Search Results - "Sarmady, Mahdi"

Transcriptome analysis of IL-10-stimulated (M2c) macrophages by next-generation sequencing by Lurier, Emily B, Dalton, Donald, Dampier, Will, Raman, Pichai, Nassiri, Sina, Ferraro, Nicole M, Rajagopalan, Ramakrishan, Sarmady, Mahdi, Spiller, Kara L

“…Abstract Alternatively activated “M2” macrophages are believed to function during late stages of wound healing, behaving in an anti-inflammatory manner to…”
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Diagnosing Cornelia de Lange syndrome and related neurodevelopmental disorders using RNA sequencing by Rentas, Stefan, Rathi, Komal S., Kaur, Maninder, Raman, Pichai, Krantz, Ian D., Sarmady, Mahdi, Tayoun, Ahmad Abou

“…Purpose Neurodevelopmental disorders represent a frequent indication for clinical exome sequencing. Fifty percent of cases, however, remain undiagnosed even…”
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mtDNA Variation and Analysis Using Mitomap and Mitomaster by Lott, Marie T, Leipzig, Jeremy N, Derbeneva, Olga, Xie, H Michael, Chalkia, Dimitra, Sarmady, Mahdi, Procaccio, Vincent, Wallace, Douglas C

“…The Mitomap database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and…”
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Clinical utility of custom-designed NGS panel testing in pediatric tumors by Surrey, Lea F, MacFarland, Suzanne P, Chang, Fengqi, Cao, Kajia, Rathi, Komal S, Akgumus, Gozde T, Gallo, Daniel, Lin, Fumin, Gleason, Adam, Raman, Pichai, Aplenc, Richard, Bagatell, Rochelle, Minturn, Jane, Mosse, Yael, Santi, Mariarita, Tasian, Sarah K, Waanders, Angela J, Sarmady, Mahdi, Maris, John M, Hunger, Stephen P, Li, Marilyn M

“…Somatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or…”
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Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach by Wu, Chao, Devkota, Batsal, Evans, Perry, Zhao, Xiaonan, Baker, Samuel W, Niazi, Rojeen, Cao, Kajia, Gonzalez, Michael A, Jayaraman, Pushkala, Conlin, Laura K, Krock, Bryan L, Deardorff, Matthew A, Spinner, Nancy B, Krantz, Ian D, Santani, Avni B, Tayoun, Ahmad N Abou, Sarmady, Mahdi

“…Clinical exome sequencing (CES) has become the preferred diagnostic platform for complex pediatric disorders with suspected monogenic etiologies. Despite rapid…”
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Automated Clinical Exome Reanalysis Reveals Novel Diagnoses by Baker, Samuel W., Murrell, Jill R., Nesbitt, Addie I., Pechter, Kieran B., Balciuniene, Jorune, Zhao, Xiaonan, Yu, Zhenming, Denenberg, Elizabeth H., DeChene, Elizabeth T., Wilkens, Alisha B., Bhoj, Elizabeth J., Guan, Qiaoning, Dulik, Matthew C., Conlin, Laura K., Abou Tayoun, Ahmad N., Luo, Minjie, Wu, Chao, Cao, Kajia, Sarmady, Mahdi, Bedoukian, Emma C., Tarpinian, Jennifer, Medne, Livija, Skraban, Cara M., Deardorff, Matthew A., Krantz, Ian D., Krock, Bryan L., Santani, Avni B.

“…Clinical exome sequencing (CES) has a reported diagnostic yield of 20% to 30% for most clinical indications. The ongoing discovery of novel gene–disease and…”
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Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases by Zhao, Mengge, Havrilla, James M, Fang, Li, Chen, Ying, Peng, Jacqueline, Liu, Cong, Wu, Chao, Sarmady, Mahdi, Botas, Pablo, Isla, Julián, Lyon, Gholson J, Weng, Chunhua, Wang, Kai

“…Abstract Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO…”
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AUDIOME: a tiered exome sequencing–based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss by Guan, Qiaoning, Balciuniene, Jorune, Cao, Kajia, Fan, Zhiqian, Biswas, Sawona, Wilkens, Alisha, Gallo, Daniel J, Bedoukian, Emma, Tarpinian, Jennifer, Jayaraman, Pushkala, Sarmady, Mahdi, Dulik, Matthew, Santani, Avni, Spinner, Nancy, Abou Tayoun, Ahmad N, Krantz, Ian D, Conlin, Laura K, Luo, Minjie

“…Hereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing…”
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HIV protein sequence hotspots for crosstalk with host hub proteins by Sarmady, Mahdi, Dampier, William, Tozeren, Aydin

“…HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of…”
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Diagnosing Cornelia de Lange syndrome and related neurodevelopmental disorders using RNA sequencing by Rentas, Stefan, Rathi, Komal S., Kaur, Maninder, Raman, Pichai, Krantz, Ian D., Sarmady, Mahdi, Tayoun, Ahmad Abou

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Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef by Sarmady, Mahdi, Dampier, William, Tozeren, Aydin

“…Virus proteins alter protein pathways of the host toward the synthesis of viral particles by breaking and making edges via binding to host proteins. In this…”
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Evaluating the impact of in silico predictors on clinical variant classification by Wilcox, Emma H., Sarmady, Mahdi, Wulf, Bryan, Wright, Matt W., Rehm, Heidi L., Biesecker, Leslie G., Abou Tayoun, Ahmad N.

“…According to the American College of Medical Genetics and Genomics/Association of Medical Pathology (ACMG/AMP) guidelines, in silico evidence is applied at the…”
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Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets by Evans, Perry, Wu, Chao, Lindy, Amanda, McKnight, Dianalee A, Lebo, Matthew, Sarmady, Mahdi, Abou Tayoun, Ahmad N

“…Recent advances in DNA sequencing have expanded our understanding of the molecular basis of genetic disorders and increased the utilization of clinical genomic…”
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Using Machine Learning to Identify True Somatic Variants from Next-Generation Sequencing by Wu, Chao, Zhao, Xiaonan, Welsh, Mark, Costello, Kellianne, Cao, Kajia, Abou Tayoun, Ahmad, Li, Marilyn, Sarmady, Mahdi

“…Abstract BACKGROUND Molecular profiling has become essential for tumor risk stratification and treatment selection. However, cancer genome complexity and…”
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Targeted and complete genomic sequencing of the Major Histocompatibility Complex in haplotypic form of individual heterozygous samples by Hu, Taishan, Mosbruger, Timothy L, Tairis, Nikolaos G, Dinou, Amalia, Jayaraman, Pushkala, Sarmady, Mahdi, Brewster, Kingham, Li, Yang, Hayeck, Tristan J, Duke, Jamie L, Monos, Dimitri S

“…The human Major Histocompatibility Complex (MHC) is an approximately 4 Mb genomic segment on Chromosome 6 that plays a pivotal role in the immune response…”
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Exome Sequencing Analysis Reveals Variants in Primary Immunodeficiency Genes in Patients With Very Early Onset Inflammatory Bowel Disease by Kelsen, Judith R, Dawany, Noor, Moran, Christopher J, Petersen, Britt-Sabina, Sarmady, Mahdi, Sasson, Ariella, Pauly-Hubbard, Helen, Martinez, Alejandro, Maurer, Kelly, Soong, Joanne, Rappaport, Eric, Franke, Andre, Keller, Andreas, Winter, Harland S, Mamula, Petar, Piccoli, David, Artis, David, Sonnenberg, Gregory F, Daly, Mark, Sullivan, Kathleen E, Baldassano, Robert N, Devoto, Marcella

“…Background & Aims Very early onset inflammatory bowel disease (VEO-IBD), IBD diagnosed at 5 years of age or younger, frequently presents with a different and…”
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A mutation update for the PCDH19 gene causing early‐onset epilepsy in females with an unusual expression pattern by Niazi, Rojeen, Fanning, Elizabeth A., Depienne, Christel, Sarmady, Mahdi, Abou Tayoun, Ahmad N.

“…The PCDH19 gene consists of six exons encoding a 1,148 amino acid transmembrane protein, Protocadherin 19, which is involved in brain development. Heterozygous…”
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Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing by Mosbruger, Timothy L., Dinou, Amalia, Duke, Jamie L., Ferriola, Deborah, Mehler, Hilary, Pagkrati, Ioanna, Damianos, Georgios, Mbunwe, Eric, Sarmady, Mahdi, Lyratzakis, Ioannis, Tishkoff, Sarah A., Dinh, Anh, Monos, Dimitri S.

“…The comprehensive characterization of human leukocyte antigen (HLA) genomic sequences remains a challenging problem. Despite the significant advantages of…”
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AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies by Jayaraman, Pushkala, Mosbruger, Timothy, Hu, Taishan, Tairis, Nikolaos G, Wu, Chao, Clark, Peter M, D’Arcy, Monica, Ferriola, Deborah, Mackiewicz, Katarzyna, Gai, Xiaowu, Monos, Dimitrios, Sarmady, Mahdi

“…Abstract Summary A number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, region-specific extraction…”
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The Development and Validation of Clinical Exome-Based Panels Using ExomeSlicer: Considerations and Proof of Concept Using an Epilepsy Panel by Niazi, Rojeen, Gonzalez, Michael A, Balciuniene, Jorune, Evans, Perry, Sarmady, Mahdi, Abou Tayoun, Ahmad N

“…Exome-based panels are becoming the preferred diagnostic strategy in clinical laboratories. This approach enables dynamic gene content update and, if needed,…”
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