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1. Full Text Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands
by Weinreb, Ilan and Piscuoglio, Salvatore and Martelotto, Luciano G and Waggott, Daryl and Ng, Charlotte K Y and Perez-Ordonez, Bayardo and Harding, Nicholas J and Alfaro, Javier and Chu, Kenneth C and Viale, Agnes and Fusco, Nicola and Da Cruz Paula, Arnaud and Marchio, Caterina and Sakr, Rita A and Lim, Raymond and Thompson, Lester D R and Chiosea, Simion I and Seethala, Raja R and Skalova, Alena and Stelow, Edward B and Fonseca, Isabel and Assaad, Adel and How, Christine and Wang, Jianxin and De Borja, Richard and Chan-Seng-Yue, Michelle and Howlett, Christopher J and Nichols, Anthony C and Wen, Y Hannah and Katabi, Nora and Buchner, Nicholas and Mullen, Laura and Kislinger, Thomas and Wouters, Bradly G and Liu, Fei-Fei and Norton, Larry and McPherson, John D and Rubin, Brian P and Clarke, Blaise A and Weigelt, Britta and Boutros, Paul C and Reis-Filho, Jorge S
Nature Genetics, ISSN 1061-4036, 11/2014, Volume 46, Issue 11, pp. 1166 - 1169
Polymorphous low-grade adenocarcinoma (PLGA) is the second most frequent type of malignant tumor of the minor salivary glands. We identified PRKD1 hotspot... 
Immunohistochemistry | Amino Acid Sequence | NIH 3T3 Cells | Protein Kinase C - genetics | Adenocarcinoma - pathology | Immunoprecipitation | Salivary Gland Neoplasms - genetics | Humans | Models, Molecular | Molecular Sequence Data | Sequence Analysis, DNA | Mutation, Missense - genetics | Microscopy, Confocal | Sequence Alignment | Animals | Mutagenesis | Protein Kinase C - chemistry | Adenocarcinoma - genetics | Mice | Salivary Gland Neoplasms - pathology | Adenocarcinoma | Genetic aspects | Gene mutations | Salivary gland tumors | Health aspects | Protein kinases | Studies | Medical research | Mutation | Kinases | Index Medicus
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2. Full Text Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
by Frésard, Laure and Smail, Craig and Ferraro, Nicole M and Teran, Nicole A and Li, Xin and Smith, Kevin S and Bonner, Devon and Kernohan, Kristin D and Marwaha, Shruti and Zappala, Zachary and Balliu, Brunilda and Davis, Joe R and Liu, Boxiang and Prybol, Cameron J and Kohler, Jennefer N and Zastrow, Diane B and Reuter, Chloe M and Fisk, Dianna G and Grove, Megan E and Davidson, Jean M and Hartley, Taila and Joshi, Ruchi and Strober, Benjamin J and Utiramerur, Sowmithri and Adams, David R and Aday, Aaron and Alejandro, Mercedes E and Allard, Patrick and Ashley, Euan A and Azamian, Mahshid S and Bacino, Carlos A and Baker, Eva and Balasubramanyam, Ashok and Barseghyan, Hayk and Batzli, Gabriel F and Beggs, Alan H and Behnam, Babak and Bellen, Hugo J and Bernstein, Jonathan A and Berry, Gerard T and Bican, Anna and Bick, David P and Birch, Camille L and Bonner, Devon and Boone, Braden E and Bostwick, Bret L and Briere, Lauren C and Brokamp, Elly and Brown, Donna M and Brush, Matthew and Burke, Elizabeth A and Burrage, Lindsay C and Butte, Manish J and Chen, Shan and Clark, Gary D and Coakley, Terra R and Cogan, Joy D and Colley, Heather A and Cooper, Cynthia M and Cope, Heidi and Craigen, William J and D’Souza, Precilla and Davids, Mariska and Davidson, Jean M and Dayal, Jyoti G and Dell’Angelica, Esteban C and Dhar, Shweta U and Dipple, Katrina M and Donnell-Fink, Laurel A and Dorrani, Naghmeh and Dorset, Daniel C and Douine, Emilie D and Draper, David D and Dries, Annika M and Duncan, Laura and Eckstein, David J and Emrick, Lisa T and Eng, Christine M and Enns, Gregory M and Eskin, Ascia and Esteves, Cecilia and Estwick, Tyra and Fernandez, Liliana and Ferreira, Carlos and Fieg, Elizabeth L and Fisher, Paul G and Fogel, Brent L and Friedman, Noah D and Gahl, William A and Glanton, Emily and Godfrey, Rena A and Goldman, Alica M and Goldstein, David B and Gould, Sarah E and Gourdine, Jean-Philippe F and Groden, Catherine A and Gropman, Andrea L and Haendel, Melissa and Hamid, Rizwan and Hanchard, Neil A and ... and Care4Rare Canada Consortium and Undiagnosed Diseases Network and Medicinska fakulteten and Klinisk epidemiologi and Medicinska och farmaceutiska vetenskapsområdet and Uppsala universitet and Institutionen för medicinska vetenskaper
Nature Medicine, ISSN 1078-8956, 06/2019, Volume 25, Issue 6, pp. 911 - 919
It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene . The current... 
Rare Diseases - genetics | Acid Ceramidase - genetics | Rare Diseases - blood | Humans | Child, Preschool | Male | Case-Control Studies | Potassium Channels - genetics | RNA - genetics | Whole Exome Sequencing | Genetic Variation | Sequence Analysis, RNA | RNA Splicing - genetics | Female | Oxidoreductases Acting on CH-CH Group Donors - genetics | Models, Genetic | Mutation | Child | RNA - blood | Cohort Studies | Disease | Splicing | Muscles | Ribonucleic acid--RNA | Gene expression | Disease control | Blood | Gene sequencing | Diseases | Mitochondria | Biopsy | Diagnostic software | Fibroblasts | Diagnostic systems | Basic Medicine | Medical Genetics | Medicinsk genetik | Medical and Health Sciences | Medicin och hälsovetenskap | Medicinska och farmaceutiska grundvetenskaper
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3. Full Text Spatial genomic heterogeneity within localized, multifocal prostate cancer
by Boutros, Paul C and Fraser, Michael and Harding, Nicholas J and de Borja, Richard and Trudel, Dominique and Lalonde, Emilie and Meng, Alice and Hennings-Yeomans, Pablo H and McPherson, Anew and Sabelnykova, Veronica Y and Zia, Amin and Fox, Natalie S and Livingstone, Julie and Shiah, Yu-Jia and Wang, Jianxin and Beck, Timothy A and Have, Cherry L and Chong, Taryne and Sam, Michelle and Johns, Jeremy and Timms, Lee and Buchner, Nicholas and Wong, Ada and Watson, John D and Simmons, Trent T and P'ng, Christine and Zafarana, Gaetano and Nguyen, Francis and Luo, Xuemei and Chu, Kenneth C and Prokopec, Stephenie D and Sykes, Jenna and Dal Pra, Alan and Berlin, Alejano and Brown, Anew and Chan-Seng-Yue, Michelle A and Yousif, Fouad and Denroche, Robert E and Chong, Lauren C and Chen, Gregory M and Jung, Esther and Fung, Clement and Starmans, Maud H. W and Chen, Hanbo and Govind, Shaylan K and Hawley, James and D'Costa, Alister and Pintilie, Melania and Waggott, Daryl and Hach, Faraz and Lambin, Philippe and Muthuswamy, Lakshmi B and Cooper, Colin and Eeles, Rosalind and Neal, David and Tetu, Bernard and Sahinalp, Cenk and Stein, Lincoln D and Fleshner, Neil and Shah, Sohrab P and Collins, Colin C and Hudson, Thomas J and McPherson, John D and van der Kwast, Theodorus and Bristow, Robert G
Nature Genetics, ISSN 1061-4036, 07/2015, Volume 47, Issue 7, pp. 736 - +
Herein we provide a detailed molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer to delineate new oncogenes or... 
GENE | LANDSCAPE | GENETICS & HEREDITY | C-MYC | GENERATION | MUTATIONS | RADIOTHERAPY | COPY-NUMBER ALTERATION | DNA-SEQUENCING DATA | EXPRESSION | FEATURES | Prostatic Neoplasms - pathology | Genetic Association Studies | Humans | Middle Aged | Male | Genetic Heterogeneity | DNA Copy Number Variations | Point Mutation | Neoplasm Grading | Prostatic Neoplasms - genetics | Cell Line, Tumor | Polymorphism, Single Nucleotide | Proto-Oncogene Proteins c-myc - genetics | Genome, Human | Copy number variations | Development and progression | Genetic aspects | Properties | Prostate cancer | Identification and classification | Oncogenes | Medical research | Mortality | Genomes | Gene expression | Cancer therapies | Patients | Studies | Pathology | Biopsy | Men | Biomarkers | Tumors | Index Medicus
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4. Full Text Genomic hallmarks of localized, non-indolent prostate cancer
by Fraser, Michael and Sabelnykova, Veronica Y and Yamaguchi, Takafumi N and Heisler, Lawrence E and Livingstone, Julie and Huang, Vincent and Shiah, Yu-Jia and Yousif, Fouad and Lin, Xihui and Masella, Andre P and Fox, Natalie S and Xie, Michael and Prokopec, Stephenie D and Berlin, Alejandro and Lalonde, Emilie and Ahmed, Musaddeque and Trudel, Dominique and Luo, Xuemei and Beck, Timothy A and Meng, Alice and Zhang, Junyan and D'Costa, Alister and Denroche, Robert E and Kong, Haiying and Espiritu, Shadrielle Melijah G and Chua, Melvin L. K and Wong, Ada and Chong, Taryne and Sam, Michelle and Johns, Jeremy and Timms, Lee and Buchner, Nicholas B and Orain, Michèle and Picard, Valérie and Hovington, Helène and Murison, Alexander and Kron, Ken and Harding, Nicholas J and P'ng, Christine and Houlahan, Kathleen E and Chu, Kenneth C and Lo, Bryan and Nguyen, Francis and Li, Constance H and Sun, Ren X and De Borja, Richard and Cooper, Christopher I and Hopkins, Julia F and Govind, Shaylan K and Fung, Clement and Waggott, Daryl and Green, Jeffrey and Haider, Syed and Chan-Seng-Yue, Michelle A and Jung, Esther and Wang, Zhiyuan and Bergeron, Alain and Dal Pra, Alan and Lacombe, Louis and Collins, Colin C and Sahinalp, Cenk and Lupien, Mathieu and Fleshner, Neil E and He, Housheng H and Fradet, Yves and Tetu, Bernard and Van Der Kwast, Theodorus and McPherson, John D and Bristow, Robert G and Boutros, Paul C
Nature, ISSN 0028-0836, 01/2017, Volume 541, Issue 7637, pp. 359 - 364
Prostate tumours are highly variable in their response to therapies, but clinically available prognostic factors can explain only a fraction of this... 
HETEROGENEITY | CHROMOSOMAL LOCI | SIGNATURES | CHROMATIN | LANDSCAPE | MULTIDISCIPLINARY SCIENCES | MUTATIONS | COPY-NUMBER ALTERATION | IDENTIFICATION | REARRANGEMENTS | DISCOVERY | Prostatic Neoplasms - pathology | Recurrence | Prognosis | Genomics | Humans | Male | Chromothripsis | Genome, Human - genetics | Prostatic Neoplasms, Castration-Resistant - genetics | Prostatic Neoplasms, Castration-Resistant - pathology | DNA Copy Number Variations | Neoplasm Metastasis - genetics | DNA Methylation | Exome - genetics | Prostatic Neoplasms - genetics | Mutation | Relapse | Analysis | Development and progression | Genetic aspects | Research | Prostate cancer | Cancer | Diseases | Studies | Genes | Medical prognosis | Genomes | Metastasis | Cancer therapies | Aggressiveness | Tumors | Index Medicus
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5. Full Text A comprehensive iterative approach is highly effective in diagnosing individuals who are exome negative
by Shashi, Vandana and Schoch, Kelly and Spillmann, Rebecca and Cope, Heidi and Tan, Queenie K.-G and Walley, Nicole and Pena, Loren and McConkie-Rosell, Allyn and Jiang, Yong-Hui and Stong, Nicholas and Need, Anna C and Goldstein, David B and Adams, David R and Alejandro, Mercedes E and Allard, Patrick and Ashley, Euan A and Azamian, Mahshid S and Bacino, Carlos A and Balasubramanyam, Ashok and Barseghyan, Hayk and Batzli, Gabriel F and Beggs, Alan H and Behnam, Babak and Bellen, Hugo J and Bernstein, Jonathan A and Bican, Anna and Bick, David P and Birch, Camille L and Bonner, Devon and Boone, Braden E and Bostwick, Bret L and Briere, Lauren C and Brown, Donna M and Brush, Matthew and Burke, Elizabeth A and Burrage, Lindsay C and Butte, Manish J and Chen, Shan and Clark, Gary D and Coakley, Terra R and Cogan, Joy D and Cooper, Cynthia M and Cope, Heidi and Craigen, William J and D’Souza, Precilla and Davids, Mariska and Davidson, Jean M and Dayal, Jyoti G and Dell’Angelica, Esteban C and Dhar, Shweta U and Dipple, Katrina M and Donnell-Fink, Laurel A and Dorrani, Naghmeh and Dorset, Daniel C and Douine, Emilie D and Draper, David D and Dries, Annika M and Eckstein, David J and Emrick, Lisa T and Eng, Christine M and Enns, Gregory M and Eskin, Ascia and Esteves, Cecilia and Estwick, Tyra and Fernandez, Liliana and Ferreira, Carlos and Fisher, Paul G and Fogel, Brent L and Friedman, Noah D and Gahl, William A and Glanton, Emily and Godfrey, Rena A and Goldstein, David B and Gould, Sarah E and Gourdine, Jean-Philippe F and Groden, Catherine A and Gropman, Andrea L and Haendel, Melissa and Hamid, Rizwan and Hanchard, Neil A and Handley, Lori H and Herzog, Matthew R and Holm, Ingrid A and Hom, Jason and Howerton, Ellen M and Huang, Yong and Jacob, Howard J and Jain, Mahim and Jiang, Yong-hui and Johnston, Jean M and Jones, Angela L and Koeller, David M and Kohane, Isaac S and Kohler, Jennefer N and Krasnewich, Donna M and Krieg, Elizabeth L and Krier, Joel B and Kyle, Jennifer E and Lalani, Seema R and Lau, C. Christopher and ... and Undiagnosed Dis Network and Undiagnosed Diseases Network
Genetics in Medicine, ISSN 1098-3600, 01/2019, Volume 21, Issue 1, pp. 161 - 172
Purpose: Sixty to seventy-five percent of individuals with rare and undiagnosed phenotypes remain undiagnosed after exome sequencing (ES). With standard ES... 
Rare diseases | Genome sequencing | Undiagnosed diseases | Exome sequencing | Phenotyping | REANALYSIS | VARIANTS | GENETICS & HEREDITY | MEDICAL GENETICS | WHOLE GENOME | whole genome sequencing | rare diseases | undiagnosed diseases | Whole exome sequencing | phenotyping
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6. Full Text Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
by Ewing, Adam D and Houlahan, Kathleen E and Hu, Yin and Ellrott, Kyle and Caloian, Cristian and Yamaguchi, Takafumi N and Bare, J Christopher and P'Ng, Christine and Waggott, Daryl and Sabelnykova, Veronica Y and Kellen, Michael R and Norman, Thea C and Haussler, David and Friend, Stephen H and Stolovitzky, Gustavo and Margolin, Adam A and Stuart, Joshua M and Boutros, Paul C and ICGC-TCGA Dream Somatic Mutation and ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants
Nature Methods, ISSN 1548-7091, 06/2015, Volume 12, Issue 7, pp. 623 - 630
The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response... 
POINT MUTATIONS | MUTATIONAL PROCESSES | CHALLENGE | READ ALIGNMENT | CANCER GENOMICS | SIGNATURES | BIOCHEMICAL RESEARCH METHODS | SEQUENCING DATA | RANDOM FOREST | IDENTIFICATION | DISCOVERY | Crowdsourcing | Algorithms | Neoplasms - genetics | Humans | Benchmarking | Polymorphism, Single Nucleotide | Genome | Care and treatment | Analysis | Genomes | Aberration | Research | Simulation methods | Cancer | Index Medicus
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7. Full Text Accuracy in wrist-worn, sensor-based measurements of heart rate and energy expenditure in a diverse cohort
by Shcherbina, Anna and Mikael Mattsson, C and Waggott, Daryl and Salisbury, Heidi and Christle, Jeffrey W and Hastie, Trevor and Wheeler, Matthew T and Ashley, Euan A and Åstrandlaboratoriet and Gymnastik- och idrottshögskolan, GIH and Institutionen för idrotts- och hälsovetenskap
Journal of Personalized Medicine, ISSN 2075-4426, 06/2017, Volume 7, Issue 2, p. 3
The ability to measure physical activity through wrist-worn devices provides an opportunity for cardiovascular medicine. However, the accuracy of commercial... 
Heart rate | Validation | Energy expenditure | Activity monitors | Fitness trackers | Mobile health | Cycles | Physical activity | Energy measurement | Watches | Heat measurement | Males | Telemetry | Wrist | Body mass index | Walking | Errors | Accuracy | Body mass | Calorimetry | Skin | Fitness | Wearable technology | heart rate | Medical and Health Sciences | Sport and Fitness Sciences | Medicin och hälsovetenskap | Medicine/Technology | Hälsovetenskaper | Medicin/Teknik | Idrottsvetenskap | energy expenditure | fitness trackers | mobile health | activity monitors | validation | Health Sciences
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8. Full Text Medical implications of technical accuracy in genome sequencing
by Goldfeder, Rachel L and Priest, James R and Zook, Justin M and Grove, Megan E and Waggott, Daryl and Wheeler, Matthew T and Salit, Marc and Ashley, Euan A
Genome Medicine, ISSN 1756-994X, 03/2016, Volume 8, Issue 1, p. 24
Background: As whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly... 
DIAGNOSIS | WHOLE-EXOME CAPTURE | DE-NOVO | VARIANTS | CLINICAL-APPLICATIONS | PERFORMANCE | ANNOTATION | MUTATION | GENETICS & HEREDITY | SENSITIVITY | IDENTIFICATION | Computational Biology - methods | Reproducibility of Results | Genetics, Medical - methods | Genetics, Medical - standards | Humans | Genomics - standards | High-Throughput Nucleotide Sequencing - standards | Exome | Genetic Variation | Computational Biology - standards | Genome, Human | Genomics - methods | High-Throughput Nucleotide Sequencing - methods | Databases, Nucleic Acid | Benchmarks | Genomes | Nucleotide sequencing | Analysis | Genomics | DNA sequencing
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9. Full Text Characterization of HPV and host genome interactions in primary head and neck cancers
by Michael Parfenov and Chandra Sekhar Pedamallu and Nils Gehlenborg and Samuel S. Freeman and Ludmila Danilova and Christopher A. Bristow and Semin Lee and Angela G. Hadjipanayis and Elena V. Ivanova and Matthew D. Wilkerson and Alexei Protopopov and Lixing Yang and Sahil Seth and Xingzhi Song and Jiabin Tang and Xiaojia Ren and Jianhua Zhang and Angeliki Pantazi and Netty Santoso and Andrew W. Xu and Harshad Mahadeshwar and David A. Wheeler and Robert I. Haddad and Joonil Jung and Akinyemi I. Ojesina and Natalia Issaeva and Wendell G. Yarbrough and D. Neil Hayes and Jennifer R. Grandis and Adel K. El-Naggar and Matthew Meyerson and Peter J. Park and Lynda Chin and J. G. Seidman and Peter S. Hammerman and Raju Kucherlapati and Canc Genome Atlas Network and Cancer Genome Atlas Network and the Cancer Genome Atlas Network
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2014, Volume 111, Issue 43, pp. 15544 - 15549
Previous studies have established that a subset of head and neck tumors contains human papillomavirus (HPV) sequences and that HPV-driven head and neck cancers... 
Head | Squamous cell carcinoma | Head and neck neoplasms | Genes | DNA | Genomes | Neck | Methylation | Tumors | Cancer | Head and neck | Papilloma virus | Genome rearrangement | Integration sites | CERVICAL CARCINOGENESIS | TRANSFORMATION | HUMAN-PAPILLOMAVIRUS TYPE-16 | MULTIDISCIPLINARY SCIENCES | KERATINOCYTES | integration sites | papilloma virus | INTEGRATION | genome rearrangement | OROPHARYNGEAL CANCER | PROSTATE-CANCER | SQUAMOUS-CELL CARCINOMA | head and neck | cancer | TUMORIGENESIS | Virus Integration - genetics | Head and Neck Neoplasms - virology | Host-Pathogen Interactions - genetics | Base Sequence | Genes, Neoplasm | Humans | Gene Expression Regulation, Neoplastic | Molecular Sequence Data | Head and Neck Neoplasms - genetics | DNA Methylation - genetics | Papillomaviridae - physiology | Genome, Human - genetics | Oncology, Experimental | Host-parasite relationships | Head and neck cancer | Development and progression | Genetic aspects | Research | Gene expression | Virus research | Papillomavirus infections | Biological Sciences
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