francis, Joe, Southern, James, Zemzemi, Nejib, Gavaghan, David J.
Publicado em 2013

A call to strengthen the global strategy for schistosomiasis and soil-transmitted helminthiasis: the time is now

Por Lo, Nathan C., Addiss, David G., Hotez, Peter J., King, Charles H., Stothard, J. Russell, Evans, Darin S., Colley, Daniel G., Lin, William, Coulibaly, Jean T., Bustinduy, Amaya L., Raso, Giovanna, Bendavid, Eran, Bogoch, Isaac I., Fenwick, Alan, Savioli, Lorenzo, Molyneux, David, Utzinger, Jürg, Andrews, Jason R.
Publicado no Lancet Infect Dis (2016)

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

Por Bardwell, David A., Adjiman, Claire S., Arnautova, Yelena A., Bartashevich, Ekaterina, Boerrigter, Stephan X. M., Braun, Doris E., Cruz-Cabeza, Aurora J., Day, Graeme M., Della Valle, Raffaele G., Desiraju, Gautam R., van Eijck, Bouke P., Facelli, Julio C., Ferraro, Marta B., Grillo, Damian, Habgood, Matthew, Hofmann, Detlef W. M., Hofmann, Fridolin, Jose, K. V. Jovan, Karamertzanis, Panagiotis G., Kazantsev, Andrei V., Kendrick, John, Kuleshova, Liudmila N., Leusen, Frank J. J., Maleev, Andrey V., Misquitta, Alston J., Mohamed, Sharmarke, Needs, Richard J., Neumann, Marcus A., Nikylov, Denis, Orendt, Anita M., Pal, Rumpa, Pantelides, Constantinos C., Pickard, Chris J., Price, Louise S., Price, Sarah L., Scheraga, Harold A., van de Streek, Jacco, Thakur, Tejender S., Tiwari, Siddharth, Venuti, Elisabetta, Zhitkov, Ilia K.
Publicado em 2011

A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

Por Regier, Jerome C., Mitter, Charles, Zwick, Andreas, Bazinet, Adam L., Cummings, Michael P., Kawahara, Akito Y., Sohn, Jae-Cheon, Zwickl, Derrick J., Cho, Soowon, Davis, Donald R., Baixeras, Joaquin, Brown, John, Parr, Cynthia, Weller, Susan, Lees, David C., Mitter, Kim T.
Publicado em 2013

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

Por Duncan K Ralph, Frederick A Matsen
Publicado em 2016-01-01

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues,...

Por Kozłowska, Urszula, Liwo, Adam, Scheraga, Harold A.
Publicado em 2010

PET imaging of patients with non-small cell lung cancer employing an EGF receptor targeting drug as tracer

Por Memon, A A, Weber, B, Winterdahl, M, Jakobsen, S, Meldgaard, P, Madsen, H H T, Keiding, S, Nexo, E, Sorensen, B S
Publicado em 2011

Biophysics and the Genomic Sciences

Por Schwartz, David C.
Publicado no Biophys J (2019)

Photoswitching of DNA Hybridization Using a Molecular Motor

Por Lubbe, Anouk S., Liu, Qing, Smith, Sanne J., de Vries, Jan Willem, Kistemaker, Jos C. M., de Vries, Alex H., Faustino, Ignacio, Meng, Zhuojun, Szymanski, Wiktor, Herrmann, Andreas, Feringa, Ben L.
Publicado no J Am Chem Soc (2018)

Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review

Por Mubashir Hassan, Faryal Mehwish Awan, Anam Naz, Enrique J. deAndrés-Galiana, Oscar Alvarez, Ana Cernea, Lucas Fernández-Brillet, Juan Luis Fernández-Martínez, Andrzej Kloczkowski
Publicado em 2022-04-01

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Por Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R., Lee, Alexandra J., Kacsoh, Balint Z., Crocker, Alex W., Lewis, Kimberley A., Georghiou, George, Nguyen, Huy N., Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S., Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L., Freddolino, Peter L., Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M., Gemovic, Branislava, Perovic, Vladimir R., Davidović, Radoslav S., Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C., Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A., Antczak, Magdalena, Fabris, Fabio, Wass, Mark N., Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E., Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J., Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W., Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T., Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L., Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B., Reeb, Jonas, Ritchie, David W., Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S., Jo, Dane, Suh, Erica, Dayton, Jonathan B., Larsen, Dallas J., Omdahl, Ashton R., McGuffin, Liam J., Brackenridge, Danielle A., Babbitt, Patricia C., Yunes, Jeffrey M., Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E., Orengo, Christine A., Jeffery, Constance J., Bosco, Giovanni, Hogan, Deborah A., Martin, Maria J., O’Donovan, Claire, Mooney, Sean D., Greene, Casey S., Radivojac, Predrag, Friedberg, Iddo
Publicado no Genome Biol (2019)

Machine Learning Model Analysis and Data Visualization with Small Molecules Tested in a Mouse Model of Mycobacterium tuberculosis Infection (2014–2015)

Por Ekins, Sean, Perryman, Alexander L., Clark, Alex M., Reynolds, Robert C., Freundlich, Joel S.
Publicado no J Chem Inf Model (2016)

Short-term prediction of suicidal thoughts and behaviors in adolescents: Can recent developments in technology and computational science provide a breakthrough?

Por Allen, Nicholas B., Nelson, Benjamin W., Brent, David, Auerbach, Randy P.
Publicado no J Affect Disord (2019)

Smart Grid Wide-Area Transmission System Visualization

Por Thomas J. Overbye, James Weber
Publicado em 2015-12-01