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1. Visibility, skulls, and kernels in convexity spaces
by Schuierer, Sven and Rawlins, Gregory J. E and Wood, Derick and University of Waterloo. Dept. of Computer Science
1989, Volume CS-89-48., 21
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2. Full Text The exon quantification pipeline (EQP): A comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data
by Schuierer, Sven and Roma, Guglielmo
Nucleic Acids Research, ISSN 0305-1048, 09/2016, Volume 44, Issue 16, pp. e132 - e132
The quantification of transcriptomic features is the basis of the analysis of RNA-seq data. We present an integrated alignment workflow and a simple... 
ACCURATE | ALIGNMENT | TRANSCRIPTOME | MODELS | BIOCHEMISTRY & MOLECULAR BIOLOGY | NONUNIFORM READ DISTRIBUTION | GENOMIC FEATURES | INFERENCE | ISOFORM EXPRESSION | ABUNDANCE | Introns - genetics | Genes | Humans | Gene Expression Regulation | Exons - genetics | Statistics as Topic | Sequence Alignment | Sequence Analysis, RNA | Time Factors | Computer Simulation | Statistics, Nonparametric | Software | Quality Control | Methods Online
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3. Full Text SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice
by Palacino, James and Swalley, Susanne E and Song, Cheng and Cheung, Atwood K and Shu, Lei and Zhang, Xiaolu and Van Hoosear, Mailin and Shin, Youngah and Chin, Donovan N and Keller, Caroline Gubser and Beibel, Martin and Renaud, Nicole A and Smith, Thomas M and Salcius, Michael and Shi, Xiaoying and Hild, Marc and Servais, Rebecca and Jain, Monish and Deng, Lin and Bullock, Caroline and McLellan, Michael and Schuierer, Sven and Murphy, Leo and Blommers, Marcel J J and Blaustein, Cecile and Berenshteyn, Frada and Lacoste, Arnaud and Thomas, Jason R and Roma, Guglielmo and Michaud, Gregory A and Tseng, Brian S and Porter, Jeffery A and Myer, Vic E and Tallarico, John A and Hamann, Lawrence G and Curtis, Daniel and Fishman, Mark C and Dietrich, William F and Dales, Natalie A and Sivasankaran, Rajeev
Nature Chemical Biology, ISSN 1552-4450, 07/2015, Volume 11, Issue 7, pp. 511 - 517
Spinal muscular atrophy (SMA), which results from the loss of expression of the survival of motor neuron-1 (SMN1) gene, represents the most common genetic... 
SURVIVAL | SYSTEM | PROTEIN | SPINAL MUSCULAR-ATROPHY | MESSENGER-RNA | GENE | BIOCHEMISTRY & MOLECULAR BIOLOGY | IDENTIFICATION | EXPRESSION | BINDING | SINGLE NUCLEOTIDE | RNA Precursors - chemistry | Ribonucleoprotein, U1 Small Nuclear - metabolism | Small Molecule Libraries - pharmacology | Alternative Splicing | Humans | Small Molecule Libraries - metabolism | Survival of Motor Neuron 2 Protein - metabolism | Proteolysis | Survival of Motor Neuron 2 Protein - chemistry | Protein Binding - drug effects | Survival of Motor Neuron 2 Protein - genetics | Ribonucleoprotein, U1 Small Nuclear - chemistry | Female | RNA Precursors - metabolism | RNA, Double-Stranded - metabolism | Binding Sites | RNA, Double-Stranded - chemistry | Disease Models, Animal | RNA, Double-Stranded - agonists | Muscular Atrophy, Spinal - mortality | Gene Expression | Muscular Atrophy, Spinal - metabolism | Ribonucleoprotein, U1 Small Nuclear - agonists | Models, Molecular | Small Molecule Libraries - chemical synthesis | Mice, Transgenic | RNA Precursors - agonists | Muscular Atrophy, Spinal - pathology | Animals | Protein Stability - drug effects | Survival Analysis | Muscular Atrophy, Spinal - drug therapy | Mice | Molecular biology | Rodents | Neurological disorders
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4. Full Text A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples
by Schuierer, Sven and Carbone, Walter and Knehr, Judith and Petitjean, Virginie and Fernandez, Anita and Sultan, Marc and Roma, Guglielmo
BMC Genomics, ISSN 1471-2164, 06/2017, Volume 18, Issue 1, pp. 442 - 13
Background: RNA-sequencing (RNA-seq) has emerged as one of the most sensitive tool for gene expression analysis. Among the library preparation methods... 
Low quality | RNA-sequencing | Benchmarking | Expression profiling | Differential expression | Low quantity | CELLS | MICROARRAY | QUANTIFICATION | IDENTIFICATION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | GENE-EXPRESSION | HUMAN TRANSCRIPTOME | CAPTURE | REVEALS | Sequence Analysis, RNA - methods | Sequence Alignment | Humans | RNA, Messenger - genetics | RNA, Messenger - chemistry | Taq Polymerase - metabolism | RNA Stability | RNA, Messenger - metabolism | Quality Control | RNA sequencing | Research | Gene expression | Ribosomal RNA | Performance evaluation | Poly(A) | rRNA | Genomics | Genomes | Gene sequencing | Degradation | Consortia | Studies | Depletion | Ribonucleic acids | Polyadenylation | Quality control | Libraries | Kits | Methods
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5. Full Text CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
by Wegmann, R and Neri, M and Schuierer, S and Bilican, B and Hartkopf, H and Nigsch, F and Mapa, F and Waldt, A and Cuttat, R and Salick, MR and Raymond, J and Kaykas, A and Roma, G and Keller, CG
GENOME BIOLOGY, ISSN 1474-760X, 07/2019, Volume 20, Issue 1, p. 142
We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq... 
Choroid plexus | Data analysis | REELIN | TRAJECTORIES | Benchmarking | Rare cell types | Clustering | IDENTITY | HETEROGENEITY | CORTICAL-NEURONS | Single-cell RNA sequencing | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PACKAGE | GENETICS & HEREDITY | Cortical development | Software | Human pluripotent stem cells | SEQUENCING DATA | Lineage mapping | EXPRESSION | Biomedical research | Genomics | Population studies | Identification | Genomes | Ribonucleic acid--RNA | Gene expression | Cell differentiation | Datasets | Archives & records | Stem cells | Quality control | Cell cycle | Bioinformatics | Pluripotency
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6. Full Text Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening
by Kiessling, Michael K and Schuierer, Sven and Stertz, Silke and Beibel, Martin and Bergling, Sebastian and Knehr, Judith and Carbone, Walter and de Vallière, Cheryl and Tchinda, Joelle and Bouwmeester, Tewis and Seuwen, Klaus and Rogler, Gerhard and Roma, Guglielmo
BMC Genomics, ISSN 1471-2164, 09/2016, Volume 17, Issue 1
Background: Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of... 
NRAS | Driver mutations | Kinase | Negative selection | EGFR | Whole genome CRISPR screen | Dropout | CELLS | DISCOVERY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GROWTH | GENES | GENETICS & HEREDITY | Genome-wide association studies | Usage | Research | Gene mutations | Cancer cells
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7. Full Text CAG repeat expansion in Huntington disease determines age at onset in a fully dominant fashion
by Lee, J.-M and Ramos, E.M and Lee, J.-H and Gillis, T and Mysore, J.S and Hayden, M.R and Warby, S.C and Morrison, P and Nance, M and Ross, C.A and Margolis, R.L and Squitieri, F and Orobello, S and Di Donato, S and Gomez-Tortosa, E and Ayuso, C and Suchowersky, O and Trent, R.J.A and McCusker, E and Novelletto, A and Frontali, M and Jones, R and Ashizawa, T and Frank, S and Saint-Hilaire, M.H and Hersch, S.M and Rosas, H.D and Lucente, D and Harrison, M.B and Zanko, A and Abramson, R.K and Marder, K and Sequeiros, J and Paulsen, J.S and Landwehrmeyer, G.B and Myers, R.H and MacDonald, M.E and Gusella, J.F and HD-MAPS Study Grp and PREDICT-HD Study Huntington and COHORT Study HSG and REGISTRY Study European and PREDICT-HD study of the Huntington Study Group (HSG) and HD-MAPS Study Group and COHORT study of the HSG and REGISTRY study of the European Huntington's Disease Network and on behalf of the COHORT study of the HSG and on behalf of the REGISTRY study of the European Huntington's Disease Network and on behalf of the HD-MAPS Study Group and on behalf of the PREDICT-HD study of the Huntington Study Group (HSG)
Neurology, ISSN 0028-3878, 03/2012, Volume 78, Issue 10, pp. 690 - 695
Objective: Age at onset of diagnostic motor manifestations in Huntington disease (HD) is strongly correlated with an expanded CAG trinucleotide repeat. The... 
HOMOZYGOSITY | ALLELE | OF-ONSET | GENE | LENGTH | MUTATION | CHROMOSOMES | CLINICAL NEUROLOGY | TRINUCLEOTIDE REPEAT | Humans | Age of Onset | Alleles | Huntington Disease - genetics | Adult | Female | Genotype | Huntington Disease - diagnosis | Male | Trinucleotide Repeat Expansion | 164
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8. Full Text Discovery of a ZIP7 inhibitor from a Notch pathway screen
by Nolin, Erin and Gans, Sara and Llamas, Luis and Bandyopadhyay, Somnath and Brittain, Scott M and Bernasconi-Elias, Paula and Carter, Kyle P and Loureiro, Joseph J and Thomas, Jason R and Schirle, Markus and Yang, Yi and Guo, Ning and Roma, Guglielmo and Schuierer, Sven and Beibel, Martin and Lindeman, Alicia and Sigoillot, Frederic and Chen, Amy and Xie, Kevin X and Ho, Samuel and Reece-Hoyes, John and Weihofen, Wilhelm A and Tyskiewicz, Kayla and Hoepfner, Dominic and McDonald, Richard I and Guthrie, Nicolette and Dogra, Abhishek and Guo, Haibing and Shao, Jian and Ding, Jian and Canham, Stephen M and Boynton, Geoff and George, Elizabeth L and Kang, Zhao B and Antczak, Christophe and Porter, Jeffery A and Wallace, Owen and Tallarico, John A and Palmer, Amy E and Jenkins, Jeremy L and Jain, Rishi K and Bushell, Simon M and Fryer, Christy J
Nature Chemical Biology, ISSN 1552-4450, 2019, Volume 15, Issue 2, pp. 179 - 179
The identification of activating mutations in NOTCH1 in 50% of T cell acute lymphoblastic leukemia has generated interest in elucidating how these mutations... 
MECHANISM | BIOCHEMISTRY & MOLECULAR BIOLOGY | DRUG DISCOVERY | RESISTANCE | GAMMA-SECRETASE INHIBITORS | ZINC TRANSPORTERS | ENDOPLASMIC-RETICULUM | TARGET IDENTIFICATION | OPINION | ACTIVATING MUTATIONS | PREDICTION | Transformation | Sequences | Acute lymphatic leukemia | Target recognition | Leukemia | Trafficking | Lymphocytes T | Lymphatic leukemia | Zinc | Organic chemistry | Zinc compounds | Lymphocytes | Mutation | Endoplasmic reticulum | Apoptosis
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9. Full Text Identification of a novel NAMPT inhibitor by CRISPR/Cas9 chemogenomic profiling in mammalian cells
by Estoppey, David and Hewett, Jeffrey W and Guy, Chantale T and Harrington, Edmund and Thomas, Jason R and Schirle, Markus and Cuttat, Rachel and Waldt, Annick and Gerrits, Bertran and Yang, Zinger and Schuierer, Sven and Pan, Xuewen and Xie, Kevin and Carbone, Walter and Knehr, Judith and Lindeman, Alicia and Russ, Carsten and Frias, Elizabeth and Hoffman, Gregory R and Varadarajan, Malini and Ramadan, Nadire and Reece-Hoyes, John S and Wang, Qiong and Chen, Xin and McAllister, Gregory and Roma, Guglielmo and Bouwmeester, Tewis and Hoepfner, Dominic
Scientific Reports, ISSN 2045-2322, 02/2017, Volume 7, Issue 1, p. 42728
Chemogenomic profiling is a powerful and unbiased approach to elucidate pharmacological targets and the mechanism of bioactive compounds. Until recently,... 
TARGET | SCREENS | CANCER | MYC | MULTIDISCIPLINARY SCIENCES | NADPH | CRISPR | Clonal deletion | Bioactive compounds | Hypersensitivity | Nicotinamide phosphoribosyltransferase | Genomes | Mammalian cells
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10. Full Text A comparative transcriptomic analysis of replicating and dormant liver stages of the relapsing malaria parasite Plasmodium cynomolgi
by Voorberg-van der Wel, A and Roma, G and Gupta, DK and Schuierer, S and Nigsch, F and Carbone, W and Zeeman, AM and Lee, BH and Hofman, SO and Faber, BW and Knehr, J and Pasini, E and Kinzel, B and Bifani, P and Bonamy, GMC and Bouwmeester, T and Kocken, CHM and Diagna, TT
ELIFE, ISSN 2050-084X, 12/2017, Volume 6
Plasmodium liver hypnozoites, which cause disease relapse, are widely considered to be the last barrier towards malaria eradication. The biology of this... 
TARGET | HOMEOSTASIS | TRANSPORTER | FALCIPARUM | PERSISTENCE | COMPOUND | BIOLOGY | HYPNOZOITE | ACTS | Plasmodium cynomolgi - growth & development | Animals | Schizonts - genetics | Plasmodium cynomolgi - genetics | Female | Male | Schizonts - growth & development | Gene Expression Profiling | Macaca mulatta - parasitology | Liver - parasitology | Plasmodium falciparum | Relapse | Malaria | Analysis | Liver | Genomics | Physiological aspects | Genomes | Drug discovery | Diseases | Schizonts | Liver diseases | Homeostasis | Infections | Parasites | Artificial chromosomes | Gene expression | Heavy metals | Tropical diseases | Dormancy | Archives & records | Physiology
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11. Full Text Identification and Evaluation of Novel Acetolactate Synthase Inhibitors as Antifungal Agents
by Daryl L. Richie and Katherine V. Thompson and Christian Studer and Vivian C. Prindle and Thomas Aust and Ralph Riedl and David Estoppey and Jianshi Tao and Jessica A. Sexton and Thomas Zabawa and Joseph Drumm and Simona Cotesta and Jürg Eichenberger and Sven Schuierer and Nicole Hartmann and N. Rao Movva and John A. Tallarico and Neil S. Ryder and Dominic Hoepfner
Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, 05/2013, Volume 57, Issue 5, pp. 2272 - 2280
Classifications Services AAC Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit... 
YEAST | SURVIVAL | ACETOHYDROXYACID SYNTHASE | PATHWAY | BIOSYNTHESIS | DRUG DISCOVERY | MICROBIOLOGY | PHARMACOLOGY & PHARMACY | CHAIN AMINO-ACIDS | VIRULENCE | Catalytic Domain - drug effects | Serum - metabolism | Saccharomyces cerevisiae - genetics | Amino Acids, Branched-Chain - metabolism | Humans | Saccharomyces cerevisiae - drug effects | Antifungal Agents - chemistry | Sulfonylurea Compounds - chemistry | Pyrimidines - chemistry | Acetolactate Synthase - chemistry | Microbial Sensitivity Tests | Sulfonylurea Compounds - pharmacology | Acetolactate Synthase - genetics | Antifungal Agents - pharmacology | Sulfonamides - chemistry | Saccharomyces cerevisiae Proteins - antagonists & inhibitors | Pyrimidines - pharmacology | Saccharomyces cerevisiae Proteins - genetics | Sulfonamides - pharmacology | High-Throughput Screening Assays | Amino Acids, Branched-Chain - pharmacology | Saccharomyces cerevisiae Proteins - metabolism | Protein Binding | Saccharomyces cerevisiae - enzymology | Acetolactate Synthase - metabolism | Molecular Docking Simulation | Mutation | Acetolactate Synthase - antagonists & inhibitors | Saccharomyces cerevisiae Proteins - chemistry | Serum - chemistry | Index Medicus | Mechanisms of Action | Physiological Effects
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12. Full Text FR171456 is a specific inhibitor of mammalian NSDHL and yeast Erg26p
by Helliwell, Stephen B and Karkare, Shantanu and Bergdoll, Marc and Rahier, Alain and Leighton-Davis, Juliet R and Fioretto, Celine and Aust, Thomas and Filipuzzi, Ireos and Frederiksen, Mathias and Gounarides, John and Hoepfner, Dominic and Hofmann, Andreas and Imbert, Pierre-Eloi and Jeker, Rolf and Knochenmuss, Richard and Krastel, Philipp and Margerit, Anais and Memmert, Klaus and Miault, Charlotte V and Rao Movva, N and Muller, Alban and Naegeli, Hans-Ulrich and Oberer, Lukas and Prindle, Vivian and Riedl, Ralph and Schuierer, Sven and Sexton, Jessica A and Tao, Jianshi and Wagner, Trixie and Yin, Hong and Zhang, Juan and Roggo, Silvio and Reinker, Stefan and Parker, Christian N
Nature Communications, ISSN 2041-1723, 10/2015, Volume 6, Issue 1, p. 8613
FR171456 is a natural product with cholesterol-lowering properties in animal models, but its molecular target is unknown, which hinders further drug... 
DRUG | ACID | MINIMA NO. 15604 | MULTIDISCIPLINARY SCIENCES | TARGETS | IDENTIFICATION | SACCHAROMYCES-CEREVISIAE | CHOLESTEROL-BIOSYNTHESIS | Candida albicans | Cholesterol - chemistry | 3-Hydroxysteroid Dehydrogenases - antagonists & inhibitors | Cholesterol - analogs & derivatives | Saccharomyces cerevisiae - genetics | Saccharomyces cerevisiae Proteins - antagonists & inhibitors | Ergosterol - biosynthesis | Antifungal Agents - chemistry | Drug Resistance, Fungal - genetics | Mutation | Saccharomyces cerevisiae Proteins - genetics | 3-Hydroxysteroid Dehydrogenases - genetics
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13. Full Text Transcriptomic analysis reveals reduced transcriptional activity in the malaria parasite Plasmodium cynomolgi during progression into dormancy
by Bertschi, Nicole L and Bertschi, Nicole L and Voorberg-Van der Wel, Annemarie and Zeeman, Anne-Marie and Schuierer, Sven and Schuierer, Sven and Nigsch, Florian and Nigsch, Florian and Carbone, Walter and Carbone, Walter and Knehr, Judith and Knehr, Judith and Gupta, Devendra K and Hofman, Sam O and van der Werff, Nicole and Nieuwenhuis, Ivonne and Klooster, Els and Faber, Bart W and Flannery, Erika L and Flannery, Erika L and Mikolajczak, Sebastian A and Chuenchob, Vorada and Shrestha, Binesh and Shrestha, Binesh and Beibel, Martin and Beibel, Martin and Bouwmeester, Tewis and Bouwmeester, Tewis and Kangwanrangsan, Niwat and Sattabongkot, Jetsumon and Sattabongkot, Jetsumon and Diagana, Thierry T and Diagana, Thierry T and Kocken, Clemens Hm and Kocken, Clemens H. M and Roma, Guglielmo and Roma, Guglielmo
eLife, ISSN 2050-084X, 12/2018, Volume 7
Relapses of Plasmodium dormant liver hypnozoites compromise malaria eradication efforts. New radical cure drugs are urgently needed, yet the vast gap in... 
maturation | infectious disease | plasmodium | microbiology | transcriptomics | liver stages | malaria | hypnozoites | TARGET | LIVER-STAGE DEVELOPMENT | PROTEIN | COMMITMENT | VIVAX | PERSISTENCE | BIOLOGY | TOXOPLASMA-GONDII | TRANSLOCON | IDENTIFICATION | DISCOVERY | Plasmodium cynomolgi - growth & development | Animals | Time Factors | Plasmodium cynomolgi - genetics | Primates | Gene Expression Profiling | Liver - parasitology | Energy metabolism | Malaria | Disease | Transcription | Liver | Infections | Genomes | Biology | Parasites | Gene expression | Kinases | Tropical diseases | Dormancy | Quality
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