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1. Full Text Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software
by Cameron, Daniel L and Di Stefano, Leon and Papenfuss, Anthony T
Nature communications, ISSN 2041-1723, 07/2019, Volume 10, Issue 1, pp. 3240 - 11
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Cell Line | Computational Biology - methods | Diploidy | Reproducibility of Results | Humans | Genomic Structural Variation - genetics | Software | Whole Genome Sequencing - methods | Genomics - methods | High-Throughput Nucleotide Sequencing - methods | Genome, Human - genetics | Evaluation | Algorithms | Software packages | Computer simulation | Cell lines | Genomes | Calibration | Computer programs | Gene sequencing | Index Medicus
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2. Full Text PathOS: A decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories
by Doig, Kenneth D and Fellowes, Andrew and Bell, Anthony H and Seleznev, Andrei and Ma, David and Ellul, Jason and Li, Jason and Doyle, Maria A and Thompson, Ella R and Kumar, Amit and Lara, Luis and Vedururu, Ravikiran and Reid, Gareth and Conway, Thomas and Papenfuss, Anthony T and Fox, Stephen B
Genome medicine, ISSN 1756-994X, 04/2017, Volume 9, Issue 1, pp. 38 - 38
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Clinical Laboratory Services | Neoplasms - genetics | Humans | Neoplasms - diagnosis | Software | Genomics - methods | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | Precision Medicine | Laboratories | Decision making | Genomics | Quality control | Data processing | Mutation | Bioinformatics | DNA sequencing | Computer programs | Cancer | Index Medicus | Capture Panel | Somatic Variant | Issue Tracking System | Molecular Pathology Laboratory | Bioinformatics Pipeline
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3. Full Text Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer
by Murchison, Elizabeth P and Schulz-Trieglaff, Ole B and Ning, Zemin and Alexandrov, Ludmil B and Bauer, Markus J and Fu, Beiyuan and Hims, Matthew and Ding, Zhihao and Ivakhno, Sergii and Stewart, Caitlin and Ng, Bee Ling and Wong, Wendy and Aken, Bronwen and White, Simon and Alsop, Amber and Becq, Jennifer and Bignell, Graham R and Cheetham, R. Keira and Cheng, William and Connor, Thomas R and Cox, Anthony J and Feng, Zhi-Ping and Gu, Yong and Grocock, Russell J and Harris, Simon R and Khrebtukova, Irina and Kingsbury, Zoya and Kowarsky, Mark and Kreiss, Alexandre and Luo, Shujun and Marshall, John and McBride, David J and Murray, Lisa and Pearse, Anne-Maree and Raine, Keiran and Rasolonjatovo, Isabelle and Shaw, Richard and Tedder, Philip and Tregidgo, Carolyn and Vilella, Albert J and Wedge, David C and Woods, Gregory M and Gormley, Niall and Humphray, Sean and Schroth, Gary and Smith, Geoffrey and Hall, Kevin and Searle, Stephen M.J and Carter, Nigel P and Papenfuss, Anthony T and Futreal, P. Andrew and Campbell, Peter J and Yang, Fengtang and Bentley, David R and Evers, Dirk J and Stratton, Michael R
Cell (Cambridge), ISSN 0092-8674, 02/2012, Volume 148, Issue 4, pp. 780 - 791
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Genomic Instability | Genome-Wide Association Study | Marsupialia - genetics | Facial Neoplasms - veterinary | Molecular Sequence Data | Male | Facial Neoplasms - genetics | Animals | Tasmania - epidemiology | Facial Neoplasms - epidemiology | Female | Mutation | Endangered Species | Facial Neoplasms - pathology | Clonal Evolution | Analysis | Genomics | Genetic research | Genomes | Genetic aspects | Universities and colleges | Nucleotide sequencing | DNA sequencing | Cancer | Index Medicus | Carnivores | Genomic analysis | RNA-mediated interference | Biting | Negative selection | Amino acid substitution | Environmental conditions | Eye | Genotyping | Evolution | Fitness | Tumors
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4. Full Text Whole genome analysis of a schistosomiasis-transmitting freshwater snail
by Adema, Coen M and Hillier, LaDeana W and Jones, Catherine S and Loker, Eric S and Knight, Matty and Minx, Patrick and Oliveira, Guilherme and Raghavan, Nithya and Shedlock, Anew and do Amaral, Laurence Roigues and Arican-Goktas, Halime D and Assis, Juliana G and Baba, Elio Hideo and Baron, Olga L and Bayne, Christopher J and Bickham-Wright, Utibe and Biggar, Kyle K and Blouin, Michael and Bonning, Bryony C and Botka, Chris and Bridger, Joanna M and Buckley, Katherine M and Buddenborg, Sarah K and Lima Caldeira, Roberta and Carleton, Julia and Carvalho, Omar S and Castillo, Maria G and Chalmers, Iain W and Christensens, Mikkel and Clifton, Sana and Cosseau, Celine and Coustau, Christine and Cripps, Richard M and Cuesta-Astroz, Yesid and Cummins, Scott F and di Stephano, Leon and Dinguirard, Nathalie and Duval, David and Emrich, Scott and Feschotte, Céic and Feyereisen, Rene and FitzGerald, Peter and Fronick, Catrina and Fulton, Lucinda and Galinier, Richard and Gava, Sana G and Geusz, Michael and Geyer, Kathrin K and Giraldo-Calderón, Gloria I and de Souza Gomes, Matheus and Gordy, Michelle A and Gourbal, Benjamin and Grunau, Christoph and Hanington, Patrick C and Hoffmann, Karl F and Hughes, Daniel and Humphries, Judith and Jackson, Daniel J and Jannotti-Passos, Liana K and de Jesus Jeremias, Wander and Jobling, Susan and Kamel, Bishoy and Kapusta, Aurélie and Kaur, Satwant and Koene, Joris M and Kohn, Anea B and Lawson, Dan and Lawton, Scott P and Liang, D.C and Limpanont, Yanin and Liu, Sijun and Lockyer, Anne E and Lovato, TyAnna L and Ludolf, Fernanda and Magrini, Vince and McManus, Donald P and Medina, Monica and Misra, Milind and Mitta, Guillaume and Mkoji, Gerald M and Montague, Michael J and Montelongo, Cesar and Moroz, Leonid L and Munoz-Torres, Monica C and Niazi, Umar and Noble, Leslie R and Oliveira, Francislon S and Pais, Fabiano S and Papenfuss, Anthony T and Peace, Rob and Pena, Janeth J and Pila, Emmanuel A and Quelais, Titouan and Raney, Brian J and Rast, Jonathan P and Rollinson, David and Rosse, Izinara C and Rotgans, Bronwyn and Routledge, Edwin J and Ryan, Kathryn M and ... and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Nature communications, ISSN 2041-1723, 05/2017, Volume 8, Issue 1, pp. 15451 - 15451
Journal Article | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Biomphalaria - genetics | Schistosoma mansoni | Gene Expression Regulation | Stress, Physiological | Biomphalaria - parasitology | Proteome | Pheromones | Sequence Analysis, DNA | DNA Transposable Elements | Animals | Schistosomiasis mansoni - transmission | Fresh Water | Host-Parasite Interactions | Genome | Animal Communication | Biomphalaria - immunology | Evolution, Molecular | Index Medicus | Invertebrate Zoology | Parasitology | Biomphalaria/immunology | Biochemistry, Molecular Biology | Genomics | Biomphalaria/genetics | Animal biology | Biomphalaria/parasitology | Life Sciences | Microbiology and Parasitology | Schistosomiasis mansoni/transmission | BASIC BIOLOGICAL SCIENCES | 60 APPLIED LIFE SCIENCES
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5. Full Text A statistical framework for analyzing deep mutational scanning data
by Rubin, Alan F and Gelman, Hannah and Lucas, Nathan and Bajjalieh, Sandra M and Papenfuss, Anthony T and Speed, Terence P and Fowler, Douglas M
Genome Biology, ISSN 1474-7596, 08/2017, Volume 18, Issue 1, pp. 150 - 150
Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Design | Hypothesis testing | Proteins | Scanning | Libraries | Mathematical models | Bioinformatics | Methods
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6. Full Text GRIDSS: Sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
by Cameron, Daniel L and Schröder, Jan and Penington, Jocelyn Sietsma and Do, Hongdo and Molania, Ramyar and Dobrovic, Alexander and Speed, Terence P and Papenfuss, Anthony T
Genome research, ISSN 1088-9051, 12/2017, Volume 27, Issue 12, pp. 2050 - 2060
Biochemistry & Molecular Biology | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Cell Line | Genomic Structural Variation | Neoplasms - genetics | Computer Simulation | Gene Rearrangement | Humans | Plasmodium falciparum - genetics | Sensitivity and Specificity | Software | Genome | Genomics - methods | Genome-wide association studies | Usage | Research | Gene mutations | Genetic variation | Genomics | Index Medicus | Method
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7. Full Text The immune gene repertoire of an important viral reservoir, the Australian black flying fox
by Papenfuss, Anthony T and Baker, Michelle L and Feng, Zhi-Ping and Tachedjian, Mary and Crameri, Gary and Cowled, Chris and Ng, Justin and Janardhana, Vijaya and Field, Hume E and Wang, Lin-Fa
BMC genomics, ISSN 1471-2164, 06/2012, Volume 13, Issue 1, pp. 261 - 261
Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Histocompatibility Antigens - genetics | Chiroptera - virology | Conserved Sequence - genetics | Receptors, Immunologic - chemistry | Chiroptera - immunology | Disease Reservoirs - virology | Horses - genetics | Humans | Histocompatibility Antigens - chemistry | Immunity, Innate - genetics | Molecular Sequence Data | Phylogeny | RNA, Messenger - metabolism | Adaptive Immunity - genetics | Amino Acid Sequence | Molecular Sequence Annotation | RNA, Messenger - genetics | Transcriptome - genetics | Sequence Homology, Nucleic Acid | Sequence Alignment | Animals | Immune System - metabolism | Disease Vectors | Australia | Receptors, Immunologic - genetics | Chiroptera - genetics | Receptors, Immunologic - metabolism | Ebola virus | Antiviral agents | Bats | Immune response | Multiprocessing | Immunotherapy | Genes | Genomics | Genomes | Viruses | Infections | Mortality | Index Medicus | Adaptations | Enzymes | Energy metabolism | Data processing | Gene expression | Immunity | Infection | Databases | Reviews | Rabies | Replication | genomics
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8. Full Text Malaria parasite DNA-harbouring vesicles activate cytosolic immune sensors
by Sisquella, Xavier and Ofir-Birin, Yifat and Pimentel, Matthew A and Cheng, Lesley and Abou Karam, Paula and Sampaio, Natália G and Penington, Jocelyn Sietsma and Connolly, Dympna and Giladi, Tal and Scicluna, Benjamin J and Sharples, Robyn A and Waltmann, Andreea and Avni, Dror and Schwartz, Eli and Schofield, Louis and Porat, Ziv and Hansen, Diana S and Papenfuss, Anthony T and Eriksson, Emily M and Gerlic, Motti and Hill, Andrew F and Bowie, Andrew G and Regev-Rudzki, Neta
Nature communications, ISSN 2041-1723, 12/2017, Volume 8, Issue 1, pp. 1985 - 15
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | DNA, Protozoan - immunology | Phosphorylation | Extracellular Vesicles - ultrastructure | Cytosol - immunology | Humans | Erythrocytes | Plasmodium falciparum - immunology | Extracellular Vesicles - metabolism | Cell Nucleus - metabolism | Extracellular Vesicles - immunology | Extracellular Vesicles - genetics | Plasmodium falciparum - genetics | Membrane Proteins - metabolism | Protein-Serine-Threonine Kinases - metabolism | Interferon Regulatory Factor-3 - immunology | Cell Line | RNA, Protozoan - immunology | Signal Transduction | Membrane Proteins - immunology | Immunity, Innate | Cryoelectron Microscopy | Malaria, Falciparum - parasitology | RNA, Protozoan - metabolism | Monocytes | DNA, Protozoan - metabolism | Malaria, Falciparum - immunology | Interferon Regulatory Factor-3 - metabolism | Plasmodium falciparum - pathogenicity | Cytosol - metabolism | Primary Cell Culture | Vector-borne diseases | Malaria | Blood cells | Virulence | Parasites | Leukocytes | Gene expression | Ribonucleic acid--RNA | Cytosol | Nuclei | Blood | White blood cells | Receptors | Vesicles | Red blood cells | Interferon regulatory factor 3 | Parasitic diseases | Internalization | Sensors | Deoxyribonucleic acid--DNA | Immune system | Index Medicus
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9. Full Text A Naturally Occurring Peptide with an Elementary Single Disulfide-Directed β-Hairpin Fold
by Robinson, Samuel D and Chhabra, Sandeep and Belgi, Alessia and Chittoor, Balasubramanyam and Safavi-Hemami, Helena and Robinson, Andrea J and Papenfuss, Anthony T and Purcell, Anthony W and Norton, Raymond S
Structure (London), ISSN 0969-2126, 02/2016, Volume 24, Issue 2, pp. 293 - 299
Biochemistry & Molecular Biology | Biophysics | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Cysteine | Animals | Peptides - chemistry | Protein Structure, Secondary | Mass Spectrometry | Models, Molecular | Mollusk Venoms - chemistry | Protein Folding | Snails - chemistry | Neuropeptides - chemistry | Index Medicus
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