% BibTeX Exporter written in LotusScript by Uwe Brahm, % Please send bug reports via email to . Thanks. % Exported: Saturday, 27. April 2024, 13:04, Server: domino/MPII/DE @INCOLLECTION{Adams2008, AUTHOR = {Adams, Ben and McHardy, Alice and Lundegaard, C. and Lengauer, Thomas}, EDITOR = {Frishman, Dmitrij and Valencia, Alfonso}, TITLE = {Viral Bioinformatics}, BOOKTITLE = {Modern Genome Annotation : the Biosapiens Network}, CHAPTER = {8.1}, TYPE = {Hardcover}, ADDRESS = {New York, NY}, PUBLISHER = {Springer}, ISBN = {978-3-211-75122-0}, DOI = {10.1007/978-3-211-75123-7_19}, YEAR = {2009}, PAGES = {429--452}, } @ARTICLE{Adams2010, AUTHOR = {Adams, Ben and McHardy, Alice}, JOURNAL = {Proceedings of the Royal Society / B, Biological Sciences}, TITLE = {The impact of seasonal and year-round transmission regimes on the evolution of influenza {A} virus}, ADDRESS = {London}, NUMBER = {1716}, PUBLISHER = {The Royal Society}, MONTH = {August}, VOLUME = {278}, ISBN = {0950-1193}, DOI = {10.1098/rspb.2010.2191}, YEAR = {2011}, PAGES = {2249--2256}, } @ARTICLE{Gartemann2008, AUTHOR = {Gartemann, K. H. and Abt, B. and Bekel, T. and Burger, A. and Engemann, J. and Fl{\"u}gel, M. and Gaigalat, L. and Goesmann, A. and Gr{\"a}fen, I. and Kalinowski, J. and Kaup, O. and Kirchner, O. and Krause, L. and Linke, B. and McHardy, Alice and Meyer, F. and Pohle, S. and R{\"u}ckert, C. and Schneiker, S. and Zellermann, E. M. and P{\"u}hler, A. and Eichenlaub, R. and Kaiser, O. and Bartels, D.}, JOURNAL = {The Journal of Bacteriology}, TITLE = {The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity}, ADDRESS = {Washington, USA}, NUMBER = {6}, PUBLISHER = {American Society for Microbiology}, MONTH = {March}, VOLUME = {190}, ISBN = {0021-9193}, DOI = {10.1128/JB.01595-07}, YEAR = {2008}, PAGES = {2138--2149}, } @ARTICLE{Holland2008, AUTHOR = {Holland, L. Z. and Albalat, R. and Azumi, K. and Benito-Guti{\'e}rrez, E. and Blow, M. J. and Bronner-Fraser, M. and Brunet, F. and Butts, T. and Candiani, S. and Dishaw, L. J. and Ferrier, D. E. and Garcia-Fern{\`a}ndez, J. and Gibson-Brown, J. J. and Gissi, C. and Godzik, A. and Hallb{\"o}{\"o}k, F. and Hirose, D. and Hosomichi, K. and Ikuta, T. and Inoko, H. and Kasahara, M. and Kasamatsu, J. and Kawashima, T. and Kimura, A. and Kobayashi, M. and Kozmik, Z. and Kubokawa, K. and Laudet, V. and Litman, G. W. and McHardy, Alice and Meulemans, D. and Nonaka, M. and Olinski, R. P. and Pancer, Z. and Pennacchio, L. A. and Pestarino, M. and Rast, J. P. and Rigoutsos, I. and Robinson-Rechavi, M. and Roch, G. and Saiga, H. and Sasakura, Y. and Satake, M. and Satou, Y. and Schubert, M. and Sherwood, N. and Shiina, T. and Takatori, N. and Tello, J. and Vopalensky, P. and Wada, S. and Xu, A. and Ye, Y. and Yoshida, K. and Yoshizaki, F. and Yu, J. K. and Zhang, Q. and Zmasek, C. M. and de Jong, P. J. and Osoegawa, K. and Putnam, N. H. and Rokhsar, D. S. and Satoh, N. and Holland, P. W.}, JOURNAL = {Genome Research}, TITLE = {The amphioxus genome illuminates vertebrate origins and cephalochordate biology}, ADDRESS = {Cold Spring Harbour, USA}, NUMBER = {7}, PUBLISHER = {Cold Spring Harbour Lab. Press}, MONTH = {July}, VOLUME = {18}, ISBN = {1088-9051}, DOI = {10.1101/gr.073676.107}, YEAR = {2008}, PAGES = {1100--1111}, } @ARTICLE{Kalyuzhnaya2008, AUTHOR = {Kalyuzhnaya, M. G. and Lapidus, A. and Ivanova, N. and Copeland, A. C. and McHardy, Alice and Szeto, E. and Salamov, A. and Grigoriev, I. V. and Suciu, D. and Levine, S. R. and Markowitz, V. M. and Rigoutsos, I. and Tringe, S. G. and Bruce, D. C. and Richardson, P. M. and Lidstrom, M. E. and Chistoserdova, L.}, JOURNAL = {Nature Biotechnology}, TITLE = {High-resolution metagenomics targets specific functional types in complex microbial communities}, ADDRESS = {New York, USA}, NUMBER = {9}, PUBLISHER = {Nature American Pub.}, MONTH = {September}, VOLUME = {26}, ISBN = {1087-0156}, DOI = {10.1038/nbt.1488}, YEAR = {2008}, PAGES = {1029--34}, } @ARTICLE{KON2011, AUTHOR = {Konietzny, Sebastian G.A. and Dietz, Laura and McHardy, Alice}, JOURNAL = {BMC Bioinformatics}, TITLE = {Inferring functional modules of protein families with probabilistic topic models}, NUMBER = {1}, VOLUME = {12}, DOI = {10.1186/1471-2105-12-141}, YEAR = {2011}, PAGES = {141}, } @ARTICLE{Mavromatis2007, AUTHOR = {Mavromatis, K. and Ivanova, N. and Barry, K. and Shapiro, H. and Goltsman, E. and McHardy, Alice and Rigoutsos, I. and Salamov, A. and Korzeniewski, F. and Land, M. and Lapidus, A. and Grigoriev, I. and Richardson, P. and Hugenholtz, P. and Kyrpides, N. C.}, JOURNAL = {Nature Methods}, TITLE = {Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.}, NUMBER = {6}, VOLUME = {4}, YEAR = {2007}, PAGES = {495--500}, } @ARTICLE{MCH2011b, AUTHOR = {Pope, P. B. and Smith, W. and Denman, S. E. and Tringe, S. G. and Barry, K. and Hugenholtz, P. and McSweeney, C. S. and McHardy, Alice and Morrison, M.}, JOURNAL = {Science}, TITLE = {Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from {Tammar} Wallabies}, NUMBER = {6042}, PUBLISHER = {AAAS}, VOLUME = {333}, DOI = {10.1126/science.1205760}, YEAR = {2011}, PAGES = {646--648}, } @ARTICLE{MCH2011c, AUTHOR = {Gilbert, Jack A. and Steele, Joshua A. and Caporaso, J. Gregory and Steinbr{\"u}ck, Lars and Reeder, Jens and Temperton, Ben and Huse, Susan and McHardy, Alice C. and Knight, Rob and Joint, Ian and Somerfield, Paul and Fuhrman, Jed A. and Field, Dawn}, JOURNAL = {The ISME Journal}, TITLE = {Defining seasonal marine microbial community dynamics}, ADDRESS = {Basingstoke}, PUBLISHER = {Nature Publishing Group}, VOLUME = {6}, ISBN = {1751-7362}, DOI = {10.1038/ismej.2011.107}, YEAR = {2012}, PAGES = {298--308}, } @ARTICLE{McHardy2007a, AUTHOR = {McHardy, Alice and Rigoutsos, I.}, JOURNAL = {Current Opinion in Microbiology}, TITLE = {What's in the mix? {M}ethods for the phylogenetic classification of metagenome sequence samples.}, NUMBER = {5}, PUBLISHER = {Elsevier}, VOLUME = {10}, YEAR = {2007}, PAGES = {499--503}, } @ARTICLE{McHardy2007b, AUTHOR = {McHardy, Alice and Martin, H. G. and Tsirigos, A. and Hugenholtz, P. and Rigoutsos, I.}, JOURNAL = {Nature Methods}, TITLE = {Accurate phylogenetic classification of variable-length {DNA} fragments.}, NUMBER = {1}, VOLUME = {4}, YEAR = {2007}, PAGES = {63--72}, } @ARTICLE{McHardy2007c, AUTHOR = {McHardy, Alice and Krause, L. and Nattkemper, T. W. and Puhler, A. and Stoye, J. and Meyer, F.}, JOURNAL = {Nucleic Acids Research}, TITLE = {{GISMO} - prokaryotic gene identification using a support vector machine for {ORF} classification.}, NUMBER = {4}, VOLUME = {32}, YEAR = {2007}, PAGES = {540--549}, } @INCOLLECTION{McHardy2008, AUTHOR = {McHardy, Alice}, EDITOR = {Keith, Jonathan M.}, JOURNAL = {Methods in Molecular Biology}, TITLE = {Finding genes in genome sequence}, BOOKTITLE = {Bioinformatics. - Vol. 1, Data, Sequence Analysis and Evolution}, CHAPTER = {2}, ADDRESS = {Clifton, N.J., USA}, PUBLISHER = {Humana Press}, SERIES = {Methods in Molecular Biology}, VOLUME = {452}, ISBN = {978-1-58829-707-5}, YEAR = {2008}, PAGES = {163--77}, } @ARTICLE{McHardy2009x, AUTHOR = {McHardy, Alice and Adams, Ben}, JOURNAL = {PLOS Pathogens}, TITLE = {The role of genomics in tracking the evolution of influenza A virus}, ADDRESS = {San Francisco, CA}, NUMBER = {10}, PUBLISHER = {Public Library of Science (PLoS)}, MONTH = {October}, VOLUME = {5}, ISBN = {1553-7366}, DOI = {10.1371/journal.ppat.1000566}, YEAR = {2009}, PAGES = {e1000566:1--e1000566:6}, } @ARTICLE{mchardy2010aht, AUTHOR = {Pope, P. B. and Denman, S. E. and Jones, M. and Tringe, S. G. and Barry, K. and Malfatti, S. A. and McHardy, Alice and Cheng, J.-F. and Hugenholtz, P. and McSweeney, C. S. and Morrison, M.}, JOURNAL = {Proceedings of the National Academy of Sciences of the United States of America}, TITLE = {Adaptation to herbivory by the {Tammar} wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores}, ADDRESS = {Washington, DC}, NUMBER = {33}, PUBLISHER = {National Academy of Sciences}, VOLUME = {107}, ISBN = {0027-8424}, DOI = {10.1073/pnas.1005297107}, YEAR = {2010}, PAGES = {14793--14798}, } @ARTICLE{mchardy2010msi, AUTHOR = {Lykidis, Athanasios and Chen, Chia-Lung and Tringe, Susannah G. and McHardy, Alice and Copeland, Alex and Kyrpides, Nikos C. and Hugenholtz, Philip and Macarie, Herv{\'e} and Olmos, Alejandro and Monroy, Oscar and Liu, Wen-Tso}, JOURNAL = {The ISME Journal}, TITLE = {Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium}, ADDRESS = {London}, NUMBER = {1}, PUBLISHER = {Nature Publishing Group}, VOLUME = {5}, ISBN = {1751-7362}, DOI = {10.1038/ismej.2010.125}, YEAR = {2011}, PAGES = {122--130}, } @ARTICLE{mchardy2010ogt, AUTHOR = {Turnbaugh, Peter J. and Quince, Christopher and Faith, Jeremiah J. and McHardy, Alice and Yatsunenko, Tanya and Niazi, Faheem and Affourtit, Jason and Egholm, Michael and Henrissat, Bernhard and Knight, Rob and Gordon, Jeffrey I.}, JOURNAL = {Proceedings of the National Academy of Sciences of the United States of America}, TITLE = {Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins}, ADDRESS = {Washington, DC}, NUMBER = {16}, PUBLISHER = {National Academy of Sciences}, MONTH = {April}, VOLUME = {107}, ISBN = {0027-8424}, DOI = {10.1073/pnas.1002355107}, YEAR = {2010}, PAGES = {7503--7508}, } @INCOLLECTION{McHardyPatil2011, AUTHOR = {McHardy, Alice and Patil, Kaustubh R.}, EDITOR = {de Bruijn, Frans J.}, TITLE = {Phylogenetic binning of metagenome sequence samples}, BOOKTITLE = {Handbook of molecular microbial ecology. - Vol. 1, Metagenomics and complementary approaches}, ADDRESS = {Chichester}, PUBLISHER = {Wiley-Blackwell}, ISBN = {978-0-470-64479-0}, YEAR = {2011}, PAGES = {353--358}, } @INCOLLECTION{MCHJahrbuch09, AUTHOR = {McHardy, Alice and Patil, Kaustubh}, TITLE = {{Informatik f{\"u}r die Metagenomforschung: Einblicke in die Welt der unkultivierbaren Mikroorganismen}}, BOOKTITLE = {T{\"a}tigkeitsberichte 2009 der Institute}, ADDRESS = {M{\"u}nchen, Germany}, PUBLISHER = {Max-Planck-Gesellschaft}, SERIES = {Jahrbuch der Max-Planck-Gesellschaft}, VOLUME = {2009}, YEAR = {2009}, PAGES = {1--6}, } @MISC{MCHSBPatent09, AUTHOR = {McHardy, Alice and Steinbr{\"u}ck, Lars}, TITLE = {Method and system for building a phylogeny from genetic sequences and using the same for recommendation of vaccine strain candidates for the influenza virus}, HOWPUBLISHED = {European Patent No. 08020835.7 - 2201}, MONTH = {November}, YEAR = {2008}, } @ARTICLE{Meisinger-Henschel2007, AUTHOR = {Meisinger-Henschel, Christine and Schmidt, Michaela and Lukassen, Susanne and Linke, Burkhard and Krause, Lutz and Konietzny, Sebastian and Goesmann, Alexander and Howley, Paul and Chaplin, Paul and Suter, Mark and Hausmann, J{\"u}rgen}, JOURNAL = {Journal of General Virology}, TITLE = {Genomic sequence of chorioallantois vaccinia virus {A}nkara, the ancestor of modified vaccinia virus {A}nkara}, NUMBER = {12}, VOLUME = {88}, YEAR = {2007}, PAGES = {3249--3259}, } @ARTICLE{Patil2008a, AUTHOR = {Patil, Kaustubh and Akerkar, Rajendra}, JOURNAL = {Journal of Hybrid Computing Research}, TITLE = {Tackling Traveling Salesman Problem with Random Key Genetic Algorithm}, NUMBER = {1}, VOLUME = {1}, YEAR = {2008}, PAGES = {10--10}, } @ARTICLE{Patil2011, AUTHOR = {Patil, Kaustubh R. and Haider, Peter and Pope, Philip B. and Turnbaugh, Peter J. and Morrison, Mark and Scheffer, Tobias and McHardy, Alice}, JOURNAL = {Nature Methods}, TITLE = {Taxonomic metagenome sequence assignment with structured output models}, ADDRESS = {London}, NUMBER = {3}, PUBLISHER = {Nature Publishing Group}, VOLUME = {8}, ISBN = {1548-7091}, DOI = {10.1038/nmeth0311-191}, YEAR = {2011}, PAGES = {191--192}, } @ARTICLE{Patil2012, AUTHOR = {Patil, Kaustubh Raosaheb and Roune, Linus and McHardy, Alice Carolyn}, JOURNAL = {PLoS ONE}, TITLE = {The {PhyloPythiaS} Web Server for Taxonomic Assignment of Metagenome Sequences}, ADDRESS = {San Francisco, CA}, NUMBER = {6}, PUBLISHER = {Public Library of Science}, VOLUME = {7}, ISBN = {1932-6203}, DOI = {10.1371/journal.pone.0038581}, YEAR = {2012}, PAGES = {e38581,1--e38581,9}, } @ARTICLE{PatKulk2007, AUTHOR = {Patil, Kaustubh and Kulkarni, Abhijit}, JOURNAL = {Biotechnology Progress}, TITLE = {A simple visualization technique to understand the system dynamics in bioreactors}, NUMBER = {5}, VOLUME = {23}, YEAR = {2007}, PAGES = {1101--1105}, } @ARTICLE{Pope2012, AUTHOR = {Pope, Phillip B. and Mackenzie, Alasdair K. and Gregor, Ivan and Smith, Wendy and Sundset, Monica A. and McHardy, Alice C. and Morrison, Mark and Eijsink, Vincent G.H.}, JOURNAL = {PLoS ONE}, TITLE = {Metagenomics of the {Svalbard} Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci}, ADDRESS = {San Francisco, CA}, NUMBER = {6}, PUBLISHER = {Public Library of Science}, VOLUME = {7}, ISBN = {1932-6203}, DOI = {10.1371/journal.pone.0038571}, YEAR = {2012}, PAGES = {e38571,1--e38571,10}, } @ARTICLE{PSJK2008, AUTHOR = {Patil, Kaustubh and Shelokar, P. S. and Jayaraman, V. K. and Kulkarni, B. D.}, JOURNAL = {Journal of Hybrid Computing Research}, TITLE = {Ant Colony Optimization in the Direct Ordering Gene Expression Data}, NUMBER = {1}, MONTH = {June}, VOLUME = {1}, ISBN = {0974-5858}, YEAR = {2008}, PAGES = {10--10}, } @ARTICLE{Richardson2007, AUTHOR = {Warnecke, F. and Luginb{\"u}hl, P. and Ivanova, N. and Ghassemian, M. and Richardson, T. H. and Stege, J. T. and Cayouette, M. and McHardy, Alice and Djordjevic, G. and Aboushadi, N. and Sorek, R. and Tringe, S. G. and Podar, M. and Martin, H. G. and Kunin, V. and Dalevi, D. and Madejska, J. and Kirton, E. and Platt, D. and Szeto, E. and Salamov, A. and Barry, K. and Mikhailova, N. and Kyrpides, N. C. and Matson, E. G. and Ottesen, E. A. and Zhang, X. and Hern{\'a}ndez, M. and Murillo, C. and Acosta, L. G. and Rigoutsos, I. and Tamayo, G. and Green, B. D. and Chang, C. and Rubin, E. M. and Mathur, E. J. and Robertson, D. E. and Hugenholtz, P. and Leadbetter, J. R.}, JOURNAL = {Nature}, TITLE = {Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite}, NUMBER = {7169}, VOLUME = {450}, YEAR = {2007}, PAGES = {560--565}, } @ARTICLE{Schneiker2007, AUTHOR = {Schneiker, Susanne and Perlova, Olena and Kaiser, Olaf and Gerth, Klaus and Alici, Aysel and Altmeyer, Matthias and Bartels, Daniela and Bekel, Thomas and Beyer, Stefan and Bode, Edna and Bode, Helge and Bolten, Christoph and Choudhuri, Jomuna and Doss, Sabrina and Elnakady, Yasser and Frank, Bettina and Gaigalat, Lars and Goesmann, Alexander and Groeger, Carolin and Gross, Frank and Jelsbak, Lars and Jelsbak, Lotte and Kalinowski, J{\"o}rn and Kegler, Carsten and Knauber, Tina and Konietzny, Sebastian and Kopp, Maren and Krause, Lutz and Krug, Daniel and Linke, Bukhard and Mahmud, Taifo and Martinez-Arias, Rosa and McHardy, Alice and Merai, Michelle and Meyer, Folker and Mormann, Sascha and Muñoz-Dorado, Jose and Perez, Juana and Pradella, Silke and Rachid, Shwan and Raddatz, G{\"u}nter and Rosenau, Frank and R{\"u}ckert, Christian and Sasse, Florenz and Scharfe, Maren and Schuster, Stephan C. and Suen, Garret and Treuner-Lange, Anke and Velicer, Gregory and Vorh{\"o}lter, Frank-J{\"o}rg and Weissman, Kira J. and Welch, Roy D. and Wenzel, Silke C. and Whitworth, David E. and Wilhelm, Susanne and Wittmann, Christoph and Bl{\"o}cker, Helmut and P{\"u}hler, Alfred and M{\"u}ller, Rolf}, JOURNAL = {Nature Biotechnology}, TITLE = {Complete genome sequence of the myxobacterium {S}orangium cellulosum.}, NUMBER = {11}, VOLUME = {27}, YEAR = {2007}, PAGES = {281--1289}, } @ARTICLE{Schoen2008, AUTHOR = {Schoen, Christoph and Blom, Jochen and Claus, Heike and Schramm-Gl{\"u}ck, Anja and Brandt, Petra and M{\"u}ller, Tobias and Goesmann, Alexander and Joseph, Biju and Konietzny, Sebastian and Kurzai, Oliver and Schmitt, Corinna and Friedrich, Torben and Linke, Burkhard and Vogel, Ulrich and Frosch, Matthias}, JOURNAL = {Proceedings of the National Academy of Sciences of the United States of America}, TITLE = {Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in {Neisseria} meningitidis}, ADDRESS = {Washington, DC}, NUMBER = {9}, PUBLISHER = {NAS}, VOLUME = {105}, ISBN = {1091-6490}, DOI = {10.1073/pnas.0800151105}, YEAR = {2008}, PAGES = {3473--3478}, } @ARTICLE{steinbrueck2010adp, AUTHOR = {Steinbr{\"u}ck, Lars and McHardy, Alice}, JOURNAL = {Nucleic Acids Research}, TITLE = {Allele dynamics plots for the study of evolutionary dynamics in viral populations}, ADDRESS = {Oxford, UK}, NUMBER = {1}, PUBLISHER = {Oxford University Press}, VOLUME = {39}, ISBN = {1362-4962}, DOI = {10.1093/nar/gkq909}, YEAR = {2010}, PAGES = {1--12}, } @ARTICLE{Steinbrueck2012, AUTHOR = {Steinbr{\"u}ck, Lars and McHardy, Alice Carolyn}, JOURNAL = {PLoS Computational Biology}, TITLE = {Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza {A} {(H3N2)} Viruses}, ADDRESS = {San Francisco, CA}, NUMBER = {4}, PUBLISHER = {Public Library of Science}, VOLUME = {8}, ISBN = {1553-734X}, DOI = {10.1371/journal.pcbi.1002492}, YEAR = {2012}, PAGES = {e1002492,1--e1002492,9}, } @ARTICLE{Tusche2012, AUTHOR = {Tusche, Christina and Steinbr{\"u}ck, Lars and McHardy, Alice Carolyn}, JOURNAL = {Molecular Biology and Evolution}, TITLE = {Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection}, ADDRESS = {Oxford}, NUMBER = {8}, PUBLISHER = {Oxford University Press}, VOLUME = {29}, ISBN = {0737-4038}, DOI = {10.1093/molbev/mss095}, YEAR = {2012}, PAGES = {2063--2071}, } @ARTICLE{VCPP2007, AUTHOR = {Vieira, J and Cardoso, CS and Pinto, JP and Patil, Kaustubh and Brazdil, P and Cruz, E and Mascarenhas, C and Lacerda, R and Gartner, A and Almeida, S and Alves, H and Porto, G}, JOURNAL = {American Journal of Hematology}, TITLE = {Location of a putative gene contributing to the setting of {CD8+T} lymphocytes: A modifier of hereditary hemochromatosis expression?}, VOLUME = {82}, YEAR = {2007}, PAGES = {509--509}, } @ARTICLE{VCPP2007a, AUTHOR = {Vieira, J and Cardoso, CS and Pinto, JP and Patil, Kaustubh and Brazdil, P and Cruz, E and Mascarenhas, C and Lacerda, R and Gartner, A and Almeida, S and Alves, H and Porto, G}, JOURNAL = {International Journal of Immunogenetics}, TITLE = {A Putative Gene Located at the {MHC-CLASS I} Region Around the {D6S105} Marker Contributes to the Setting of {CD8+ T} Lymphocyte Numbers in Humans}, NUMBER = {5}, VOLUME = {34}, YEAR = {2007}, PAGES = {359--367}, }