INGA 2.0: improving protein function prediction for the dark proteome

Por Piovesan, Damiano, Tosatto, Silvio C E
Publicado no Nucleic Acids Res (2019)

Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis

Por Liu, Donglin, Brockman, J. Michael, Dass, Brinda, Hutchins, Lucie N., Singh, Priyam, McCarrey, John R., MacDonald, Clinton C., Graber, Joel H.
Publicado em 2007

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

Por Paez-Espino, David, Roux, Simon, Chen, I-Min A, Palaniappan, Krishna, Ratner, Anna, Chu, Ken, Huntemann, Marcel, Reddy, T B K, Pons, Joan Carles, Llabrés, Mercè, Eloe-Fadrosh, Emiley A, Ivanova, Natalia N, Kyrpides, Nikos C
Publicado no Nucleic Acids Res (2019)

DBSI: DNA-binding site identifier

Por Zhu, Xiaolei, Ericksen, Spencer S., Mitchell, Julie C.
Publicado em 2013

The Biomolecular Interaction Network Database and related tools 2005 update

Por Alfarano, C., Andrade, C. E., Anthony, K., Bahroos, N., Bajec, M., Bantoft, K., Betel, D., Bobechko, B., Boutilier, K., Burgess, E., Buzadzija, K., Cavero, R., D'Abreo, C., Donaldson, I., Dorairajoo, D., Dumontier, M. J., Dumontier, M. R., Earles, V., Farrall, R., Feldman, H., Garderman, E., Gong, Y., Gonzaga, R., Grytsan, V., Gryz, E., Gu, V., Haldorsen, E., Halupa, A., Haw, R., Hrvojic, A., Hurrell, L., Isserlin, R., Jack, F., Juma, F., Khan, A., Kon, T., Konopinsky, S., Le, V., Lee, E., Ling, S., Magidin, M., Moniakis, J., Montojo, J., Moore, S., Muskat, B., Ng, I., Paraiso, J. P., Parker, B., Pintilie, G., Pirone, R., Salama, J. J., Sgro, S., Shan, T., Shu, Y., Siew, J., Skinner, D., Snyder, K., Stasiuk, R., Strumpf, D., Tuekam, B., Tao, S., Wang, Z., White, M., Willis, R., Wolting, C., Wong, S., Wrong, A., Xin, C., Yao, R., Yates, B., Zhang, S., Zheng, K., Pawson, T., Ouellette, B. F. F., Hogue, C. W. V.
Publicado em 2005

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity

Por Taxis, Tasia M., Wolff, Sara, Gregg, Sarah J., Minton, Nicholas O., Zhang, Chiqian, Dai, Jingjing, Schnabel, Robert D., Taylor, Jeremy F., Kerley, Monty S., Pires, J. Chris, Lamberson, William R., Conant, Gavin C.
Publicado no Nucleic Acids Res (2015)

Analyzing large biological datasets with association networks

Por Karpinets, Tatiana V., Park, Byung H., Uberbacher, Edward C.
Publicado em 2012

Genome engineering of isogenic human ES cells to model autism disorders

Por Martinez, Refugio A., Stein, Jason L., Krostag, Anne-Rachel F., Nelson, Angelique M., Marken, John S., Menon, Vilas, May, Ryan C., Yao, Zizhen, Kaykas, Ajamete, Geschwind, Daniel H., Grimley, Joshua S.
Publicado no Nucleic Acids Res (2015)

Gene Ontology annotations at SGD: new data sources and annotation methods

Por Hong, Eurie L., Balakrishnan, Rama, Dong, Qing, Christie, Karen R., Park, Julie, Binkley, Gail, Costanzo, Maria C., Dwight, Selina S., Engel, Stacia R., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Krieger, Cynthia J., Livstone, Michael S., Miyasato, Stuart R., Nash, Robert S., Oughtred, Rose, Skrzypek, Marek S., Weng, Shuai, Wong, Edith D., Zhu, Kathy K., Dolinski, Kara, Botstein, David, Cherry, J. Michael
Publicado em 2008

funtrp: identifying protein positions for variation driven functional tuning

Por Miller, Maximilian, Vitale, Daniel, Kahn, Peter C, Rost, Burkhard, Bromberg, Yana
Publicado no Nucleic Acids Res (2019)

A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity

Por Garton, Michael, Najafabadi, Hamed S., Schmitges, Frank W., Radovani, Ernest, Hughes, Timothy R., Kim, Philip M.
Publicado no Nucleic Acids Res (2015)

A large-scale association study for nanoparticle C60 uncovers mechanisms of nanotoxicity disrupting the native conformations of DNA/RNA

Por Xu, Xue, Wang, Xia, Li, Yan, Wang, Yonghua, Yang, Ling
Publicado em 2012

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

Por Blin, Kai, Wolf, Thomas, Chevrette, Marc G., Lu, Xiaowen, Schwalen, Christopher J., Kautsar, Satria A., Suarez Duran, Hernando G., de los Santos, Emmanuel L. C., Kim, Hyun Uk, Nave, Mariana, Dickschat, Jeroen S., Mitchell, Douglas A., Shelest, Ekaterina, Breitling, Rainer, Takano, Eriko, Lee, Sang Yup, Weber, Tilmann, Medema, Marnix H.
Publicado no Nucleic Acids Res (2017)

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

Por Folkes, Leighton, Moxon, Simon, Woolfenden, Hugh C., Stocks, Matthew B., Szittya, Gyorgy, Dalmay, Tamas, Moulton, Vincent
Publicado em 2012

New insights into the structures and interactions of bacterial Y-family DNA polymerases

Por Timinskas, Kęstutis, Venclovas, Česlovas
Publicado no Nucleic Acids Res (2019)

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae

Por Monteiro, Pedro T., Mendes, Nuno D., Teixeira, Miguel C., d’Orey, Sofia, Tenreiro, Sandra, Mira, Nuno P., Pais, Hélio, Francisco, Alexandre P., Carvalho, Alexandra M., Lourenço, Artur B., Sá-Correia, Isabel, Oliveira, Arlindo L., Freitas, Ana T.
Publicado em 2008

Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing

Por Sathirapongsasuti, J. Fah, Sathira, Nuankanya, Suzuki, Yutaka, Huttenhower, Curtis, Sugano, Sumio
Publicado em 2011

Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans

Por Dumesic, Phillip A., Rosenblad, Magnus A., Samuelsson, Tore, Nguyen, Tiffany, Moresco, James J., Yates, John R., Madhani, Hiten D.
Publicado no Nucleic Acids Res (2015)

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

Por Jia, Baofeng, Raphenya, Amogelang R., Alcock, Brian, Waglechner, Nicholas, Guo, Peiyao, Tsang, Kara K., Lago, Briony A., Dave, Biren M., Pereira, Sheldon, Sharma, Arjun N., Doshi, Sachin, Courtot, Mélanie, Lo, Raymond, Williams, Laura E., Frye, Jonathan G., Elsayegh, Tariq, Sardar, Daim, Westman, Erin L., Pawlowski, Andrew C., Johnson, Timothy A., Brinkman, Fiona S.L., Wright, Gerard D., McArthur, Andrew G.
Publicado no Nucleic Acids Res (2017)

RNASEQR—a streamlined and accurate RNA-seq sequence analysis program

Por Chen, Leslie Y., Wei, Kuo-Chen, Huang, Abner C.-Y., Wang, Kai, Huang, Chiung-Yin, Yi, Danielle, Tang, Chuan Yi, Galas, David J., Hood, Leroy E.
Publicado em 2012