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Analytical chemistry, ISSN 0003-2700, 01/2020, Volume 92, Issue 2, pp. 1796 - 1803
Advancements in molecular separations coupled with mass spectrometry have enabled metabolome analyses for clinical cohorts. A population of interest for... 
Journal Article
Journal of medical toxicology : official journal of the American College of Medical Toxicology, ISSN 1556-9039, 01/2020, Volume 16, Issue 1, pp. 49 - 60
Non-medical use and abuse of prescription opioids is a growing problem in both the civilian and military communities, with minimal technologies for detecting... 
Journal Article
Toxicology and Applied Pharmacology, ISSN 0041-008X, 03/2013, Volume 267, Issue 2
The co-occurrence of environmental factors is common in complex human diseases and, as such, understanding the molecular responses involved is essential to... 
ANTIOXIDANTS | MACROPHAGES | LUNGS | 60 APPLIED LIFE SCIENCES | OXYGEN | TOBACCO SMOKES | DIET | LYMPHOKINES | BIOLOGICAL MARKERS | ENZYMES | INFLAMMATION | ENZYME IMMUNOASSAY | MICE | METABOLIC DISEASES
Journal Article
Chemical Research in Toxicology, ISSN 0893-228X, 05/2018, Volume 31, Issue 5, pp. 308 - 318
Cytochrome P450 monooxygenase (P450) enzymes metabolize critical endogenous chemicals and oxidize nearly all xenobiotics. Dysregulated P450 activities lead to... 
Index Medicus
Journal Article
Journal of Proteome Research, ISSN 1535-3893, 07/2012, Volume 11, Issue 7, pp. 3690 - 3703
Journal Article
Methods in molecular biology (Clifton, N.J.), ISSN 1064-3745, 2009, Volume 492, pp. 453 - 460
Accurate identification of peptides is a current challenge in mass spectrometry (MS)-based proteomics. The standard approach uses a search routine to compare... 
Tandem Mass Spectrometry | Reproducibility of Results | Algorithms | Peptides - chemistry | Artificial Intelligence | Databases, Protein | Sensitivity and Specificity | Benchmarking | Peptides - classification | Peptides - analysis
Journal Article
by Ramoni, Rachel B and Mulvihill, John J and Adams, Christopher J and Adams, David R and Allard, Patrick and Ashley, Euan A and Bernstein, Jonathan A and Gahl, William A and Hamid, Rizwan and Loscalzo, Joseph and McCray, Alexa T and Shashi, Vandana and Tifft, Cynthia J and Alejandro, Mercedes E and Azamian, Mashid S and Bacino, Carlos A and Balasubramanyam, Ashok and Barseghyan, Hayk and Beggs, Alan H and Bellen, Hugo J and Bernick, David and Bican, Anna and Bick, David P and Birch, Camille L and Boone, Braden E and Briere, Lauren C and Brown, Donna M and Brownstein, Catherine A and Brush, Matthew and Burke, Elizabeth A and Burrage, Lindsay C and Chao, Katherine R and Clark, Gary D and Cogan, Joy D and Cooper, Cynthia M and Craigen, William J and Davids, Mariska 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 Draper, David D and Dries, Annika M and Eastwood, Rachel and Eckstein, David J and Emrick, Lisa T and Eng, Christine M and Esteves, Cecilia and Estwick, Tyra and Fisher, Paul G and Frisby, Trevor S and Frost, Kate and Gartner, Valerie and Godfrey, Rena A and Goheen, Mitchell and Golas, Gretchen A and Goldstein, David B and Gordon, Mary “Gracie” G and Gould, Sarah E and Gourdine, Jean-Philippe F and Graham, Brett H and Groden, Catherine A and Gropman, Andrea L and Hackbarth, Mary E and Haendel, Melissa and Hanchard, Neil A and Handley, Lori H and Hardee, Isabel and Herzog, Matthew R and Holm, Ingrid A and Howerton, Ellen M and Iglesias, Brenda and Jacob, Howard J and Jain, Mahim and Jiang, Yong-hui and Johnston, Jean M and Jones, Angela L and Koehler, Alanna E 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 Latham, Lea and Latour, Yvonne L and Lau, C. Christopher and Lazar, Jozef and Lee, Paul R and Lee, Brendan H and Lee, Hane and Levy, Denise J and Levy, Shawn E and Lewis, Richard A and Liebendorder, Adam P and ... and Undiag Dis Network and Undiagnosed Diseases Network
The American Journal of Human Genetics, ISSN 0002-9297, 02/2017, Volume 100, Issue 2, pp. 185 - 192
Journal Article
ISSN 1757-9694, 10/2013, Volume 5, Issue 11, pp. 1393 - 146
To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or... 
Journal Article
Cell metabolism, ISSN 1550-4131, 01/2020
Type 1 diabetes (T1D) results from the progressive loss of β cells, a process propagated by pro-inflammatory cytokine signaling that disrupts the balance... 
Journal Article
by Wang, Julia and Al-Ouran, Rami and Hu, Yanhui and Kim, Seon-Young and Wan, Ying-Wooi and Wangler, Michael F and Yamamoto, Shinya and Chao, Katherine R and Chao, Hsiao-Tuan and Comjean, Aram and Mohr, Stephanie E and Adams, David R and Adams, Christopher J and Alejandro, Mercedes E and Allard, Patrick and Ashley, Euan A and Azamian, Mashid S and Bacino, Carlos A and Balasubramanyam, Ashok and Barseghyan, Hayk and Beggs, Alan H and Bellen, Hugo J and Bernstein, Jonathan A and Bican, Anna and Bick, David P and Birch, Camille L and Boone, Braden E and Briere, Lauren C and Brown, Donna M and Brush, Matthew and Burke, Elizabeth A and Burrage, Lindsay C and Clark, Gary D and Cogan, Joy D and Cooper, Cynthia M and Craigen, William J and Davids, Mariska 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 Draper, David D and Dries, Annika M and Eckstein, David J and Emrick, Lisa T and Eng, Christine M and Esteves, Cecilia and Estwick, Tyra and Fisher, Paul G and Frisby, Trevor S and Frost, Kate and Gahl, William A and Gartner, Valerie and Godfrey, Rena A and Goheen, Mitchell and Golas, Gretchen A and Goldstein, David B and Gordon, Mary G and Gould, Sarah E and Gourdine, Jean-Philippe F and Graham, Brett H and Groden, Catherine A and Gropman, Andrea L and Hackbarth, Mary E and Haendel, Melissa and Hamid, Rizwan and Hanchard, Neil A and Handley, Lori H and Hardee, Isabel and Herzog, Matthew R and Holm, Ingrid A and Howerton, Ellen M and Jacob, Howard J and Jain, Mahim and Jiang, Yong-hui and Johnston, Jean M and Jones, Angela L and Koehler, Alanna E 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 Latham, Lea and Latour, Yvonne L and Lau, C. Christopher and Lazar, Jozef and Lee, Paul R and Lee, Hane and Lee, Brendan H and Levy, Shawn E and Levy, Denise J and Lewis, Richard A and Liebendorfer, Adam P and ... and UDN
The American Journal of Human Genetics, ISSN 0002-9297, 06/2017, Volume 100, Issue 6, pp. 843 - 853
One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on... 
rare diseases | genetic diseases | Diopt | Geno2MP | ExAC | Zfin | variants of unknown significance | FlyBase | MGI | ClinVar | SEQUENCE VARIANTS | PHENOTYPES | DATABASE | GENETICS & HEREDITY | Genetic Variation | Databases, Genetic | Software | Genome, Human | Humans | Molecular Sequence Annotation | Genetic research | Technology application | Research | Genetic variation
Journal Article
JOURNAL OF PROTEOME RESEARCH, ISSN 1535-3893, 03/2019, Volume 18, Issue 3, pp. 1426 - 1432
The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research... 
INTENSITIES | visualization | software | proteomics | PRINCIPAL COMPONENT ANALYSIS | reproducibility | BIOCHEMICAL RESEARCH METHODS | IDENTIFICATION | web service | MASS-SPECTROMETRY | SEQUEST | exploratory data analysis | COMPUTATIONAL PLATFORM | SCIENCE | statistics | TOOL | Index Medicus | MATHEMATICS AND COMPUTING | BASIC BIOLOGICAL SCIENCES
Journal Article
JOURNAL OF PROTEOME RESEARCH, ISSN 1535-3893, 03/2019, Volume 18, Issue 3, pp. 1418 - 1425
Prior to statistical analysis of mass spectrometry (MS) data, quality control (QC) of the identified biomolecule peak intensities is imperative for reducing... 
visualization | IMPUTATION | quantification | quality control | BIOCHEMICAL RESEARCH METHODS | QUANTITATIVE-ANALYSIS | R package | SOFTWARE | BIOCONDUCTOR | normalization | mass spectrometry | statistics | PROTEOMICS | TOOL | Technical Note
Journal Article
Toxicological Sciences, ISSN 1096-6080, 2011, Volume 120, Issue 1, pp. 123 - 135
Reflecting their exceptional potential to advance a range of biomedical, aeronautic, and other industrial products, carbon nanotube (CNT) production and the... 
Nanomaterials | Asbestos | Risk assessment | Proteomics | SWCNT | risk assessment | BRONCHOALVEOLAR LAVAGE FLUID | DIESEL EXHAUST PARTICLES | OXIDATIVE STRESS | proteomics | asbestos | C57BL/6 MICE | ACCURATE MASS | nanomaterials | FTICR MASS-SPECTROMETRY | MOUSE MODEL | TOXICOLOGY | BETA INTEGRINS | EXPRESSION | EXPOSURE | Instillation, Drug | Pneumonia - pathology | Bronchoalveolar Lavage Fluid - immunology | Soot - toxicity | Chromatography, High Pressure Liquid | Tandem Mass Spectrometry | Nanotubes, Carbon - toxicity | Peptides - metabolism | Pneumonia - chemically induced | Pneumonia - immunology | Female | Bronchoalveolar Lavage Fluid - cytology | Lung - metabolism | Pulmonary Fibrosis - metabolism | Proteomics - methods | Cytokines - immunology | Lung - pathology | Mice, Inbred C57BL | Pulmonary Fibrosis - immunology | Pulmonary Fibrosis - pathology | Asbestos, Crocidolite - toxicity | Particle Size | Animals | Proteins - metabolism | Lung - drug effects | Pulmonary Fibrosis - chemically induced | Mice | Bronchoalveolar Lavage Fluid - chemistry | Pneumonia - metabolism | Proteome - metabolism | Index Medicus | GRANULOMAS | PROTEIN | LUNGS | SENSITIVITY | 60 APPLIED LIFE SCIENCES | ABUNDANCE | CARBON BLACK | NANOTUBES | MICE | ASBESTOS | PRODUCTION | FIBROSIS | CARBON | RODENTS | BASIC BIOLOGICAL SCIENCES | TOXICITY | LYMPHOKINES | INFLAMMATION | PROTEINS | Nanotoxicology
Journal Article
PLoS Computational Biology, ISSN 1553-734X, 05/2008, Volume 4, Issue 5
  Computational biology is replete with high-dimensional (high-D) discrete prediction and inference problems, including sequence alignment, RNA structure... 
Studies | Phylogenetics | Genomes | Gene expression | Bioinformatics
Journal Article
by Chao, Hsiao-Tuan and Chao, Katherine R and Davids, Mariska and Burke, Elizabeth and Pappas, John G and Rosenfeld, Jill A and McCarty, Alexandra J and Davis, Taylor and Wolfe, Lynne and Toro, Camilo and Tifft, Cynthia and Xia, Fan and Stong, Nicholas and Johnson, Travis K and Warr, Coral G and Adams, David R and Adams, Christopher J and Alejandro, Mercedes E and Allard, Patrick and Ashley, Euan A and Bacino, Carlos A and Balasubramanyam, Ashok and Barseghyan, Hayk and Beggs, Alan H and Bellen, Hugo J and Bernstein, Jonathan A and Bick, David P and Birch, Camille L and Boone, Braden E and Briere, Lauren C and Brown, Donna M and Brush, Matthew and Burrage, Lindsay C and Clark, Gary D and Cogan, Joy D and Cooper, Cynthia M and Craigen, William J 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, Dan C and Draper, David D and Dries, Annika M and Eckstein, David J and Emrick, Lisa T and Eng, Christine M and Esteves, Cecilia and Estwick, Tyra and Fisher, Paul G and Frisby, Trevor S and Frost, Kate and Gahl, William A and Gartner, Valerie and Godfrey, Rena A and Goheen, Mitchell and Golas, Gretchen A and Goldstein, David B and Gordon, Mary “Gracie” G and Gould, Sarah E and Gourdine, Jean-Philippe F and Graham, Brett H and Groden, Catherine A and Gropman, Andrea L and Hackbarth, Mary E and Haendel, Melissa and Hamid, Rizwan and Hanchard, Neil A and Handley, Lori H and Hardee, Isabel and Herzog, Matthew R and Holm, Ingrid A and Howerton, Ellen M and Jacob, Howard J and Jain, Mahim and Jiang, Yong-hui and Johnston, Jean M and Jones, Angela L and Koehler, Alanna E 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 Latham, Lea and Latour, Yvonne L and Lau, C. Christopher and Lazar, Jozef and Lee, Hane and Lee, Paul R and Lee, Brendan H and Levy, Denise J and Levy, Shawn E and Lewis, Richard A and Liebendorder, Adam P and ... and Undiag Dis Network and Undiagnosed Diseases Network
The American Journal of Human Genetics, ISSN 0002-9297, 01/2017, Volume 100, Issue 1, pp. 128 - 137
Journal Article