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Items: 13

1.
Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes
Maria A. Spyrou, Marcel Keller, Rezeda I. Tukhbatova, Christiana L. Scheib, Elizabeth A. Nelson, Aida Andrades Valtueña, Gunnar U. Neumann, Don Walker, Amelie Alterauge, Niamh Carty, Craig Cessford, Hermann Fetz, Michaël Gourvennec, Robert Hartle, Michael Henderson, Kristin von Heyking, Sarah A. Inskip, Sacha Kacki, Felix M. Key, Elizabeth L. Knox, Christian Later, Prishita Maheshwari-Aplin, Joris Peters, John E. Robb, Jürgen Schreiber, Toomas Kivisild, Dominique Castex, Sandra Lösch, Michaela Harbeck, Alexander Herbig, Kirsten I. Bos, Johannes Krause
Nat Commun. 2019; 10: 4470. Published online 2019 Oct 2. doi: 10.1038/s41467-019-12154-0
PMCID:
PMC6775055
AbstractArticlePDF–8.6M
2.
Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)
Marcel Keller, Maria A. Spyrou, Christiana L. Scheib, Gunnar U. Neumann, Andreas Kröpelin, Brigitte Haas-Gebhard, Bernd Päffgen, Jochen Haberstroh, Albert Ribera i Lacomba, Claude Raynaud, Craig Cessford, Raphaël Durand, Peter Stadler, Kathrin Nägele, Jessica S. Bates, Bernd Trautmann, Sarah A. Inskip, Joris Peters, John E. Robb, Toomas Kivisild, Dominique Castex, Michael McCormick, Kirsten I. Bos, Michaela Harbeck, Alexander Herbig, Johannes Krause
Proc Natl Acad Sci U S A. 2019 Jun 18; 116(25): 12363–12372. Published online 2019 Jun 4. doi: 10.1073/pnas.1820447116
PMCID:
PMC6589673
AbstractArticlePDF–1.4M
3.
Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague
Maria A. Spyrou, Rezeda I. Tukhbatova, Chuan-Chao Wang, Aida Andrades Valtueña, Aditya K. Lankapalli, Vitaly V. Kondrashin, Victor A. Tsybin, Aleksandr Khokhlov, Denise Kühnert, Alexander Herbig, Kirsten I. Bos, Johannes Krause
Nat Commun. 2018; 9: 2234. Published online 2018 Jun 8. doi: 10.1038/s41467-018-04550-9
PMCID:
PMC5993720
AbstractArticlePDF–2.9M
4.
Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes
Nina Luhmann, Daniel Doerr, Cedric Chauve
Microb Genom. 2017 Sep; 3(9): e000123. Published online 2017 Jul 8. doi: 10.1099/mgen.0.000123
PMCID:
PMC5643016
AbstractArticlePDF–1.4M
5.
PsRNA: A Computing Engine for the Comparative Identification of Putative Small RNA Locations within Intergenic Regions
Jayavel Sridhar, Govindaraj Sowmiya, Kanagaraj Sekar, Ziauddin Ahamed Rafi
Genomics Proteomics Bioinformatics. 2010 Jun; 8(2): 127–134. Published online 2010 Aug 4. doi: 10.1016/S1672-0229(10)60014-9
PMCID:
PMC5054453
AbstractArticlePDF–684K
6.
Dynamics of CRISPR Loci in Microevolutionary Process of Yersinia pestis Strains
Maria Paloma S. Barros, Camila T. França, Rosanny Holanda F. B. Lins, Milena Danda V. Santos, Ednaldo J. Silva, Maria Betânia M. Oliveira, Vladimir M. Silveira-Filho, Antônio M. Rezende, Valdir Q. Balbino, Tereza Cristina Leal-Balbino
PLoS One. 2014; 9(9): e108353. Published online 2014 Sep 29. doi: 10.1371/journal.pone.0108353
PMCID:
PMC4180756
AbstractArticlePDF–847K
7.
Probabilistic models for CRISPR spacer content evolution
Anne Kupczok, Jonathan P Bollback
BMC Evol Biol. 2013; 13: 54. Published online 2013 Feb 26. doi: 10.1186/1471-2148-13-54
PMCID:
PMC3704272
AbstractArticlePDF–1.0M
8.
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
Elena S Peterson, Lee Ann McCue, Alexandra C Schrimpe-Rutledge, Jeffrey L Jensen, Hyunjoo Walker, Markus A Kobold, Samantha R Webb, Samuel H Payne, Charles Ansong, Joshua N Adkins, William R Cannon, Bobbie-Jo M Webb-Robertson
BMC Genomics. 2012; 13: 131. Published online 2012 Apr 5. doi: 10.1186/1471-2164-13-131
PMCID:
PMC3364912
AbstractArticlePDF–3.2M
9.
Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae
Alexandra C. Schrimpe-Rutledge, Marcus B. Jones, Sadhana Chauhan, Samuel O. Purvine, James A. Sanford, Matthew E. Monroe, Heather M. Brewer, Samuel H. Payne, Charles Ansong, Bryan C. Frank, Richard D. Smith, Scott N. Peterson, Vladimir L. Motin, Joshua N. Adkins
PLoS One. 2012; 7(3): e33903. Published online 2012 Mar 27. doi: 10.1371/journal.pone.0033903
Correction in:
PLoS One. 2012; 7(8): 10.1371/annotation/03110e8b-3e10-4334-9ff7-969c85ad25d8.
PMCID:
PMC3313959
AbstractArticlePDF–787K
10.
Structure and Function of the d-Galactose Network in Enterobacteria
Zsolt Csiszovszki, Sandeep Krishna, László Orosz, Sankar Adhya, Szabolcs Semsey
mBio. 2011 Jul-Aug; 2(4): e00053-11. Published online 2011 Jun 28. doi: 10.1128/mBio.00053-11
PMCID:
PMC3119520
AbstractArticlePDF–3.8M
11.
Trends of the Major Porin Gene (ompF) Evolution: Insight from the Genus Yersinia
Anna M. Stenkova, Marina P. Isaeva, Felix N. Shubin, Valeri A. Rasskazov, Alexander V. Rakin
PLoS One. 2011; 6(5): e20546. Published online 2011 May 31. doi: 10.1371/journal.pone.0020546
PMCID:
PMC3105102
AbstractArticlePDF–734K
12.
Single-stranded DNA transposition is coupled to host replication
Bao Ton Hoang, Cécile Pasternak, Patricia Siguier, Catherine Guynet, Alison Burgess Hickman, Fred Dyda, Suzanne Sommer, Michael Chandler
Cell. Author manuscript; available in PMC 2011 Aug 6.
Published in final edited form as: Cell. 2010 Aug 6; 142(3): 398–408. doi: 10.1016/j.cell.2010.06.034
PMCID:
PMC2919506
AbstractArticlePDF–1.9M
13.
Insight into Microevolution of Yersinia pestis by Clustered Regularly Interspaced Short Palindromic Repeats
Yujun Cui, Yanjun Li, Olivier Gorgé, Mikhail E. Platonov, Yanfeng Yan, Zhaobiao Guo, Christine Pourcel, Svetlana V. Dentovskaya, Sergey V. Balakhonov, Xiaoyi Wang, Yajun Song, Andrey P. Anisimov, Gilles Vergnaud, Ruifu Yang
PLoS One. 2008; 3(7): e2652. Published online 2008 Jul 9. doi: 10.1371/journal.pone.0002652
PMCID:
PMC2440536
AbstractArticlePDF–383K

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