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1. Full Text GOFAST: An integrated approach for efficient and comprehensive membrane proteome analysis
by Yu, Yanbao and Xie, Ling and Gunawardena, Harsha P and Khatun, Jainab and Maier, Christopher and Spitzer, Wendy and Leerkes, Maarten and Giddings, Morgan C and Chen, Xian
Analytical Chemistry, ISSN 0003-2700, 11/2012, Volume 84, Issue 21, pp. 9008 - 9014
Membrane proteomics, the large-scale analysis of membrane proteins, is often constrained by the difficulties of achieving fully resolvable separation and... 
DIGESTION | CHEMISTRY, ANALYTICAL | SAMPLE PREPARATION METHOD | EXTRACTION | SHOTGUN PROTEOMICS | INTACT PROTEINS | TOP-DOWN | IN-DEPTH ANALYSIS | CHROMATOGRAPHY-MASS SPECTROMETRY | IDENTIFICATION | CELL-LINE | Membrane Proteins - isolation & purification | Filtration | Humans | Protein Isoforms - analysis | Proteome - analysis | Proteome - chemistry | Membrane Proteins - analysis | Membrane Proteins - chemistry | Analytic Sample Preparation Methods - methods | Protein Isoforms - chemistry | K562 Cells | Electrophoresis - methods | Proteomics - methods | Enzymes | Usage | Synthesis | Proteolysis | Analysis | Research | Mathematical optimization | Membrane proteins | Proteins | Analytical chemistry | Membranes | Integrated approach | Medical technology | Leukemia | Proteomics | Index Medicus
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2. Full Text Modulation of B-cell exosome proteins by gamma herpesvirus infection
by David G. Meckes, Jr and Harsha P. Gunawardena and Robert M. Dekroon and Phillip R. Heaton and Rachel H. Edwards and Sezgin Ozgur and Jack D. Griffith and Blossom Damania and Nancy Raab-Traub
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 07/2013, Volume 110, Issue 31, pp. E2925 - E2933
The human gamma herpesviruses, Kaposi sarcoma-associated virus (KSHV) and EBV, are associated with multiple cancers. Recent evidence suggests that EBV and... 
Microparticles | Microvesicles | Oncosomes | LMP1 | MULTIDISCIPLINARY SCIENCES | SARCOMA-ASSOCIATED HERPESVIRUS | PRIMARY EFFUSION LYMPHOMA | microparticles | RECEPTOR | microvesicles | NASOPHARYNGEAL CARCINOMA-CELLS | KAPOSIS-SARCOMA | ENDOTHELIAL-CELLS | CLASS-I | oncosomes | EXPRESSION | PROTEOMICS | Exosomes - metabolism | Protein Biosynthesis | Epstein-Barr Virus Infections - virology | Signal Transduction | Cell Survival | Sarcoma, Kaposi - metabolism | Humans | Exosomes - pathology | Sarcoma, Kaposi - virology | Neoplasm Proteins - metabolism | Sarcoma, Kaposi - pathology | Epstein-Barr Virus Infections - pathology | Herpesvirus 8, Human - metabolism | Cell Death | Cell Line, Tumor | Epstein-Barr Virus Infections - diagnosis | B-Lymphocytes - pathology | Herpesvirus 4, Human - metabolism | Epstein-Barr Virus Infections - metabolism | B-Lymphocytes - metabolism | Cell Line, Transformed | Exosomes - virology | Sarcoma, Kaposi - diagnosis | Proteins | Cellular biology | Herpes viruses | Proteomics | Mass spectrometry | Cancer | Tumors | Index Medicus | Biological Sciences | PNAS Plus
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3. Full Text An integrated encyclopedia of DNA elements in the human genome
by Dunham, Ian and Kundaje, Anshul and Aldred, Shelley F and Collins, Patrick J and Davis, Carrie A and Doyle, Francis and Epstein, Charles B and Frietze, Seth and Harrow, Jennifer and Kaul, Rajinder and Khatun, Jainab and Lajoie, Bryan R and Landt, Stephen G and Lee, Bum-Kyu and Pauli, Florencia and Rosenbloom, Kate R and Sabo, Peter and Safi, Alexias and Sanyal, Amartya and Shoresh, Noam and Simon, Jeremy M and Song, Lingyun and Trinklein, Nathan D and Altshuler, Robert C and Birney, Ewan and Brown, James B and Cheng, Chao and Djebali, Sarah and Dong, Xianjun and Ernst, Jason and Furey, Terrence S and Gerstein, Mark and Giardine, Belinda and Greven, Melissa and Hardison, Ross C and Harris, Robert S and Herrero, Javier and Hoffman, Michael M and Iyer, Sowmya and Kellis, Manolis and Kheradpour, Pouya and Lassmann, Timo and Li, Qunhua and Lin, Xinying and Marinov, Georgi K and Merkel, Angelika and Mortazavi, Ali and Parker, Stephen C. J and Reddy, Timothy E and Rozowsky, Joel and Schlesinger, Felix and Thurman, Robert E and Wang, Jie and Ward, Lucas D and Whitfield, Troy W and Wilder, Steven P and Wu, Weisheng and Xi, Hualin S and Yip, Kevin Y and Zhuang, Jiali and Bernstein, Bradley E and Green, Eric D and Gunter, Chris and Snyder, Michael and Pazin, Michael J and Lowdon, Rebecca F and Dillon, Laura A. L and Adams, Leslie B and Kelly, Caroline J and Zhang, Julia and Wexler, Judith R and Good, Peter J and Feingold, Elise A and Crawford, Gregory E and Dekker, Job and Elnitski, Laura and Farnham, Peggy J and Giddings, Morgan C and Gingeras, Thomas R and Guigó, Roderic and Hubbard, Timothy J and Kent, W. James and Lieb, Jason D and Margulies, Elliott H and Myers, Richard M and Stamatoyannopoulos, John A and Tenenbaum, Scott A and Weng, Zhiping and White, Kevin P and Wold, Barbara and Yu, Yanbao and Wrobel, John and Risk, Brian A and Gunawardena, Harsha P and Kuiper, Heather C and Maier, Christopher W and Xie, Ling and Chen, Xian and Mikkelsen, Tarjei S and Gillespie, Shawn and ... and ENCODE Project Consortium and The ENCODE Project Consortium
Nature, ISSN 0028-0836, 09/2012, Volume 489, Issue 7414, pp. 57 - 74
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA... 
TRANSCRIPTION FACTOR-BINDING | CHROMATIN | MAPS | DETERMINANTS | HUMAN-CELLS | MULTIDISCIPLINARY SCIENCES | IN-VIVO | REGIONS | MOUSE | WIDE | CHROMOSOME CONFORMATION CAPTURE | Mammals - genetics | Chromatin - metabolism | Histones - chemistry | Genomics | Humans | Promoter Regions, Genetic - genetics | Encyclopedias as Topic | DNA-Binding Proteins - metabolism | Chromatin Immunoprecipitation | Neoplasms - genetics | Genetic Predisposition to Disease - genetics | Genome-Wide Association Study | Chromosomes, Human - genetics | Molecular Sequence Annotation | Exons - genetics | DNA Methylation - genetics | Binding Sites - genetics | Chromosomes, Human - metabolism | Genome, Human - genetics | Regulatory Sequences, Nucleic Acid - genetics | DNA - genetics | DNA Footprinting | Proteins - genetics | Transcription Factors - metabolism | Deoxyribonuclease I - metabolism | Animals | Sequence Analysis, RNA | Alleles | Polymorphism, Single Nucleotide - genetics | Genetic Variation - genetics | Histones - metabolism | Transcription, Genetic - genetics | Chromatin - genetics | Genetic research | Genetic transcription | Research | Human genome | Proteins | Studies | Genes | DNA methylation | Genetics | Deoxyribonucleic acid--DNA | Index Medicus | Genètica | Genòmica | Genoma humà | Life Sciences
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4. Full Text Long noncoding RNAs are rarely translated in two human cell lines
by Bánfai, Balázs and Jia, Hui and Khatun, Jainab and Wood, Emily and Risk, Brian and Gundling Jr, William E and Kundaje, Anshul and Gunawardena, Harsha P and Yu, Yanbao and Xie, Ling and Krajewski, Krzysztof and Strahl, Brian D and Chen, Xian and Bickel, Peter and Giddings, Morgan C and Brown, James B and Lipovich, Leonard
Genome Research, ISSN 1088-9051, 09/2012, Volume 22, Issue 9, pp. 1646 - 1657
Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (IncRNAs), yet only 100 have... 
RELATIVE PROTEIN ABUNDANCE | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | IDENTIFICATION | MASS-SPECTROMETRY | DISCOVERY | GENOME | COMPARING PROTEIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EMBRYONIC STEM-CELLS | GENETICS & HEREDITY | GENE-EXPRESSION | PROTEOMICS | Amino Acid Sequence | Cell Line | Gene Expression | Protein Biosynthesis | Humans | Molecular Sequence Annotation | RNA, Messenger - genetics | Gene Expression Regulation | Peptides - genetics | Molecular Sequence Data | Gene Expression Profiling | RNA, Long Noncoding - genetics | RNA, Messenger - metabolism | Sequence Alignment | Base Sequence | K562 Cells | RNA, Long Noncoding - metabolism | Tandem Mass Spectrometry - methods | Index Medicus | Research
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5. Full Text Rapid Screening of Ellagitannins in Natural Sources via Targeted Reporter Ion Triggered Tandem Mass Spectrometry
by Bowers, Jeremiah J and Gunawardena, Harsha P and Cornu, Anaëlle and Narvekar, Ashwini S and Richieu, Antoine and Deffieux, Denis and Quideau, Stéphane and Tharayil, Nishanth
Scientific Reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 10399 - 10
Complex biomolecules present in their natural sources have been difficult to analyze using traditional analytical approaches. Ultrahigh-performance liquid... 
ANTIOXIDANT ACTIVITY | INVERSE FOURIER-TRANSFORM | IN-VITRO | C-GLYCOSIDIC ELLAGITANNINS | MULTIDISCIPLINARY SCIENCES | BIOLOGICAL-ACTIVITY | ELECTRON-TRANSFER DISSOCIATION | COLLISION-INDUCED DISSOCIATION | ELLAGIC ACID | THERMOCHEMICAL DETERMINATIONS | FRAGARIA X ANANASSA | Anions | Classification | Data processing | Mass spectroscopy | Ions | Liquid chromatography | Isomers
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6. Full Text Micro-Data-Independent Acquisition for High-Throughput Proteomics and Sensitive Peptide Mass Spectrum Identification
by Heaven, Michael R and Cobbs, Archie L and Nei, Yuan-Wei and Gutierrez, Danielle B and Herren, Anthony W and Gunawardena, Harsha P and Caprioli, Richard M and Norris, Jeremy L
Analytical Chemistry, ISSN 0003-2700, 08/2018, Volume 90, Issue 15, pp. 8905 - 8911
State-of-the-art strategies for proteomics are not able to rapidly interrogate complex peptide mixtures in an untargeted manner with sensitive peptide and... 
MIXTURES | SPECTROMETRY DATA | CHEMISTRY, ANALYTICAL | ASSAY | QUANTIFICATION | STRATEGY | LIBRARY | MS/MS | Humans | Workflow | Escherichia coli - chemistry | Proteome - chemistry | Algorithms | Databases, Protein | Chromatography, Liquid | Software | HeLa Cells | Proteomics - methods | Escherichia coli Proteins - chemistry | Tandem Mass Spectrometry - methods | Peptides - analysis | High-Throughput Screening Assays - methods | Proteins | Deconvolution | Peptides | Search algorithms | Data acquisition systems | Escherichia coli | Proteomics | Liquid chromatography | Software development tools | Mass spectrometry | Mass spectra | Index Medicus
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7. Full Text Proteogenomic integration reveals therapeutic targets in breast cancer xenografts
by Huang, Kuan-Lin and Li, Shunqiang and Mertins, Philipp and Cao, Song and Gunawardena, Harsha P and Ruggles, Kelly V and Mani, D.R and Clauser, Karl R and Tanioka, Maki and Usary, Jerry and Kavuri, Shyam M and Xie, Ling and Yoon, Christopher and Qiao, Jana W and Wrobel, John and Wyczalkowski, Matthew A and Erdmann-Gilmore, Petra and Snider, Jacqueline E and Hoog, Jeremy and Singh, Purba and Niu, Beifung and Guo, Zhanfang and Sun, Sam Qiancheng and Sanati, Souzan and Kawaler, Emily and Wang, Xuya and Scott, Adam and Ye, Kai and McLellan, Michael D and Wendl, Michael C and Malovannaya, Anna and Held, Jason M and Gillette, Michael A and Fenyö, David and Kinsinger, Christopher R and Mesri, Mehdi and Rodriguez, Henry and Davies, Sherri R and Perou, Charles M and Ma, Cynthia and Reid Townsend, R and Chen, Xian and Carr, Steven A and Ellis, Matthew J and Ding, Li
Nature Communications, ISSN 2041-1723, 03/2017, Volume 8, Issue 1, pp. 14864 - 14864
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein... 
TUMOR XENOGRAFTS | GENOMICS | PATHWAY | QUANTIFICATION | MULTIDISCIPLINARY SCIENCES | MUTATIONS | INHIBITOR | DISCOVERY | MTOR | Index Medicus
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8. Full Text Whole human genome proteogenomic mapping for ENCODE cell line data: Identifying protein-coding regions
by Khatun, Jainab and Yu, Yanbao and Wrobel, John A and Risk, Brian A and Gunawardena, Harsha P and Secrest, Ashley and Spitzer, Wendy J and Xie, Ling and Wang, Li and Chen, Xian and Giddings, Morgan C
BMC Genomics, ISSN 1471-2164, 02/2013, Volume 14, Issue 1, pp. 141 - 141
Background: Proteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating... 
Genome annotation | MS/MS spectra | Proteogenomic mapping | Genomics | Proteomics | PEPTIDE IDENTIFICATION | SHOTGUN PROTEOMICS | HIDDEN MARKOV MODEL | DISCOVERY | BREAST-CANCER | SCORING FUNCTION | OPEN READING FRAMES | GENE | TRANSLATION START SITES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MASS | GENETICS & HEREDITY | Cell Line | Humans | Mass Spectrometry | Molecular Sequence Annotation | Computational Biology | Databases, Genetic | Chromosome Mapping | Genome, Human | Open Reading Frames - genetics | Sequence Analysis, DNA | Chromosome mapping | Usage | Research | Human genome | Methods | Web browsers | Proteins | Studies | Reading | Pilot projects | Encyclopedias | Genetics | Genomes | Mass spectrometry | Deoxyribonucleic acid--DNA | Data bases | Index Medicus
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