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1. Full Text Recurrent R-spondin fusions in colon cancer
by Seshagiri, Somasekar and Stawiski, Eric W and Durinck, Steffen and Modrusan, Zora and Storm, Elaine E and Conboy, Caitlin B and Chaudhuri, Subhra and Guan, Yinghui and Janakiraman, Vasantharajan and Jaiswal, Bijay S and Guillory, Joseph and Ha, Connie and Dijkgraaf, Gerrit J. P and Stinson, Jeremy and Gnad, Florian and Huntley, Melanie A and Degenhardt, Jeremiah D and Haverty, Peter M and Bourgon, Richard and Wang, Weiru and Koeppen, Hartmut and Gentleman, Robert and Starr, Timothy K and Zhang, Zemin and Largaespada, David A and Wu, Thomas D and De Sauvage, Frederic J
Nature, ISSN 0028-0836, 08/2012, Volume 488, Issue 7413, pp. 660 - 664
Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics(1). Here we analyse systematically more than... 
HUMAN BREAST | SEQUENCES | WNT/BETA-CATENIN | COLORECTAL-CANCER | MULTIDISCIPLINARY SCIENCES | ALGORITHM | MUTATIONS | RECEPTORS | LGR5 | CIRCULAR BINARY SEGMENTATION | DISCOVERY | Colonic Neoplasms - genetics | Thrombospondins - genetics | Humans | Molecular Sequence Data | Gene Expression Profiling | Wnt Proteins - metabolism | Colonic Neoplasms - metabolism | Genes, APC | Insulin-Like Growth Factor II - genetics | Base Sequence | Tumor Suppressor Proteins - genetics | Cell Cycle Proteins - genetics | Genes, Neoplasm - genetics | Gene Expression Regulation, Neoplastic - genetics | Transcription Factor 7-Like 2 Protein - genetics | Intercellular Signaling Peptides and Proteins - genetics | Protein-Serine-Threonine Kinases - genetics | Proto-Oncogene Proteins - genetics | DNA Copy Number Variations - genetics | Signal Transduction - genetics | Ataxia Telangiectasia Mutated Proteins | Receptor, ErbB-3 - genetics | DNA-Binding Proteins - genetics | Mutation - genetics | Gene Fusion - genetics | Exome - genetics | Dioxygenases - genetics | Sequence Analysis, RNA | Colonic Neoplasms - pathology | Polymorphism, Single Nucleotide - genetics | Care and treatment | Colon cancer | Gene mutations | Genomics | Patient outcomes | Genetic aspects | Research | Proteins | Mutation | Colon | Genes
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2. Full Text Discovery of Novel Blood-Brain Barrier Targets to Enhance Brain Uptake of Therapeutic Antibodies
by Zuchero, Y. Joy Yu and Chen, Xiaocheng and Bien-Ly, Nga and Bumbaca, Daniela and Tong, Raymond K and Gao, Xiaoying and Zhang, Shuo and Hoyte, Kwame and Luk, Wilman and Huntley, Melanie A and Phu, Lilian and Tan, Christine and Kallop, Dara and Weimer, Robby M and Lu, Yanmei and Kirkpatrick, Donald S and Ernst, James A and Chih, Ben and Dennis, Mark S and Watts, Ryan J
Neuron, ISSN 0896-6273, 01/2016, Volume 89, Issue 1, pp. 70 - 82
The blood-brain barrier (BBB) poses a major challenge for developing effective antibody therapies for neurological diseases. Using transcriptomic and proteomic... 
HUMAN INSULIN-RECEPTOR | AMINO-ACID TRANSPORTER | LOCALIZATION | HEAVY-CHAIN | TRANSFERRIN RECEPTOR | PRIMATE | PERMEABILITY | TRANSCYTOSIS | IN-VIVO | MONOCLONAL-ANTIBODY | NEUROSCIENCES | Brain - metabolism | Fusion Regulatory Protein 1, Heavy Chain - immunology | Antibodies - therapeutic use | Animals | Transcytosis - physiology | Endothelial Cells - metabolism | Antibodies - immunology | Biological Transport - physiology | Mice | Proteomics - methods | Receptors, Transferrin - metabolism | Blood-Brain Barrier - metabolism | Proteins | Viral antibodies | Nervous system diseases | Neurosciences | Antibodies | Health aspects | Biopharmaceutics | Brain | Antigens | Immunoglobulins | Blood-brain barrier | Rodents | Proteomics | Scientific imaging | Gene expression | Experiments | Mass spectrometry
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3. Full Text Complex regulation of ADAR-mediated RNA-editing across tissues
by Huntley, MA and Lou, M and Goldstein, LD and Lawrence, M and Dijkgraaf, GJP and Kaminker, JS and Gentleman, R
BMC GENOMICS, ISSN 1471-2164, 01/2016, Volume 17, Issue 1, p. 61
Background: RNA-editing is a tightly regulated, and essential cellular process for a properly functioning brain. Dysfunction of A-to-I RNA editing can have... 
ADENOSINE-DEAMINASE | MOUSE | BINDING DOMAIN | DIMERIZATION | ADAR | RNA-DNA difference | IDENTIFICATION | INTERFERON | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | GENE FAMILY | RECEPTOR FUNCTION | MUTATIONS | EXPRESSION | RNA-editing | RNA-Binding Proteins - genetics | Introns - genetics | Adenosine Deaminase - genetics | RNA Editing - genetics | Humans | Gene Expression Regulation | Adenosine Deaminase - biosynthesis | Brain - growth & development | Brain - metabolism | Organ Specificity - genetics | RNA-Binding Proteins - biosynthesis | Animals | Transcription, Genetic | Mice | Protein Isoforms - genetics | Physiological aspects | Research | Genetic regulation | RNA processing
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4. Full Text Changes in the Synaptic Proteome in Tauopathy and Rescue of Tau-Induced Synapse Loss by C1q Antibodies
by Dejanovic, Borislav and Huntley, Melanie A and De Mazière, Ann and Meilandt, William J and Wu, Tiffany and Srinivasan, Karpagam and Jiang, Zhiyu and Gandham, Vineela and Friedman, Brad A and Ngu, Hai and Foreman, Oded and Carano, Richard A.D and Chih, Ben and Klumperman, Judith and Bakalarski, Corey and Hanson, Jesse E and Sheng, Morgan
Neuron, ISSN 0896-6273, 12/2018, Volume 100, Issue 6, pp. 1322 - 1336.e7
Synapse loss and Tau pathology are hallmarks of Alzheimer’s disease (AD) and other tauopathies, but how Tau pathology causes synapse loss is unclear. We used... 
postsynaptic density | C1q | Alzheimer’s disease | proteomics | neurodegeneration | Tau | mass spectrometry | synapse | complement | GTPase | Alzheimer's disease | DENDRITIC SPINES | ACTIN | MICROGLIA | AMYLOID-BETA | ALZHEIMERS-DISEASE | DYSFUNCTION | MUTATIONS | EXPRESSION | NEUROSCIENCES | COGNITIVE DEFICITS | PLASTICITY | Brain | Ontology | Genes | Blocking antibodies | Complement | Synaptic density | Experiments | Proteins | Dendritic spines | Neurodegeneration | Actin | Transgenic animals | Age | Statistical analysis | Neurodegenerative diseases | Therapeutic applications | Transgenic mice | Microglia | Complement component C1q | Pathology | Tau protein | Cytoskeleton | Evacuations & rescues | Regulatory proteins | Guanosinetriphosphatase
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5. Full Text Evolutionary Analysis of Amino Acid Repeats across the Genomes of 12 Drosophila Species
by Huntley, Melanie A and Clark, Andrew G
Molecular Biology and Evolution, ISSN 0737-4038, 12/2007, Volume 24, Issue 12, pp. 2598 - 2609
Repeated motifs of amino acids within proteins are an abundant feature of eukaryotic sequences and may catalyze the rapid production of genetic and even... 
Homopeptides | Protein repeats | Simple sequence | BIOCHEMISTRY & MOLECULAR BIOLOGY | protein repeats | GRADIENT | LOW-COMPLEXITY REGIONS | YEAST | EVOLUTIONARY BIOLOGY | simple sequence | DATABASE | TANDEM REPEATS | DNA | GENES | GENETICS & HEREDITY | homopeptides | PROTEINS | PROGRAM | Amino Acid Sequence | Species Specificity | Genome, Insect - genetics | Selection, Genetic | Molecular Sequence Data | Drosophila - classification | Phylogeny | Chi-Square Distribution | Trinucleotide Repeats - genetics | Repetitive Sequences, Amino Acid | Sequence Alignment | Animals | Base Sequence | Insect Proteins - chemistry | Drosophila - genetics | Evolution, Molecular | Proteins | Amino acids | Evolutionary biology | Insects | Molecular biology | Genomics
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6. Full Text Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer's Disease Not Evident in Mouse Models
by Friedman, Brad A and Srinivasan, Karpagam and Ayalon, Gai and Meilandt, William J and Lin, Han and Huntley, Melanie A and Cao, Yi and Lee, Seung-Hye and Haddick, Patrick C.G and Ngu, Hai and Modrusan, Zora and Larson, Jessica L and Kaminker, Joshua S and van der Brug, Marcel P and Hansen, David V
Cell Reports, ISSN 2211-1247, 01/2018, Volume 22, Issue 3, pp. 832 - 847
Microglia, the CNS-resident immune cells, play important roles in disease, but the spectrum of their possible activation states is not well understood. We... 
microgliosis | tauopathy | myeloid | RNA-seq | neuroinflammation | neurodegeneration | FACS | Alzheimer's disease | microglia | gene expression | NEURODEGENERATIVE DISEASE | CELLS | IMMUNE-RESPONSES | INFLAMMATION | MACROPHAGES | GENE-EXPRESSION | AMYLOID PLAQUES | CENTRAL-NERVOUS-SYSTEM | TRANSGENIC MICE | CUTTING EDGE | CELL BIOLOGY
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7. Selection and Slippage Creating Serine Homopolymers
by Huntley, Melanie A and Golding, GBrian
Molecular Biology and Evolution, ISSN 0737-4038, 11/2006, Volume 23, Issue 11, pp. 2017 - 2025
Highly repetitive sequence within proteins is an abundant feature yet is considered by some to be the protein equivalent of "junk DNA." Homopolymer sequences,... 
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8. Full Text Evolution of genes and genomes on the Drosophila phylogeny
by Clark, Andrew G and Eisen, Michael B and Smith, Douglas R and Bergman, Casey M and Oliver, Brian and Markow, Therese A and Kaufman, Thomas C and Kellis, Manolis and Gelbart, William and Iyer, Venky N and Pollard, Daniel A and Sackton, Timothy B and Larracuente, Amanda M and Singh, Nadia D and Abad, Jose P and Abt, Dawn N and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W and Aquadro, Charles F and Ardell, David H and Arguello, Roman and Artieri, Carlo G and Barbash, Daniel A and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A and Bradley, Robert K and Brand, Adrianne D and Brent, Michael R and Brooks, Angela N and Brown, Randall H and Butlin, Roger K and Caggese, Corrado and Calvi, Brian R and Bernardo De Carvalho, A and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E and Chang, Jean L and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W and Comeron, Josep M and Costello, James C and Coyne, Jerry A and Daub, Jennifer and David, Robert G and Delcher, Arthur L and Delehaunty, Kim and Do, Chuong B and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D and Filipski, Alan and Findeiß, Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C. L and Gardiner, Anastasia and Garfield, David A and Garvin, Barry E and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A and Haerty, Wilfried and Hahn, Matthew W and Halligan, Daniel L and Halpern, Aaron L and Halter, Gillian M and Han, Mira V and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S and Holmes, Ian and Hoskins, Roger A and Hubisz, Melissa J and Hultmark, Dan and Huntley, Melanie A and Jaffe, David B and Jagadeeshan, Santosh and ... and Drosophila 12 Genomes Consor and Broad Inst Whole Genome Ass and Broad Inst Genome Sequencing and Drosophila 12 Genomes Consortium and Medicinska fakulteten and Umeå centrum för molekylär patogenes (UCMP) (Medicinska fakulteten) and Umeå universitet
Nature, ISSN 0028-0836, 11/2007, Volume 450, Issue 7167, pp. 203 - 218
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing... 
SYNONYMOUS CODON USAGE | ADAPTIVE PROTEIN EVOLUTION | NONCODING DNA | FRUIT-FLY | MULTIDISCIPLINARY SCIENCES | MOLECULAR EVOLUTION | NATURAL-SELECTION | HOST-DEFENSE | MITOCHONDRIAL-DNA | FAMILY EVOLUTION | AMINO-ACID SUBSTITUTION | Multigene Family - genetics | Synteny - genetics | Genes, Insect - genetics | Genomics | Genome, Insect - genetics | Genome, Mitochondrial - genetics | Reproduction - genetics | Drosophila - classification | Phylogeny | RNA, Untranslated - genetics | Sequence Analysis, DNA | Gene Order - genetics | Sequence Alignment | Animals | DNA Transposable Elements - genetics | Drosophila - immunology | Codon - genetics | Drosophila - metabolism | Drosophila Proteins - genetics | Immunity - genetics | Drosophila - genetics | Evolution, Molecular | Comparative studies | Evolution | Genetics | Insects | Genes
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9. Full Text Dissecting gene expression at the blood-brain barrier
by Huntley, Melanie A and Bien-Ly, Nga and Daneman, Richard and Watts, Ryan J
Frontiers in Neuroscience, ISSN 1662-4548, 2014, Volume 8, p. 355
The availability of genome-wide expression data for the blood-brain barrier is an invaluable resource that has recently enabled the discovery of several genes... 
Expression profiling | Blood-brain barrier | Genomics | Transcriptome | Brain endothelial cells | blood-brain barrier | MOUSE-BRAIN | VASCULAR DEVELOPMENT | EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS | transcriptome | expression profiling | MICROVASCULAR ENDOTHELIAL-CELLS | brain endothelial cells | NEUROSCIENCES | LASER-CAPTURE MICRODISSECTION | PROTEIN EXPRESSION | INCIPIENT ALZHEIMERS-DISEASE | genomics | CENTRAL-NERVOUS-SYSTEM | RAT-BRAIN | HUMAN GLIOBLASTOMA-MULTIFORME | Blood-Brain Barrier
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10. Evolutionary Analysis of Amino Acid Repeats across the Genomes of 12 Drosophila Species
by Huntley, Melanie A and Clark, Andrew G
Molecular Biology and Evolution, ISSN 0737-4038, 12/2007, Volume 24, Issue 12, pp. 2598 - 2609
Repeated motifs of amino acids within proteins are an abundant feature of eukaryotic sequences and may catalyze the rapid production of genetic and even... 
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11. Full Text Complement C3 Is Activated in Human AD Brain and Is Required for Neurodegeneration in Mouse Models of Amyloidosis and Tauopathy
by Wu, Tiffany and Dejanovic, Borislav and Gandham, Vineela D and Gogineni, Alvin and Edmonds, Rose and Schauer, Stephen and Srinivasan, Karpagam and Huntley, Melanie A and Wang, Yuanyuan and Wang, Tzu-Ming and Hedehus, Maj and Barck, Kai H and Stark, Maya and Ngu, Hai and Foreman, Oded and Meilandt, William J and Elstrott, Justin and Chang, Michael C and Hansen, David V and Carano, Richard A.D and Sheng, Morgan and Hanson, Jesse E
Cell Reports, ISSN 2211-1247, 08/2019, Volume 28, Issue 8, pp. 2111 - 2123.e6
Complement pathway overactivation can lead to neuronal damage in various neurological diseases. Although Alzheimer’s disease (AD) is characterized by β-amyloid... 
tauopathy | amyloidosis | Alzheimer’s disease | neuroinflammation | neurodegeneration | synapse | complement | astrocyte | microglia | BETA OLIGOMERS | PROTEIN | VARIANTS | ENDOGENOUS TAU | MICROGLIA | ALZHEIMERS-DISEASE | SYNAPSE LOSS | DEFICITS | EXPRESSION | TRANSGENIC MICE | CELL BIOLOGY
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12. Full Text Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer’s Disease Not Evident in Mouse Models
by Friedman, Brad A and Srinivasan, Karpagam and Ayalon, Gai and Meilandt, William J and Lin, Han and Huntley, Melanie A and Cao, Yi and Lee, Seung-Hye and Haddick, Patrick C.G and Ngu, Hai and Modrusan, Zora and Larson, Jessica L and Kaminker, Joshua S and van der Brug, Marcel P and Hansen, David V
Cell Reports, ISSN 2211-1247, 01/2018, Volume 22, Issue 3, pp. 832 - 847
Microglia, the CNS-resident immune cells, play important roles in disease, but the spectrum of their possible activation states is not well understood. We... 
microgliosis | tauopathy | myeloid | RNA-seq | Alzheimer’s disease | neuroinflammation | neurodegeneration | FACS | microglia | gene expression
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