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1. Full Text Introducing COCOS: Codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
by Butkiewicz, Mariusz and Haines, Jonathan L and Bush, William S
Bioinformatics, ISSN 1367-4803, 05/2017, Volume 33, Issue 10, pp. 1561 - 1562
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Sequence Analysis, Protein - methods | Codon | Frameshift Mutation | Humans | Reading Frames | Software | Genomics - methods | Sequence Analysis, DNA - methods | INDEL Mutation | Index Medicus | Applications Notes
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2. In silico functional annotation of genomic variation
by Butkiewicz, Mariusz and Bush, William S
Current Protocols in Human Genetics, ISSN 1934-8266, 2016, Volume 2016, pp. 6.15.1 - 6.15.17
Genome annotation | Sequence analysis | Functional prediction | Variant annotation | Genetic Variation | Computational Biology - methods | Genetic Predisposition to Disease - genetics | Reproducibility of Results | Computer Simulation | Humans | Molecular Sequence Annotation - methods | Genome-Wide Association Study - methods | Genomics - methods | Genome, Human - genetics
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3. Full Text Rapidly progressive Alzheimer's disease features distinct structures of amyloid-β
by Cohen, Mark L and Kim, Chae and Haldiman, Tracy and ElHag, Mohamed and Mehndiratta, Prachi and Pichet, Termsarasab and Lissemore, Frances and Shea, Michelle and Cohen, Yvonne and Chen, Wei and Blevins, Janis and Appleby, Brian S and Surewicz, Krystyna and Surewicz, Witold K and Sajatovic, Martha and Tatsuoka, Curtis and Zhang, Shulin and Mayo, Ping and Butkiewicz, Mariusz and Haines, Jonathan L and Lerner, Alan J and Safar, Jiri G
Brain (London, England : 1878), ISSN 0006-8950, 04/2015, Volume 138, Issue 4, pp. 1009 - 1022
progression rate | Alzheimer | structure | β-amyloid | Neurosciences | Clinical Neurology | Neurosciences & Neurology | Life Sciences & Biomedicine | Science & Technology | Humans | Middle Aged | Male | Disease Progression | Alzheimer Disease - pathology | Time Factors | Amyloid beta-Peptides - genetics | Aged, 80 and over | Adult | Female | Aged | Alzheimer Disease - genetics | Peptide Fragments - genetics | Cohort Studies | Index Medicus | Abridged Index Medicus | Original
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4. Full Text Shared genetic etiology of autoimmune diseases in patients from a biorepository linked to de-identified electronic health records
by Restrepo, Nicole A and Butkiewicz, Mariusz and McGrath, Josephine A and Crawford, Dana C
Frontiers in genetics, ISSN 1664-8021, 10/2016, Volume 7, pp. 185 - 185
Autoimmune disease | Multiple sclerosis | Crohn's disease | Electronic health records | Rheumatoid arthritis | Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Analysis | Electronic records | Medical records | Genetic aspects | Diagnosis | Research | Autoimmune diseases | Causes and theories of causation | Risk factors | Diseases | Genetics | electronic health records | autoimmune disease | rheumatoid arthritis | multiple sclerosis | Multiple Sclerosis | Crohn’s Disease | Electronic Health Records
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5. Full Text Benchmarking ligand-based virtual high-throughput screening with the pubchem database
by Butkiewicz, Mariusz and Lowe Jr, Edward W and Mueller, Ralf and Mendenhall, Jeffrey L and Teixeira, Pedro L and Weaver, C. David and Meiler, Jens
Molecules (Basel, Switzerland), ISSN 1420-3049, 01/2013, Volume 18, Issue 1, pp. 735 - 756
Quantitative structure-Activity relations (QSAR) | Cheminformatics | PubChem | Machine learning | High-throughput screening (HTS) | Virtual screening | BCL | Biochemistry & Molecular Biology | Physical Sciences | Chemistry | Life Sciences & Biomedicine | Chemistry, Multidisciplinary | Science & Technology | Models, Chemical | Area Under Curve | Humans | Drug Discovery - standards | Support Vector Machine | Databases, Chemical - standards | Algorithms | Animals | Quality Improvement | Computer Simulation | Inhibitory Concentration 50 | High-Throughput Screening Assays - standards | Ligands | ROC Curve | Decision Trees | Quantitative Structure-Activity Relationship | Neural Networks (Computer) | Index Medicus | high-throughput screening (HTS) | virtual screening | quantitative structure-activity relations (QSAR) | machine learning | cheminformatics
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6. Full Text Functional annotation of genomic variants in studies of late-onset Alzheimer's disease
by Butkiewicz, Mariusz and Blue, Elizabeth E and Leung, Yuk Yee and Jian, Xueqiu and Marcora, Edoardo and Renton, Alan E and Kuzma, Amanda and Wang, Li-San and Koboldt, Daniel C and Haines, Jonathan L and Bush, William S
Bioinformatics, ISSN 1367-4803, 08/2018, Volume 34, Issue 16, pp. 2724 - 2731
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Index Medicus | Original Papers
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7. Full Text Pathway analysis by randomization incorporating structure - Paris: An update
by Butkiewicz, Mariusz and Cooke Bailey, Jessica N and Frase, Alex and Dudek, Scott and Yaspan, Brian L and Ritchie, Marylyn D and Pendergrass, Sarah A and Haines, Jonathan L
Bioinformatics, ISSN 1367-4803, 08/2016, Volume 32, Issue 15, pp. 2361 - 2363
Statistics & Probability | Biochemistry & Molecular Biology | Physical Sciences | Computer Science, Interdisciplinary Applications | Life Sciences & Biomedicine | Technology | Biochemical Research Methods | Computer Science | Mathematics | Biotechnology & Applied Microbiology | Science & Technology | Mathematical & Computational Biology | Genome-Wide Association Study | Software | Genomics | Humans | Databases, Factual | Index Medicus | Applications Notes
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8. Full Text BCL::EMAS - Enantioselective molecular asymmetry descriptor for 3D-QSAR
by Sliwoski, Gregory and Lowe Jr, Edward W and Butkiewicz, Mariusz and Meiler, Jens
Molecules (Basel, Switzerland), ISSN 1420-3049, 08/2012, Volume 17, Issue 8, pp. 9971 - 9989
CADD | Stereochemistry | Molecular asymmetry | QSAR | Chirality | Enantiomer | Biochemistry & Molecular Biology | Physical Sciences | Chemistry | Life Sciences & Biomedicine | Chemistry, Multidisciplinary | Science & Technology | Models, Molecular | Software | Algorithms | Stereoisomerism | Quantitative Structure-Activity Relationship | Index Medicus | molecular asymmetry | stereochemistry | enantiomer | chirality
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9. Full Text Identification of Novel Allosteric Modulators of Metabotropic Glutamate Receptor Subtype 5 Acting at Site Distinct from 2‑Methyl-6-(phenylethynyl)-pyridine Binding
by Butkiewicz, Mariusz and Rodriguez, Alice L and Rainey, Shane E and Wieting, Joshua and Luscombe, Vincent B and Stauffer, Shaun R and Lindsley, Craig W and Conn, P. Jeffrey and Meiler, Jens
ACS chemical neuroscience, ISSN 1948-7193, 08/2019, Volume 10, Issue 8, pp. 3427 - 3436
Biochemistry & Molecular Biology | Neurosciences | Life Sciences & Biomedicine | Pharmacology & Pharmacy | Neurosciences & Neurology | Chemistry, Medicinal | Science & Technology | Index Medicus | G protein-coupled receptor | virtual screening | 1-(3-fluorophenyl)-N-((3-fluorophenyl)-methylideneamino)-methanimine | N-{4-chloro-2-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-2-hydroxybenzamide | metabotropic glutamate receptor | high-throughput screening | 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)-benzamide | CPPHA | 2-methyl-6-(phenylethynyl)-pyridine | MPEP | 4-nitro-N-(1,3-diphenyl-1H-pyrazol-5-yl)-benzamide | machine learning | cheminformatics | quantitative structure–activity relationship | mGlu | BioChemistryLibrary | PubChem | QSAR | GPCR | PAM | positive allosteric modulator
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10. Full Text Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project
by Naj, Adam C and Lin, Honghuang and Vardarajan, Badri N and White, Simon and Lancour, Daniel and Ma, Yiyi and Schmidt, Michael and Sun, Fangui and Butkiewicz, Mariusz and Bush, William S and Kunkle, Brian W and Malamon, John and Amin, Najaf and Choi, Seung Hoan and Hamilton-Nelson, Kara L and van der Lee, Sven J and Gupta, Namrata and Koboldt, Daniel C and Saad, Mohamad and Wang, Bowen and Nato, Alejandro Q and Sohi, Harkirat K and Kuzma, Amanda and Wang, Li-San and Cupples, L. Adrienne and van Duijn, Cornelia and Seshadri, Sudha and Schellenberg, Gerard D and Boerwinkle, Eric and Bis, Joshua C and Dupuis, Josée and Salerno, William J and Wijsman, Ellen M and Martin, Eden R and DeStefano, Anita L and Alzheimer's Disease Sequencing Project (ADSP) and Alzheimers Dis Sequencing Project
Genomics (San Diego, Calif.), ISSN 0888-7543, 07/2019, Volume 111, Issue 4, pp. 808 - 818
GATK | Atlas | Consensus calling | Whole genome sequencing | Mendelian inconsistencies | Quality control | c_article_only_freely_accessible_via_repository | yes | Genetics | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Humans | Genotyping Techniques - standards | Genotype | Male | Whole Genome Sequencing - standards | Whole Genome Sequencing - methods | Polymorphism, Genetic | Algorithms | Female | Alzheimer Disease - genetics | Genome-Wide Association Study - methods | Genome-Wide Association Study - standards | Genotyping Techniques - methods | Quality Control | Pipelines | Analysis | Genomics | Design and construction | Alzheimer's disease | Quality management | Index Medicus | whole genome sequencing | consensus calling | quality control
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11. Full Text Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer’s Disease Sequencing Project
by Blue, Elizabeth E and Bis, Joshua C and Dorschner, Michael O and Tsuang, Debby W and Barral, Sandra M and Beecham, Gary and Below, Jennifer E and Bush, William S and Butkiewicz, Mariusz and Cruchaga, Carlos and DeStefano, Anita and Farrer, Lindsay A and Goate, Alison and Haines, Jonathan and Jaworski, Jim and Jun, Gyungah and Kunkle, Brian and Kuzma, Amanda and Lee, Jenny J and Lunetta, Kathryn L and Ma, Yiyi and Martin, Eden and Naj, Adam and Nato, Alejandro Q and Navas, Patrick and Nguyen, Hiep and Reitz, Christiane and Reyes, Dolly and Salerno, William and Schellenberg, Gerard D and Seshadri, Sudha and Sohi, Harkirat and Thornton, Timothy A and Valadares, Otto and van Duijn, Cornelia and Vardarajan, Badri N and Wang, Li-San and Boerwinkle, Eric and Dupuis, Josée and Pericak-Vance, Margaret A and Mayeux, Richard and Wijsman, Ellen M and Alzheimer's Dis Sequencing Project and on behalf of the Alzheimer’s Disease Sequencing Project
Dementia and geriatric cognitive disorders, ISSN 1420-8008, 05/2018, Volume 45, Issue 1-2, pp. 1 - 17
Original Research Article | Pathogenicity | Candidate genes | Rare variants | Frontotemporal dementia | Alzheimer's disease | ClinVar | Alzheimer genetics | Arylsulfatase A pseudodeficiency | Clinical Neurology | Neurosciences & Neurology | Life Sciences & Biomedicine | Psychiatry | Geriatrics & Gerontology | Science & Technology | Genome-Wide Association Study | Prevalence | Humans | Male | Dementia - epidemiology | Dementia - genetics | Nerve Tissue Proteins - genetics | Sequence Analysis, DNA | Case-Control Studies | Genetic Variation | Aged, 80 and over | Alzheimer Disease - epidemiology | Female | Aged | Polymorphism, Single Nucleotide | Alzheimer Disease - genetics | Cohort Studies | Advertising executives | Apolipoproteins | Genes | Index Medicus | rare variants | pathogenicity | arylsufatase A pseudodeficiency | Alzheimer’s disease | candidate genes | frontotemporal dementia
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