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1. Full Text Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 pseudomonas syringae isolates
by Baltrus, David A and Nishimura, Marc T and Romanchuk, Artur and Chang, Jeff H and Mukhtar, M. Shahid and Cherkis, Karen and Roach, Jeff and Grant, Sarah R and Jones, Corbin D and Dangl, Jeffery L
PLoS Pathogens, ISSN 1553-7366, 07/2011, Volume 7, Issue 7, p. e1002132
Closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. In... 
AVIRULENCE GENES | HOST-SPECIFICITY | MICROBIOLOGY | EFFECTOR REPERTOIRE | FUNCTIONAL SCREEN | PHASEOLICOLA 1448A | PLANT IMMUNITY | VIROLOGY | VIRULENCE EFFECTOR | PV. TOMATO DC3000 | PARASITOLOGY | III SECRETION SYSTEM | INNATE IMMUNITY | Biological Evolution | Genome, Bacterial | Virulence Factors - genetics | Base Sequence | Genomics | Alleles | Bacterial Proteins - genetics | Plasmids - genetics | Plant Diseases - genetics | Pseudomonas syringae - genetics | Phylogeny | Pseudomonas syringae - pathogenicity | Pseudomonas syringae | Research | Proteins | Medical research | Flowers & plants | Microbiology | Plasmids
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2. 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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3. Full Text Comprehensive genomic characterization of head and neck squamous cell carcinomas
by Lawrence, Michael S and Sougnez, Carrie and Lichtenstein, Lee and Cibulskis, Kristian and Lander, Eric and Gabriel, Stacey B and Getz, Gad and Ally, Adrian and Balasundaram, Miruna and Birol, Inanc and Bowlby, Reanne and Brooks, Denise and Butterfield, Yaron S. N and Carlsen, Rebecca and Cheng, Dean and Chu, Andy and Dhalla, Noreen and Guin, Ranabir 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 Wong, Tina and Protopopov, Alexei and Santoso, Netty and Lee, Semin and Parfenov, Michael and Zhang, Jianhua and Mahadeshwar, Harshad S and Tang, Jiabin and Ren, Xiaojia and Seth, Sahil and Haseley, Psalm and Zeng, Dong and Yang, Lixing and Xu, Andrew W and Song, Xingzhi and Pantazi, Angeliki and Bristow, Christopher A and Hadjipanayis, Angela and Seidman, Jonathan and Chin, Lynda and Park, Peter J and Kucherlapati, Raju and Akbani, Rehan and Casasent, Tod and Liu, Wenbin and Lu, Yiling and Mills, Gordon and Motter, Thomas and Weinstein, John and Diao, Lixia and Wang, Jing and Hong Fan, You and Liu, Jinze and Wang, Kai and Auman, J. Todd and Balu, Saianand and Bodenheimer, Thomas and Buda, Elizabeth and Hayes, D. Neil and Hoadley, Katherine A and Hoyle, Alan P and Jefferys, Stuart R and Jones, Corbin D and Kimes, Patrick K and Liu, Yufeng and Marron, J.S and Meng, Shaowu and Mieczkowski, Piotr A and Mose, Lisle E and Parker, Joel S and Perou, Charles M and Prins, Jan F and Roach, Jeffrey and Shi, Yan and Simons, Janae V and Singh, Darshan and Soloway, Matthew G and Tan, Donghui and Veluvolu, Umadevi and Walter, Vonn and Waring, Scot and Wilkerson, Matthew D and Wu, Junyuan and Zhao, Ni and Cherniack, Andrew D and Hammerman, Peter S and Tward, Aaron D and Pedamallu, Chandra Sekhar and Saksena, Gordon and ... and Canc Genome Atlas Network and Cancer Genome Atlas Network and The Cancer Genome Atlas Network
Nature, ISSN 0028-0836, 01/2015, Volume 517, Issue 7536, pp. 576 - 582
The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here... 
CANCER GROWTH | ACTIVATION | GROWTH-FACTOR-RECEPTOR | MULTIDISCIPLINARY SCIENCES | RESISTANCE | CLASSIFICATION | INHIBITORS | MUTATIONS | NF-KAPPA-B | LIM PROTEIN AJUBA | EGFR | Oncogenes - genetics | Carcinoma, Squamous Cell - genetics | Genomics | Humans | Male | DNA Copy Number Variations - genetics | Signal Transduction - genetics | Molecular Targeted Therapy | Mutation - genetics | Genome, Human - genetics | Transcription Factors - metabolism | Squamous Cell Carcinoma of Head and Neck | RNA, Neoplasm - genetics | Female | Head and Neck Neoplasms - genetics | DNA, Neoplasm - genetics | Gene Expression Regulation, Neoplastic - genetics | Squamous cell carcinoma | Oncology, Experimental | Genetic research | Head and neck cancer | Genetic aspects | Research | Gene expression | Cancer | Transcription factors | Cell cycle | DNA methylation | Genomes | Mutation | Head & neck cancer | Kinases | Cancer therapies | Tumors | Apoptosis
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4. Full Text (P097) Two-and-a-Half Year Clinical Experience With Magnetic Resonance Image Guided Radiation Therapy
by Fischer-Valuck, Benjamin W., MD and Henke, Lauren, MD and Kashani, Rojano, PhD and Green, Olga, PhD and Olsen, Jeffrey, MD and Parikh, Parag, MD and Robinson, Cliff, MD and Bradley, Jeff, MD and Thomas, Maria, MD, PhD and Roach, Michael, MD and Zoberi, Imran, MD and Mazur, Thomas, PhD and Huang, Jiayi, MD and Gay, Hiram, MD and Rodriguez, Vivian, PhD and Mutic, Sasa, PhD and Michalski, Jeff M., MD, MBA
International Journal of Radiation Oncology, Biology, Physics, ISSN 0360-3016, 2017, Volume 98, Issue 2, pp. E41 - E42
Radiology | Hematology, Oncology and Palliative Medicine | Magnetic resonance imaging | Radiotherapy | Radiation
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5. Full Text The accessible chromatin landscape of the human genome
by Thurman, Robert E and Rynes, Eric and Humbert, Richard and Vierstra, Jeff and Maurano, Matthew T and Haugen, Eric and Sheffield, Nathan C and Stergachis, Andrew B and Wang, Hao and Vernot, Benjamin and Garg, Kavita and John, Sam and Sandstrom, Richard and Bates, Daniel and Boatman, Lisa and Canfield, Theresa K and Diegel, Morgan and Dunn, Douglas and Ebersol, Abigail K and Frum, Tristan and Giste, Erika and Johnson, Audra K and Johnson, Ericka M and Kutyavin, Tanya and Lajoie, Bryan and Lee, Bum-Kyu and Lee, Kristen and London, Darin and Lotakis, Dimitra and Neph, Shane and Neri, Fidencio and Nguyen, Eric D and Qu, Hongzhu and Reynolds, Alex P and Roach, Vaughn and Safi, Alexias and Sanchez, Minerva E and Sanyal, Amartya and Shafer, Anthony and Simon, Jeremy M and Song, Lingyun and Vong, Shinny and Weaver, Molly and Yan, Yongqi and Zhang, Zhancheng and Zhang, Zhuzhu and Lenhard, Boris and Tewari, Muneesh and Dorschner, Michael O and Hansen, R. Scott and Navas, Patrick A and Stamatoyannopoulos, George and Iyer, Vishwanath R and Lieb, Jason D and Sunyaev, Shamil R and Akey, Joshua M and Sabo, Peter J and Kaul, Rajinder and Furey, Terrence S and Dekker, Job and Crawford, Gregory E and Stamatoyannopoulos, John A
Nature, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 75 - 82
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including... 
LOCUS-CONTROL REGION | PROTEIN | MULTIDISCIPLINARY SCIENCES | TRANSCRIPTION | DISTINCT | NF-E2 | BINDING | BETA-GLOBIN LOCUS | Chromatin - metabolism | Genomics | Humans | Molecular Sequence Annotation | Mutation Rate | Promoter Regions, Genetic - genetics | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | Encyclopedias as Topic | DNA - genetics | DNA Footprinting | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | DNA Methylation | Transcription Initiation Site | Transcription, Genetic | Chromatin - genetics | Evolution, Molecular | Physiological aspects | Genetic research | Chromatin | Research | Human genome | DNA | Proteins | DNA methylation | Mutation | Cells
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6. Full Text An expansive human regulatory lexicon encoded in transcription factor footprints
by Neph, Shane and Vierstra, Jeff and Stergachis, Andrew B and Reynolds, Alex P and Haugen, Eric and Vernot, Benjamin and Thurman, Robert E and John, Sam and Sandstrom, Richard and Johnson, Audra K and Maurano, Matthew T and Humbert, Richard and Rynes, Eric and Wang, Hao and Vong, Shinny and Lee, Kristen and Bates, Daniel and Diegel, Morgan and Roach, Vaughn and Dunn, Douglas and Neri, Jun and Schafer, Anthony and Hansen, R. Scott and Kutyavin, Tanya and Giste, Erika and Weaver, Molly and Canfield, Theresa and Sabo, Peter and Zhang, Miaohua and Balasundaram, Gayathri and Byron, Rachel and MacCoss, Michael J and Akey, Joshua M and Bender, M.A and Groudine, Mark and Kaul, Rajinder and Stamatoyannopoulos, John A
Nature, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 83 - 90
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution 'footprints'. Using genomic... 
RNA-POLYMERASE-II | COMPLEX | HUMAN GENOME | PROTEIN-DNA INTERACTIONS | CHROMATIN | MULTIDISCIPLINARY SCIENCES | IN-VIVO | GENE-EXPRESSION | MICE | DIFFERENTIATION | BINDING | Genomic Imprinting | Genomics | Humans | Molecular Sequence Annotation | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | Encyclopedias as Topic | DNA - genetics | DNA Footprinting | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | DNA Methylation | Transcription Initiation Site | Polymorphism, Single Nucleotide - genetics | Physiological aspects | Genetic research | Transcription factors | Research | Genetic regulation | Proteins | Genes | Phylogenetics | Footprints | Genomes | Deoxyribonucleic acid--DNA | Methods | protein occupancy | regulation | chromatin | DNaseI footprinting | ENCODE
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7. Full Text Adjuvant and Salvage Radiation Therapy After Prostatectomy: American Society for Radiation Oncology/American Urological Association Guidelines
by Valicenti, Richard K., MD, MBA and Thompson, Ian, MD and Albertsen, Peter, MD, MS and Davis, Brian J., MD, PhD and Goldenberg, S. Larry, MD and Wolf, J. Stuart, MD and Sartor, Oliver, MD and Klein, Eric, MD and Hahn, Carol, MD and Michalski, Jeff, MD, MBA and Roach, Mack, MD and Faraday, Martha M., PhD and American Society for Radiation Oncology/American Urological Association
International Journal of Radiation Oncology, Biology, Physics, ISSN 0360-3016, 2013, Volume 86, Issue 5, pp. 822 - 828
Purpose The purpose of this guideline was to provide a clinical framework for the use of radiation therapy after radical prostatectomy as adjuvant or salvage... 
Radiology | Hematology, Oncology and Palliative Medicine | CONSENSUS GUIDELINES | ONCOLOGY | BIOCHEMICAL RECURRENCE | RADICAL RETROPUBIC PROSTATECTOMY | RANDOMIZED CLINICAL-TRIAL | POSTOPERATIVE RADIOTHERAPY | POSITIVE SURGICAL MARGINS | TARGET VOLUME | PROGNOSTIC-SIGNIFICANCE | CANCER | RADIOLOGY, NUCLEAR MEDICINE & MEDICAL IMAGING | PROGRESSION | Salvage Therapy - adverse effects | Prostatic Neoplasms - radiotherapy | United States | Humans | Male | Prostate-Specific Antigen - blood | Urology - standards | Salvage Therapy - standards | Societies, Medical | Radiotherapy, Adjuvant - adverse effects | Patient Education as Topic - standards | Prostatectomy | Radiotherapy, Adjuvant - standards | Radiation Oncology - standards | Sects | Medical colleges | Radiotherapy | Nuclear radiation | Surgery | PROSTATE | REVIEWS | SURGERY | PATIENTS | RECOMMENDATIONS | METASTASES | RADIOLOGY AND NUCLEAR MEDICINE | ANTIGENS | RADIOTHERAPY | SIDE EFFECTS
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8. Full Text Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)
by Klionsky, Daniel J and Abdelmohsen, Kotb and Abe, Akihisa and Abedin, Md Joynal and Abeliovich, Hagai and Acevedo Arozena, Abraham and Adachi, Hiroaki and Adams, Christopher M and Adams, Peter D and Adeli, Khosrow and Adhihetty, Peter J and Adler, Sharon G and Agam, Galila and Agarwal, Rajesh and Aghi, Manish K and Agnello, Maria and Agostinis, Patrizia and Aguilar, Patricia V and Aguirre-Ghiso, Julio and Airoldi, Edoardo M and Ait-Si-Ali, Slimane and Akematsu, Takahiko and Akporiaye, Emmanuel T and Al-Rubeai, Mohamed and Albaiceta, Guillermo M and Albanese, Chris and Albani, Diego and Albert, Matthew L and Aldudo, Jesus and Algül, Hana and Alirezaei, Mehrdad and Alloza, Iraide and Almasan, Alexandru and Almonte-Beceril, Maylin and Alnemri, Emad S and Alonso, Covadonga and Altan-Bonnet, Nihal and Altieri, Dario C and Alvarez, Silvia and Alvarez-Erviti, Lydia and Alves, Sandro and Amadoro, Giuseppina and Amano, Atsuo and Amantini, Consuelo and Ambrosio, Santiago and Amelio, Ivano and Amer, Amal O and Amessou, Mohamed and Amon, Angelika and An, Zhenyi and Anania, Frank A and Andersen, Stig U and Andley, Usha P and Andreadi, Catherine K and Andrieu-Abadie, Nathalie and Anel, Alberto and Ann, David K and Anoopkumar-Dukie, Shailendra and Antonioli, Manuela and Aoki, Hiroshi and Apostolova, Nadezda and Aquila, Saveria and Aquilano, Katia and Araki, Koichi and Arama, Eli and Aranda, Agustin and Araya, Jun and Arcaro, Alexandre and Arias, Esperanza and Arimoto, Hirokazu and Ariosa, Aileen R and Armstrong, Jane L and Arnould, Thierry and Arsov, Ivica and Asanuma, Katsuhiko and Askanas, Valerie and Asselin, Eric and Atarashi, Ryuichiro and Atherton, Sally S and Atkin, Julie D and Attardi, Laura D and Auberger, Patrick and Auburger, Georg and Aurelian, Laure and Autelli, Riccardo and Avagliano, Laura and Avantaggiati, Maria Laura and Avrahami, Limor and Awale, Suresh and Azad, Neelam and Bachetti, Tiziana and Backer, Jonathan M and Bae, Dong-Hun and Bae, Jae-sung and Bae, Ok-Nam and Bae, Soo Han and Baehrecke, Eric H and Baek, Seung-Hoon and Baghdiguian, Stephen and Bagniewska-Zadworna, Agnieszka and ... and Medicinska fakulteten and Region Östergötland and Linköpings universitet and Institutionen för klinisk och experimentell medicin and Diagnostikcentrum and Klinisk patologi och klinisk genetik and Institutionen för medicin och hälsa and Avdelningen för läkemedelsforskning and Avdelningen för cellbiologi
Autophagy, ISSN 1554-8627, 01/2016, Volume 12, Issue 1, pp. 1 - 222
stress | chaperone-mediated autophagy | vacuole | autolysosome | macroautophagy | flux | autophagosome | LC3 | lysosome | phagophore | Phagophore | Lysosome | Autolysosome | Flux | Autophagosome | Vacuole | Chaperonemediated autophagy | Macroautophagy | Stress | ACTIVATED PROTEIN-KINASE | ENDOPLASMIC-RETICULUM STRESS | STARVATION-INDUCED AUTOPHAGY | GLUCAGON-INDUCED AUTOPHAGY | CELL BIOLOGY | PROGRAMMED CELL-DEATH | LIFE-SPAN EXTENSION | BETAINE HOMOCYSTEINE METHYLTRANSFERASE | VACUOLAR MEMBRANE DYNAMICS | NF-KAPPA-B | Autophagy - physiology | Biological Assay - methods | Animals | Biological Assay - standards | Computer Simulation | Humans | Life Sciences | Medical and Health Sciences | Medicin och hälsovetenskap
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