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1. Full Text Trans-ancestry mutational landscape of hepatocellular carcinoma genomes
by Totoki, Yasushi and Totoki, Yasushi and Tatsuno, Kenji and Covington, Kyle R and Ueda, Hiroki and Creighton, Chad J and Kato, Mamoru and Tsuji, Shingo and Donehower, Lawrence A and Slagle, Betty L and Nakamura, Hiromi and Yamamoto, Shogo and Shinbrot, Eve and Hama, Natsuko and Lehmkuhl, Megan and Hosoda, Fumie and Arai, Yasuhito and Walker, Kim and Dahdouli, Mahmoud and Gotoh, Kengo and Nagae, Genta and Gingras, Marie-Claude and Muzny, Donna M and Ojima, Hidenori and Shimada, Kazuaki and Midorikawa, Yutaka and Goss, John A and Cotton, Ronald and Hayashi, Akimasa and Shibahara, Junji and Ishikawa, Shumpei and Guiteau, Jacfranz and Tanaka, Mariko and Urushidate, Tomoko and Ohashi, Shoko and Okada, Naoko and Doddapaneni, Harsha and Wang, Min and Zhu, Yiming and Dinh, Huyen and Okusaka, Takuji and Kokudo, Norihiro and Kosuge, Tomoo and Takayama, Tadatoshi and Fukayama, Masashi and Gibbs, Richard A and Wheeler, David A and Aburatani, Hiroyuki and Shibata, Tatsuhiro
Nature Genetics, ISSN 1061-4036, 12/2014, Volume 46, Issue 12, pp. 1267 - 1273
Diverse epidemiological factors are associated with hepatocellular carcinoma (HCC) prevalence in different populations. However, the global landscape of the... 
SIGNATURES | SRCAP | TELOMERASE | RECURRENT MUTATIONS | GENETICS & HEREDITY | ACTIVATOR PROTEIN | RECEPTOR | SUSCEPTIBILITY LOCUS | WIDE ASSOCIATION | CANCER | SOMATIC MUTATIONS | Carcinoma, Hepatocellular - epidemiology | United States | Humans | Gene Expression Regulation, Neoplastic | Hepacivirus - genetics | Exome | Liver Neoplasms - epidemiology | TOR Serine-Threonine Kinases - genetics | Telomerase - genetics | DNA Mutational Analysis | Carcinoma, Hepatocellular - genetics | Principal Component Analysis | Carcinoma, Hepatocellular - ethnology | Genome, Viral | Liver Neoplasms - genetics | Japan | European Continental Ancestry Group | Models, Statistical | Liver Neoplasms - ethnology | Asian Continental Ancestry Group | Algorithms | Hepatitis B virus - genetics | CpG Islands | Mutation | Genome, Human | Medical research | Gene mutations | Medicine, Experimental | Development and progression | Genetic aspects | Hepatoma | Research | Medical statistics | Identification and classification | Liver cancer | Human papillomavirus | Data analysis | Genealogy | Research & development--R&D | Genomics | Software | Infections | Genomes | Chromosomes | Tumors
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2. Full Text PacBio-LITS: A large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations
by Wang, Min and Wang, Min and Beck, Christine R and Beck, Christine R and English, Adam C and English, Adam C and Meng, Qingchang and Meng, Qingchang and Buhay, Christian and Buhay, Christian and Han, Yi and Han, Yi and Doddapaneni, Harsha V and Doddapaneni, Harsha V and Yu, Fuli and Yu, Fuli and Boerwinkle, Eric and Boerwinkle, Eric and Lupski, James R and Lupski, James R and Muzny, Donna M and Muzny, Donna M and Gibbs, Richard A and Gibbs, Richard A
BMC Genomics, ISSN 1471-2164, 2015, Volume 16, Issue 1, pp. 1 - 12
Background: Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently,... 
Targeted sequencing | Single molecule sequencing | Complex genomic rearrangement | COPY-NUMBER VARIANTS | INSTABILITY | DISORDERS | MECHANISMS | REARRANGEMENTS | GENETIC-VARIATION | HUMAN GENOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DNA | GENETICS & HEREDITY | ARCHITECTURE | HOMOLOGOUS RECOMBINATION | Gene Library | Gene Rearrangement | Humans | Chromosome Aberrations | Genetic Association Studies - methods | Workflow | Genomics - methods | High-Throughput Nucleotide Sequencing - methods | Complications and side effects | Usage | Chromosome abnormalities | Diagnosis | Research | Nucleotide sequencing | Methods | DNA sequencing | Comparative analysis
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3. Full Text Structure and function of the healthy pre-adolescent pediatric gut microbiome
by Hollister, Emily B and Riehle, Kevin and Luna, Ruth Ann and Weidler, Erica M and Rubio-Gonzales, Michelle and Mistretta, Toni-Ann and Raza, Sabeen and Doddapaneni, Harsha V and Metcalf, Ginger A and Muzny, Donna M and Gibbs, Richard A and Petrosino, Joseph F and Shulman, Robert J and Versalovic, James
Microbiome, ISSN 2049-2618, 08/2015, Volume 3, Issue 1, p. 36
Background: The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although... 
16S rRNA | WGS | BACTERIA | SEQUENCES | MARKERS | ADULTS | MICROBIOLOGY | CHILDREN | Healthy gut microbiome | DE-BRUIJN GRAPHS | OBESITY | DISEASE | Pediatric | BRAIN | AGE | Age Factors | Humans | Gastrointestinal Microbiome | Male | Biodiversity | Healthy Volunteers | DNA Barcoding, Taxonomic | RNA, Ribosomal, 16S - genetics | Adult | Female | Child | Metagenome | Cluster Analysis | Pediatrics | Microbiota (Symbiotic organisms) | RNA | Medical care | Shotguns | Comparative analysis | Quality management
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4. Full Text Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions
by Anstead, Clare A and Korhonen, Pasi K and Young, Neil D and Hall, Ross S and Jex, Aaron R and Murali, Shwetha C and Hughes, Daniel S.T and Lee, Siu F and Perry, Trent and Stroehlein, Andreas J and Ansell, Brendan R.E and Breugelmans, Bert and Hofmann, Andreas and Qu, Jiaxin and Dugan, Shannon and Lee, Sandra L and Chao, Hsu and Dinh, Huyen and Han, Yi and Doddapaneni, Harsha V and Worley, Kim C and Muzny, Donna M and Ioannidis, Panagiotis and Waterhouse, Robert M and Zdobnov, Evgeny M and James, Peter J and Bagnall, Neil H and Kotze, Andrew C and Gibbs, Richard A and Richards, Stephen and Batterham, Philip and Gasser, Robin B
Nature Communications, ISSN 2041-1723, 06/2015, Volume 6, Issue 1, p. 7344
Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and... 
PROTEIN | INSECT IMMUNITY | DROSOPHILA-MELANOGASTER | MULTIDISCIPLINARY SCIENCES | LARVAE | SHEEP | RESISTANCE | GENE FAMILY | RECEPTORS | BLOWFLY STRIKE | EXPRESSION | Insecticides - pharmacology | Animals | Larva | Transcriptome | Gene Expression Regulation - physiology | Insect Proteins - genetics | Insecticide Resistance - genetics | Female | Male | Diptera - genetics | Genome, Insect | Insect Proteins - metabolism
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5. Full Text A global reference for human genetic variation
by Altshuler, D.M and Albers, C.A and Abecasis, G.R and et al and Genomes Project Consortium and 1000 Genomes Project Consortium and The 1000 Genomes Project Consortium
Nature, ISSN 0028-0836, 2015, Volume 526, Issue 7571, pp. 68 - 74
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set... 
BAYES FACTORS | INDIVIDUALS | COMPLEMENT FACTOR-H | POPULATION HISTORY | MULTIDISCIPLINARY SCIENCES | MUTATION | DISEASE | SUSCEPTIBILITY | MACULAR DEGENERATION | VARIANT | GENOME-WIDE ASSOCIATION | Rare Diseases - genetics | Genome-Wide Association Study | Datasets as Topic | Demography | Disease Susceptibility | Physical Chromosome Mapping | Humans | Genetics, Population - standards | Genomics - standards | Genotype | INDEL Mutation - genetics | Sequence Analysis, DNA | Genome, Human - genetics | Haplotypes - genetics | Exome - genetics | Reference Standards | Genetics, Medical | Internationality | Polymorphism, Single Nucleotide - genetics | Genetic Variation - genetics | High-Throughput Nucleotide Sequencing | Quantitative Trait Loci - genetics | Genetic research | Nucleotide sequencing | Observations | Genetic variation | Methods | DNA sequencing | Studies | Haplotypes | Genotype & phenotype | Accuracy | Genealogy | Population | Genomes | Genetic diversity | Mitochondrial DNA | Binding sites
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6. Full Text Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
by Ally, Adrian and Balasundaram, Miruna and Carlsen, Rebecca and Chuah, Eric and Clarke, Amanda and Dhalla, Noreen and Holt, Robert A and Jones, Steven J.M and Jones, Corbin D and Lee, Ju-Seog and Lee, Darlene and Lee, Sandra and Ma, Yussanne and Marra, Marco A and Mayo, Michael and Moore, Richard A and Moore, David D and Mungall, Karen and Mungall, Andrew J and Schein, Jacqueline E and Sipahimalani, Payal and Tam, Angela and Thiessen, Nina and Cheung, Dorothy and Wong, Tina and Brooks, Denise and Robertson, A. Gordon and Bowlby, Reanne and Sadeghi, Sara and Xi, Liu and Covington, Kyle and Shinbrot, Eve and Wheeler, David A and Gibbs, Richard A and Donehower, Lawrence A and Wang, Zhining and Wang, Min and Wang, Linghua and Bowen, Jay and Gastier-Foster, Julie M and Gerken, Mark and Helsel, Carmen and Leraas, Kristen M and Lichtenberg, Tara M and Ramirez, Nilsa C and Wise, Lisa and Zmuda, Erik and Gabriel, Stacey B and Meyerson, Matthew and Cibulskis, Carrie and Murray, Bradley A and Shih, Juliann and Beroukhim, Rameen and Cherniack, Andrew D and Schumacher, Steven E and Saksena, Gordon and Pedamallu, Chandra Sekhar and Chin, Lynda and Getz, Gad and Noble, Michael and Zhang, Jiashan and Zhang, Hongxin and Zhang, Jianping and Zhang, Wei and Zhang, Hailei and Heiman, David and Cho, Juok and Gehlenborg, Nils and Voet, Douglas and Lin, Pei and Frazer, Scott and Defreitas, Timothy and Meier, Sam and Lawrence, Michael and Kim, Jaegil and Creighton, Chad J and Muzny, Donna and Doddapaneni, HarshaVardhan and Hu, Jianhong and Morton, Donna and Korchina, Viktoriya and Han, Yi and Dinh, Huyen and Lewis, Lora and Bellair, Michelle and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Santibanez, Jireh and Glenn, Robert and Hale, Walker and Parker, Joel S and Wilkerson, Matthew D and Hayes, D. Neil and Reynolds, Sheila M and Shmulevich, Ilya and Iype, Lisa and Makhlouf, Hala and Torbenson, Michael S and Kakar, Sanjay and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu
Cell, ISSN 0092-8674, 06/2017, Volume 169, Issue 7, pp. 1327 - 1341.e23
Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases... 
IDH1/2 | stem cell phenotype | significantly mutated genes | sonic hedgehog signaling | promoter hypermethylation | cancer subtyping | TP53 | hepatocellular carcinoma | expression profile | metabolic reprogramming | ACCURATE | GENE | SIGNATURES | DNA | QUANTIFICATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | MUTATIONAL LANDSCAPE | PHENOTYPE | EXPRESSION | DISCOVERY | PREDICTION | CELL BIOLOGY | Liver Neoplasms - virology | DNA Methylation | Liver Neoplasms - genetics | Carcinoma, Hepatocellular - genetics | Genomics | Humans | Isocitrate Dehydrogenase - genetics | Carcinoma, Hepatocellular - virology | MicroRNAs - genetics | Mutation | RNA | Gene mutations | Analysis | Genes | Genetic aspects | Hepatoma | Nucleotide sequencing | Tumor proteins | Methylation | Gene expression | DNA sequencing | Cancer | Mortality | Stem cells | Liver cancer | TERT | CDKN2A | HCC subtyping | IDH1 | miR-122 | hepatocellular carcinoma (HCC) | CTNNB1 | immune checkpoint proteins
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7. Full Text The cancer genome atlas pan-cancer analysis project
by Weinstein, John N and Collisson, Eric A and Mills, Gordon B and Shaw, Kenna R Mills and Ozenberger, Brad A and Ellrott, Kyle and Sander, Chris and Stuart, Joshua M and Chang, Kyle and Creighton, Chad J and Davis, Caleb and Donehower, Lawrence and Drummond, Jennifer and Wheeler, David and Ally, Adrian and Balasundaram, Miruna and Birol, Inanc and Butterfield, Yaron S.N and Chu, Andy and Chuah, Eric and Chun, Hye-Jung E and Dhalla, Noreen and Guin, Ranabir and Hirst, Martin and Hirst, Carrie and Holt, Robert A and Jones, Steven J.M and Lee, Darlene and Li, Haiyan I and Marra, Marco A and Mayo, Michael and Moore, Richard A and Mungall, Andrew J and Robertson, A Gordon and Schein, Jacqueline E and Sipahimalani, Payal and Tam, Angela and Thiessen, Nina and Varhol, Richard J and Beroukhim, Rameen and Bhatt, Ami S and Brooks, Angela N and Cherniack, Andrew D and Freeman, Samuel S and Gabriel, Stacey B and Helman, Elena and Jung, Joonil and Meyerson, Matthew and Ojesina, Akinyemi I and Pedamallu, Chandra Sekhar and Saksena, Gordon and Schumacher, Steven E and Tabak, Barbara and Zack, Travis and Lander, Eric S and Bristow, Christopher A and Hadjipanayis, Angela and Haseley, Psalm and Kucherlapati, Raju and Lee, Semin and Lee, Eunjung and Luquette, Lovelace J and Mahadeshwar, Harshad S and Pantazi, Angeliki and Parfenov, Michael and Park, Peter J and Protopopov, Alexei and Ren, Xiaojia and Santoso, Netty and Seidman, Jonathan and Seth, Sahil and Song, Xingzhi and Tang, Jiabin and Xi, Ruibin and Xu, Andrew W and Yang, Lixing and Zeng, Dong and Auman, J Todd and Balu, Saianand and Buda, Elizabeth and Fan, Cheng and Hoadley, Katherine A and Jones, Corbin D and Meng, Shaowu and Mieczkowski, Piotr A and Parker, Joel S and Perou, Charles M and Roach, Jeffrey and Shi, Yan and Silva, Grace O and Tan, Donghui and Veluvolu, Umadevi and Waring, Scot and Wilkerson, Matthew D and Wu, Junyuan and Zhao, Wei and Bodenheimer, Tom and Hayes, D Neil and Hoyle, Alan P and Jeffreys, Stuart R and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and The Cancer Genome Atlas Research Network and Department of Mathematical Sciences, Mathematical Statistics and Naturvetenskapliga fakulteten and Institutionen för matematiska vetenskaper, matematisk statistik and Faculty of Sciences and Göteborgs universitet and Gothenburg University
Nature Genetics, ISSN 1061-4036, 10/2013, Volume 45, Issue 10, pp. 1113 - 1120
The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA,... 
ONCOGENE | FUSION | GENE | GENETICS & HEREDITY | MUTATIONS | IDENTIFICATION | HALLMARKS | Gene Expression Profiling | Neoplasms - genetics | Genome | Neoplasms - pathology | Humans | Medical research | Breast cancer | Mutation | Genomics | Tumors | Genetik | Medicinsk genetik | Medical Genetics | Genetics
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