ALBERT

Description: Environmental Science & Technology DOI: 10.1021/es403377p

Description: The Journal of Organic Chemistry DOI: 10.1021/jo4001433

Description: Accounts of Chemical Research DOI: 10.1021/ar3002238

Description: Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms. Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis. Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html . Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Crystal Growth & Design DOI: 10.1021/cg401230a

Description: Journal of Medicinal Chemistry DOI: 10.1021/jm401234w

Description: Gamma-ray burst (GRB) 130427A is one of the most energetic GRBs ever observed. The initial pulse up to 2.5 seconds is possibly the brightest well-isolated pulse observed to date. A fine time resolution spectral analysis shows power-law decays of the peak energy from the onset of the pulse, consistent with models of internal synchrotron shock pulses. However, a strongly correlated power-law behavior is observed between the luminosity and the spectral peak energy that is inconsistent with curvature effects arising in the relativistic outflow. It is difficult for any of the existing models to account for all of the observed spectral and temporal behaviors simultaneously.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Preece, R -- Burgess, J Michael -- von Kienlin, A -- Bhat, P N -- Briggs, M S -- Byrne, D -- Chaplin, V -- Cleveland, W -- Collazzi, A C -- Connaughton, V -- Diekmann, A -- Fitzpatrick, G -- Foley, S -- Gibby, M -- Giles, M -- Goldstein, A -- Greiner, J -- Gruber, D -- Jenke, P -- Kippen, R M -- Kouveliotou, C -- McBreen, S -- Meegan, C -- Paciesas, W S -- Pelassa, V -- Tierney, D -- van der Horst, A J -- Wilson-Hodge, C -- Xiong, S -- Younes, G -- Yu, H-F -- Ackermann, M -- Ajello, M -- Axelsson, M -- Baldini, L -- Barbiellini, G -- Baring, M G -- Bastieri, D -- Bellazzini, R -- Bissaldi, E -- Bonamente, E -- Bregeon, J -- Brigida, M -- Bruel, P -- Buehler, R -- Buson, S -- Caliandro, G A -- Cameron, R A -- Caraveo, P A -- Cecchi, C -- Charles, E -- Chekhtman, A -- Chiang, J -- Chiaro, G -- Ciprini, S -- Claus, R -- Cohen-Tanugi, J -- Cominsky, L R -- Conrad, J -- D'Ammando, F -- de Angelis, A -- de Palma, F -- Dermer, C D -- Desiante, R -- Digel, S W -- Di Venere, L -- Drell, P S -- Drlica-Wagner, A -- Favuzzi, C -- Franckowiak, A -- Fukazawa, Y -- Fusco, P -- Gargano, F -- Gehrels, N -- Germani, S -- Giglietto, N -- Giordano, F -- Giroletti, M -- Godfrey, G -- Granot, J -- Grenier, I A -- Guiriec, S -- Hadasch, D -- Hanabata, Y -- Harding, A K -- Hayashida, M -- Iyyani, S -- Jogler, T -- Johannesson, G -- Kawano, T -- Knodlseder, J -- Kocevski, D -- Kuss, M -- Lande, J -- Larsson, J -- Larsson, S -- Latronico, L -- Longo, F -- Loparco, F -- Lovellette, M N -- Lubrano, P -- Mayer, M -- Mazziotta, M N -- Michelson, P F -- Mizuno, T -- Monzani, M E -- Moretti, E -- Morselli, A -- Murgia, S -- Nemmen, R -- Nuss, E -- Nymark, T -- Ohno, M -- Ohsugi, T -- Okumura, A -- Omodei, N -- Orienti, M -- Paneque, D -- Perkins, J S -- Pesce-Rollins, M -- Piron, F -- Pivato, G -- Porter, T A -- Racusin, J L -- Raino, S -- Rando, R -- Razzano, M -- Razzaque, S -- Reimer, A -- Reimer, O -- Ritz, S -- Roth, M -- Ryde, F -- Sartori, A -- Scargle, J D -- Schulz, A -- Sgro, C -- Siskind, E J -- Spandre, G -- Spinelli, P -- Suson, D J -- Tajima, H -- Takahashi, H -- Thayer, J G -- Thayer, J B -- Tibaldo, L -- Tinivella, M -- Torres, D F -- Tosti, G -- Troja, E -- Usher, T L -- Vandenbroucke, J -- Vasileiou, V -- Vianello, G -- Vitale, V -- Werner, M -- Winer, B L -- Wood, K S -- Zhu, S -- New York, N.Y. -- Science. 2014 Jan 3;343(6166):51-4. doi: 10.1126/science.1242302. Epub 2013 Nov 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Space Science, University of Alabama in Huntsville, Huntsville, AL 35899, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24263132" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fainman, Yeshaiahu -- Porter, George -- New York, N.Y. -- Science. 2013 Oct 11;342(6155):202-3. doi: 10.1126/science.1242906.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA 92093, USA. fainman@eng.ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24115429" target="_blank"〉PubMed〈/a〉

Description: The observations of the exceptionally bright gamma-ray burst (GRB) 130427A by the Large Area Telescope aboard the Fermi Gamma-ray Space Telescope provide constraints on the nature of these unique astrophysical sources. GRB 130427A had the largest fluence, highest-energy photon (95 GeV), longest gamma-ray duration (20 hours), and one of the largest isotropic energy releases ever observed from a GRB. Temporal and spectral analyses of GRB 130427A challenge the widely accepted model that the nonthermal high-energy emission in the afterglow phase of GRBs is synchrotron emission radiated by electrons accelerated at an external shock.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ackermann, M -- Ajello, M -- Asano, K -- Atwood, W B -- Axelsson, M -- Baldini, L -- Ballet, J -- Barbiellini, G -- Baring, M G -- Bastieri, D -- Bechtol, K -- Bellazzini, R -- Bissaldi, E -- Bonamente, E -- Bregeon, J -- Brigida, M -- Bruel, P -- Buehler, R -- Burgess, J Michael -- Buson, S -- Caliandro, G A -- Cameron, R A -- Caraveo, P A -- Cecchi, C -- Chaplin, V -- Charles, E -- Chekhtman, A -- Cheung, C C -- Chiang, J -- Chiaro, G -- Ciprini, S -- Claus, R -- Cleveland, W -- Cohen-Tanugi, J -- Collazzi, A -- Cominsky, L R -- Connaughton, V -- Conrad, J -- Cutini, S -- D'Ammando, F -- de Angelis, A -- DeKlotz, M -- de Palma, F -- Dermer, C D -- Desiante, R -- Diekmann, A -- Di Venere, L -- Drell, P S -- Drlica-Wagner, A -- Favuzzi, C -- Fegan, S J -- Ferrara, E C -- Finke, J -- Fitzpatrick, G -- Focke, W B -- Franckowiak, A -- Fukazawa, Y -- Funk, S -- Fusco, P -- Gargano, F -- Gehrels, N -- Germani, S -- Gibby, M -- Giglietto, N -- Giles, M -- Giordano, F -- Giroletti, M -- Godfrey, G -- Granot, J -- Grenier, I A -- Grove, J E -- Gruber, D -- Guiriec, S -- Hadasch, D -- Hanabata, Y -- Harding, A K -- Hayashida, M -- Hays, E -- Horan, D -- Hughes, R E -- Inoue, Y -- Jogler, T -- Johannesson, G -- Johnson, W N -- Kawano, T -- Knodlseder, J -- Kocevski, D -- Kuss, M -- Lande, J -- Larsson, S -- Latronico, L -- Longo, F -- Loparco, F -- Lovellette, M N -- Lubrano, P -- Mayer, M -- Mazziotta, M N -- McEnery, J E -- Michelson, P F -- Mizuno, T -- Moiseev, A A -- Monzani, M E -- Moretti, E -- Morselli, A -- Moskalenko, I V -- Murgia, S -- Nemmen, R -- Nuss, E -- Ohno, M -- Ohsugi, T -- Okumura, A -- Omodei, N -- Orienti, M -- Paneque, D -- Pelassa, V -- Perkins, J S -- Pesce-Rollins, M -- Petrosian, V -- Piron, F -- Pivato, G -- Porter, T A -- Racusin, J L -- Raino, S -- Rando, R -- Razzano, M -- Razzaque, S -- Reimer, A -- Reimer, O -- Ritz, S -- Roth, M -- Ryde, F -- Sartori, A -- Parkinson, P M Saz -- Scargle, J D -- Schulz, A -- Sgro, C -- Siskind, E J -- Sonbas, E -- Spandre, G -- Spinelli, P -- Tajima, H -- Takahashi, H -- Thayer, J G -- Thayer, J B -- Thompson, D J -- Tibaldo, L -- Tinivella, M -- Torres, D F -- Tosti, G -- Troja, E -- Usher, T L -- Vandenbroucke, J -- Vasileiou, V -- Vianello, G -- Vitale, V -- Winer, B L -- Wood, K S -- Yamazaki, R -- Younes, G -- Yu, H-F -- Zhu, S J -- Bhat, P N -- Briggs, M S -- Byrne, D -- Foley, S -- Goldstein, A -- Jenke, P -- Kippen, R M -- Kouveliotou, C -- McBreen, S -- Meegan, C -- Paciesas, W S -- Preece, R -- Rau, A -- Tierney, D -- van der Horst, A J -- von Kienlin, A -- Wilson-Hodge, C -- Xiong, S -- Cusumano, G -- La Parola, V -- Cummings, J R -- New York, N.Y. -- Science. 2014 Jan 3;343(6166):42-7. doi: 10.1126/science.1242353. Epub 2013 Nov 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Deutsches Elektronen Synchrotron DESY, D-15738 Zeuthen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24263133" target="_blank"〉PubMed〈/a〉

Description: Background: Homology-based taxonomic assignment is impeded by differences between the unassigned read and reference database, forcing a rank-specific classification to the closest (and possibly incorrect) reference lineage. This assignment may be correct only to a general rank (e.g. order) and incorrect below that rank (e.g. family and genus). Algorithms like LCA avoid this by varying the predicted taxonomic rank based on matches to a set of taxonomic references. LCA and related approaches can be conservative, especially if best matches are taxonomically widespread because of events such as lateral gene transfer (LGT). Results: Our extension to LCA called SPANNER (similarity profile annotater) uses the set of best homology matches (the LCA Profile) for a given sequence and compares this profile with a set of profiles inferred from taxonomic reference organisms. SPANNER provides an assignment that is less sensitive to LGT and other confounding phenomena. In a series of trials on real and artificial datasets, SPANNER outperformed LCA-style algorithms in terms of taxonomic precision and outperformed best BLAST at certain levels of taxonomic novelty in the dataset. We identify examples where LCA made an overly conservative prediction, but SPANNER produced a more precise and correct prediction. Conclusions: By using profiles of homology matches to represent patterns of genomic similarity that arise because of vertical and lateral inheritance, SPANNER offers an effective compromise between taxonomic assignment based on best BLAST scores, and the conservative approach of LCA and similar approaches. Availability: C++ source code and binaries are freely available at http://kiwi.cs.dal.ca/Software/SPANNER . Contact: beiko@cs.dal.ca Supplementary information: Supplementary data are available at Bioinformatics online.