As one of my 2016 scientific resolutions I will be reading one paper every day of the year and posting each here (hopefully) daily.
Yaffe, Michael B. “Reproducibility in science.” Sci. Signal. 8, no. 371 (2015): eg5-eg5.
Naegle, Kristen, Nancy R. Gough, and Michael B. Yaffe. “Criteria for biological reproducibility: what does” n” mean?.” Science signaling 8, no. 371 (2015): fs7.
Parnas, Oren, Marko Jovanovic, Thomas M. Eisenhaure, Rebecca H. Herbst, Atray Dixit, Chun Jimmie Ye, Dariusz Przybylski et al. “A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks.” Cell 162, no. 3 (2015): 675-686.
Evers, Bastiaan, Katarzyna Jastrzebski, Jeroen PM Heijmans, Wipawadee Grernrum, Roderick L. Beijersbergen, and Rene Bernards. “CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes.” Nature biotechnology (2016).
Housden, Benjamin E., and Norbert Perrimon. “Comparing CRISPR and RNAi-based screening technologies.” Nature Biotechnology 34, no. 6 (2016): 621-623.
Qi, Xiaolong, Jiwei Zhang, Yongzhao Zhao, Tao Chen, Yi Xiang, Jialiang Hui, Danxian Cai et al. “The applications of CRISPR screen in functional genomics.” Briefings in Functional Genomics (2016): elw020.
Vickers, Claudia E. “The minimal genome comes of age.” Nature Biotechnology 34, no. 6 (2016): 623-624.
Nam, Jae-Yong, Nayoung KD Kim, Sang Cheol Kim, Je-Gun Joung, Ruibin Xi, Semin Lee, Peter J. Park, and Woong-Yang Park. “Evaluation of somatic copy number estimation tools for whole-exome sequencing data.” Briefings in bioinformatics 17, no. 2 (2016): 185-192.
Belkadi, Aziz, Alexandre Bolze, Yuval Itan, Aurelie Cobat, Quentin B. Vincent, Alexander Antipenko, Lei Shang, Bertrand Boisson, Jean-Laurent Casanova, and Laurent Abel. “Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants.” Proceedings of the National Academy of Sciences 112, no. 17 (2015): 5473-5478.
Law, Charity W., Monther Alhamdoosh, Shian Su, Gordon K. Smyth, and Matthew E. Ritchie. “RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.” F1000Research 5 (2016).
Schurch, Nicholas J., Pietá Schofield, Marek Gierliński, Christian Cole, Alexander Sherstnev, Vijender Singh, Nicola Wrobel et al. “How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?.” RNA 22, no. 6 (2016): 839-851.
Delconte, Rebecca B., Tatiana B. Kolesnik, Laura F. Dagley, Jai Rautela, Wei Shi, Eva M. Putz, Kimberley Stannard et al. “CIS is a potent checkpoint in NK cell-mediated tumor immunity.” Nature immunology (2016).
Gamon, L. F., J. M. White, and U. Wille. “Oxidative damage of aromatic dipeptides by the environmental oxidants NO 2˙ and O 3.” Organic & biomolecular chemistry 12, no. 41 (2014): 8280-8287.
Cerami, Ethan, Jianjiong Gao, Ugur Dogrusoz, Benjamin E. Gross, Selcuk Onur Sumer, Bülent Arman Aksoy, Anders Jacobsen et al. “The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.” Cancer discovery 2, no. 5 (2012): 401-404.
Pham, Thu-Hang, Julia Minderjahn, Christian Schmidl, Helen Hoffmeister, Sandra Schmidhofer, Wei Chen, Gernot Längst, Christopher Benner, and Michael Rehli. “Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU. 1.” Nucleic acids research (2013): gkt355.
Nakamura, Tetsuya, Andrew R. Gehrke, Justin Lemberg, Julie Szymaszek, and Neil H. Shubin. “Digits and fin rays share common developmental histories.” Nature (2016).
de Graaf, Carolyn A., Jarny Choi, Tracey M. Baldwin, Jessica E. Bolden, Kirsten A. Fairfax, Aaron J. Robinson, Christine Biben et al. “Haemopedia: An Expression Atlas of Murine Hematopoietic Cells.” Stem Cell Reports (2016).
Dobin, Alexander, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras. “STAR: ultrafast universal RNA-seq aligner.” Bioinformatics 29, no. 1 (2013): 15-21.
Muniz, João RC, Kunde Guo, Nadia J. Kershaw, Vikram Ayinampudi, Frank von Delft, Jeffrey J. Babon, and Alex N. Bullock. “Molecular architecture of the ankyrin SOCS box family of Cul5-dependent E3 ubiquitin ligases.” Journal of molecular biology 425, no. 17 (2013): 3166-3177.
Guillerey, Camille, Nicholas D. Huntington, and Mark J. Smyth. “Targeting natural killer cells in cancer immunotherapy.” Nature Immunology 17, no. 9 (2016): 1025-1036.
Masuda, Kazuya, and Tadamitsu Kishimoto. “CD5: A New Partner for IL-6.” Immunity 44, no. 4 (2016): 720-722.
Moss-Racusin, Corinne A., Jojanneke van der Toorn, John F. Dovidio, Victoria L. Brescoll, Mark J. Graham, and Jo Handelsman. “A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists.” CBE-Life Sciences Education 15, no. 3 (2016): ar29.
Obenauer, John C., Lewis C. Cantley, and Michael B. Yaffe. “Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.” Nucleic acids research 31, no. 13 (2003): 3635-3641.
Chen, Chang-Zheng, Ling Li, Harvey F. Lodish, and David P. Bartel. “MicroRNAs modulate hematopoietic lineage differentiation.” science 303, no. 5654 (2004): 83-86.
Mueckler, Mike, Carla Caruso, Stephen A. Baldwin, Maria Panico, Ian Blench, Howard R. Morris, W. Jeffrey Allard, Gustav E. Lienhard, and Harvey F. Lodish. “Sequence and structure of a human glucose transporter.” Science 229, no. 4717 (1985): 941-945.
Lodish, Harvey F. “Accommodating family life: mentoring future female faculty members.” Trends in cell biology 25, no. 3 (2015): 109-111.
de Koning-Ward, Tania F., Paul R. Gilson, and Brendan S. Crabb. “Advances in molecular genetic systems in malaria.” Nature Reviews Microbiology 13, no. 6 (2015): 373-387.
Koonin, Eugene V., and Mart Krupovic. “Evolution of adaptive immunity from transposable elements combined with innate immune systems.” Nature Reviews Genetics 16, no. 3 (2015): 184-192.
Sulonen, Anna-Maija, Pekka Ellonen, Henrikki Almusa, Maija Lepistö, Samuli Eldfors, Sari Hannula, Timo Miettinen et al. “Comparison of solution-based exome capture methods for next generation sequencing.” Genome biology 12, no. 9 (2011): 1.
Hodge, David R., Elaine M. Hurt, and William L. Farrar. “The role of IL-6 and STAT3 in inflammation and cancer.” European journal of cancer 41, no. 16 (2005): 2502-2512.
Shuai, Ke, and Bin Liu. “Regulation of JAK–STAT signalling in the immune system.” Nature Reviews Immunology 3, no. 11 (2003): 900-911.