Current Protocols in Bioinformatics

Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests

Posada, D., & Buckley, T. R. (2004) · Systematic Biology · doi:10.1080/10635150490522304 · Cited by 3,927

Model selection in ecology and evolution

Johnson, J. B., & Omland, K. S. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2003.10.013 · Cited by 3,838

A beginner’s guide to eukaryotic genome annotation

Yandell, M., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 588

Natural mutagenesis of human genomes by endogenous retrotransposons

Iskow, R. C., McCabe, M. T., Mills, R. E., Torene, S., Pittard, W. S., Neuwald, A. F., Van Meir, E. G., Vertino, P. M., & Devine, S. E. (2010) · Cell · doi:10.1016/j.cell.2010.05.020 · Cited by 551

Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication

Dennis, M. Y., Nuttle, X., Sudmant, P. H., Antonacci, F., Graves, T. A., Nefedov, M., Rosenfeld, J. A., Sajjadian, S., Malig, M., Kotkiewicz, H., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.033 · Cited by 407

GeneMANIA Prediction Server 2013 Update

Zuberi, K., Franz, M., Rodriguez, H., Montojo, J., Lopes, C. T., Bader, G. D., & Morris, Q. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt533 · Cited by 396

Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes

Michalski, A., Damoc, E., Lange, O., Denisov, E., Nolting, D., Müller, M., Viner, R., Schwartz, J., Remes, P., Belford, M., et al. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.013698 · Cited by 373

A Genomic Regulatory Element That Directs Assembly and Function of Immune-Specific AP-1–IRF Complexes

Glasmacher, E., Agrawal, S., Chang, A. B., Murphy, T. L., Zeng, W., Vander Lugt, B., Khan, A. A., Ciofani, M., Spooner, C. J., Rutz, S., et al. (2012) · Science · doi:10.1126/science.1228309 · Cited by 361

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers

Yugi, K., Kubota, H., Hatano, A., & Kuroda, S. (2016) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.12.013 · Cited by 258

ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry

Zamdborg, L., LeDuc, R. D., Glowacz, K. J., Kim, Y.-B., Viswanathan, V., Spaulding, I. T., Early, B. P., Bluhm, E. J., Babai, S., & Kelleher, N. L. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm371 · Cited by 251

The transcription factor IRF1 dictates the IL-21-dependent anticancer functions of TH9 cells

Végran, F., Berger, H., Boidot, R., Mignot, G., Bruchard, M., Dosset, M., Chalmin, F., Rébé, C., Dérangère, V., Ryffel, B., et al. (2014) · Nature Immunology · doi:10.1038/ni.2925 · Cited by 228

The diverse and expanding role of mass spectrometry in structural and molecular biology

Lössl, P., van de Waterbeemd, M., & Heck, A. J. (2016) · The EMBO Journal · doi:10.15252/embj.201694818 · Cited by 222

Comparative genomics of emerging pathogens in the Candida glabrata clade.

Gabaldón, T., Martin, T., Marcet-Houben, M., Durrens, P., Bolotin-Fukuhara, M., Lespinet, O., Arnaise, S., Boisnard, S., Aguileta, G., Atanasova, R., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-623 · Cited by 198

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

Prakash, A., Tomazela, D. M., Frewen, B., MacLean, B., Merrihew, G., Peterman, S., & MacCoss, M. J. (2009) · Journal of Proteome Research · doi:10.1021/pr801028b · Cited by 147

Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production

Bogen, C., Al-Dilaimi, A., Albersmeier, A., Wichmann, J., Grundmann, M., Rupp, O., Lauersen, K. J., Blifernez-Klassen, O., Kalinowski, J., Goesmann, A., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-926 · Cited by 108

Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20

McCraw, D. M., O’Donnell, J. K., Taylor, K. A., Stagg, S. M., & Chapman, M. S. (2012) · Virology · doi:10.1016/j.virol.2012.05.004 · Cited by 84

PU.1 and NFATc1 mediate osteoclastic induction of the mouse β3 integrin promoter

Crotti, T. N., Sharma, S. M., Fleming, J. D., Flannery, M. R., Ostrowski, M. C., Goldring, S. R., & McHugh, K. P. (2008) · Journal of Cellular Physiology · doi:10.1002/jcp.21344 · Cited by 76

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction

Hu, Z., Ng, D. M., Yamada, T., Chen, C., Kawashima, S., Mellor, J., Linghu, B., Kanehisa, M., Stuart, J. M., & DeLisi, C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm295 · Cited by 76

Molecular investigation of the radiation resistance of edible cyanobacterium Arthrospira sp. PCC 8005

Badri, H., Monsieurs, P., Coninx, I., Wattiez, R., & Leys, N. (2015) · MicrobiologyOpen · doi:10.1002/mbo3.229 · Cited by 56

Light whole genome sequence for SNP discovery across domestic cat breeds

Mullikin, J. C., Hansen, N. F., Shen, L., Ebling, H., Donahue, W. F., Tao, W., Saranga, D. J., Brand, A., Rubenfield, M. J., Young, A. C., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-406 · Cited by 56

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis : Implications for Isoprenoid Production

Martien, J. I., Hebert, A. S., Stevenson, D. M., Regner, M. R., Khana, D. B., Coon, J. J., & Amador-Noguez, D. (2019) · mSystems · doi:10.1128/msystems.00284-18 · Cited by 34

Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation

Foley, N. M., Harris, A. J., Bredemeyer, K. R., Ruedi, M., Puechmaille, S. J., Teeling, E. C., Criscitiello, M. F., & Murphy, W. J. (2024) · Cell Genomics · doi:10.1016/j.xgen.2023.100482 · Cited by 31

Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma

Mitra, A., Andrews, M. C., Roh, W., De Macedo, M. P., Hudgens, C. W., Carapeto, F., Singh, S., Reuben, A., Wang, F., Mao, X., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15538-9 · Cited by 27

Effect of Poria cocos Terpenes: Verifying Modes of Action Using Molecular Docking, Drug-Induced Transcriptomes, and Diffusion Network Analyses

Park, M., Yi, J.-M., Kim, N. S., Lee, S.-Y., & Lee, H. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25094636 · Cited by 11

Hepatocyte Cell Cycle Progression Depends on a Transcriptional Repressor Cascade Downstream of Wnt Signaling

Jin, Y., Anbarchian, T., Wu, P., Sarkar, A., Fish, M., & Nusse, R. (2021) · doi:10.1101/2021.10.15.464616 · Cited by 2