Search Results - "Ghaffari, Noushin"

A robust benchmark for detection of germline large deletions and insertions by Zook, Justin M., Hansen, Nancy F., Olson, Nathan D., Chapman, Lesley, Mullikin, James C., Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M., Boutros, Paul C., Sahraeian, Sayed Mohammad E., Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E., Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T., Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L., Bashir, Ali, Jackman, Shaun, Farrell, John J., Wenger, Aaron M., Alkan, Can, Soylev, Arda, Schatz, Michael C., Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C., Rosenfeld, Jeffrey A., Zhou, Weichen, Mills, Ryan E., Sage, Jay M., Davis, Jennifer R., Kaiser, Michael D., Oliver, John S., Catalano, Anthony P., Chaisson, Mark J. P., Spies, Noah, Sedlazeck, Fritz J., Salit, Marc

“…New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and…”
Get full text

Speeding genomic island discovery through systematic design of reference database composition by Yu, Steven L, Mageeney, Catherine M, Shormin, Fatema, Ghaffari, Noushin, Williams, Kelly P

“…Genomic islands (GIs) are mobile genetic elements that integrate site-specifically into bacterial chromosomes, bearing genes that affect phenotypes such as…”
Get full text

Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare by Doan, Ryan, Cohen, Noah D, Sawyer, Jason, Ghaffari, Noushin, Johnson, Charlie D, Dindot, Scott V

“…The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the…”
Get full text

HiMMe: using genetic patterns as a proxy for genome assembly reliability assessment by Abante, Jordi, Ghaffari, Noushin, Johnson, Charles D, Datta, Aniruddha

“…The information content of genomes plays a crucial role in the existence and proper development of living organisms. Thus, tremendous effort has been dedicated…”
Get full text

Author Correction: A robust benchmark for detection of germline large deletions and insertions by Zook, Justin M., Hansen, Nancy F., Olson, Nathan D., Chapman, Lesley, Mullikin, James C., Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M., Boutros, Paul C., Sahraeian, Sayed Mohammad E., Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E., Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T., Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L., Bashir, Ali, Jackman, Shaun, Farrell, John J., Wenger, Aaron M., Alkan, Can, Soylev, Arda, Schatz, Michael C., Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C., Rosenfeld, Jeffrey A., Zhou, Weichen, Mills, Ryan E., Sage, Jay M., Davis, Jennifer R., Kaiser, Michael D., Oliver, John S., Catalano, Anthony P., Chaisson, Mark J. P., Spies, Noah, Sedlazeck, Fritz J., Salit, Marc

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
Get full text

DNA methylation patterns and gene expression from amygdala tissue of mature Brahman cows exposed to prenatal stress by Baker, Emilie C., Earnhardt, Audrey L., Cilkiz, Kubra Z., Collins, Haley C., Littlejohn, Brittni P., Cardoso, Rodolfo C., Ghaffari, Noushin, Long, Charles R., Riggs, Penny K., Randel, Ronald D., Welsh, Thomas H., Riley, David G.

“…Prenatal stress can alter postnatal performance and temperament of cattle. These phenotypic effects may result from changes in gene expression caused by…”
Get full text

Inter-Individual Variation in DNA Methylation Patterns across Two Tissues and Leukocytes in Mature Brahman Cattle by Baker, Emilie C, San, Audrey E, Cilkiz, Kubra Z, Littlejohn, Brittni P, Cardoso, Rodolfo C, Ghaffari, Noushin, Long, Charles R, Riggs, Penny K, Randel, Ronald D, Welsh, Jr, Thomas H, Riley, David G

“…Quantifying the natural inter-individual variation in DNA methylation patterns is important for identifying its contribution to phenotypic variation, but also…”
Get full text

Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning by Harris, Cole, Ghaffari, Noushin

“…The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray…”
Get full text

Raw pacific biosciences and illumina sequencing reads and assembled genome data for the cattle ticks Rhipicephalus microplus and Rhipicephalus annulatus by Guerrero, Felix D., Ghaffari, Noushin, Bendele, Kylie G., Metz, Richard P., Dickens, C. Michael, Blood, Philip D., Tidwell, Jason, Miller, Robert J., de León, Adalberto A. Pérez, Teel, Pete D., Johnson, Charles D.

“…Ticks from the genus Rhipicephalus have enormous global economic impact as ectoparasites of cattle. Rhipicephalus microplus and Rhipicephalus annulatus are…”
Get full text

The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901 by Guerrero, Felix D., Bendele, Kylie G., Ghaffari, Noushin, Guhlin, Joseph, Gedye, Kristene R., Lawrence, Kevin E., Dearden, Peter K., Harrop, Thomas W.R., Heath, Allen C.G., Lun, Yanni, Metz, Richard P., Teel, Pete, Perez de Leon, Adalberto, Biggs, Patrick J., Pomroy, William E., Johnson, Charles D., Blood, Philip D., Bellgard, Stanley E., Tompkins, Daniel M.

“…The longhorned tick, Haemaphysalis longicornis, feeds upon a wide range of bird and mammalian hosts. Mammalian hosts include cattle, deer, sheep, goats,…”
Get full text

Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer-enhancer interactions by Beytebiere, Joshua R, Trott, Alexandra J, Greenwell, Ben J, Osborne, Collin A, Vitet, Helene, Spence, Jessica, Yoo, Seung-Hee, Chen, Zheng, Takahashi, Joseph S, Ghaffari, Noushin, Menet, Jerome S

“…The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of thousands of genes. Consistent with the…”
Get full text

402 Awardee Talk: Stress-Induced Dna Methylation Changes and Their Implications in Livestock Production by Baker, Emilie C, Earnhardt-San, Audrey L, Cilkiz, Kubra Z, Littlejohn, Brittni P, Cardoso, Rodolfo C, Ghaffari, Noushin, Long, Charles R, Riggs, Penny K, Randel, Ronald D, Welsh, Thomas H, Riley, David G

“…Abstract It is well known that pre- and post-natal stressors can impact livestock phenotype and performance. However, less is known about the molecular…”
Get full text

Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens by Wang, Ying, Ghaffari, Noushin, Johnson, Charles D, Braga-Neto, Ulisses M, Wang, Hui, Chen, Rui, Zhou, Huaijun

“…RNA-Seq is the recently developed high-throughput sequencing technology for profiling the entire transcriptome in any organism. It has several major advantages…”
Get full text

Specific microRNAs in stallion spermatozoa are potential biomarkers of high functionality by Ing, Nancy H., Konganti, Kranti, Ghaffar, Noushin, Johnson, Charles D., Forrest, David W., Love, Charles C., Varner, Dickson D.

“…Males of some species, from horses to humans, require medical help for subfertility problems. There is an urgent need for novel molecular assays that reflect…”
Get full text

Evaluation of Peripheral Blood Leukocytes as a Surrogate for RNA-Seq Detection of Gene Expression in Stress Axis Tissues of Mature Brahman Cows by Earnhardt, Audrey L, Baker, Emilie C, Cilkiz, Kubra Z, Riley, David G, Ghaffari, Noushin, Littlejohn, Brittni P, Collins, Haley C, Riggs, Penny K, Long, Charles R, Cardoso, Rodolfo C, Randel, Ron D, Welsh, Thomas H

“…Abstract Longitudinal studies of gene expression where sampling certain organ systems is precluded may become more feasible if a more accessible,…”
Get full text

The Potential Use of DNA Methylation Patterns from Peripheral Blood Leukocytes as a Surrogate for Stress Axis Tissues in Mature Brahman Cows by Baker, Emilie C, Earnhardt, Audrey L, Cilkiz, Kubra Z, Littlejohn, Brittni P, Collins, Haley C, Ghaffari, Noushin, Riggs, Penny K, Long, Charles R, Welsh, Thomas H, Randel, Ron D, Riley, David G

“…Abstract DNA methylation (DNAm) patterns are tissue specific and aid in tissue specific gene expression changes. The use of DNAm patterns from peripheral blood…”
Get full text

Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture by Ghaffari, Noushin, Sanchez-Flores, Alejandro, Doan, Ryan, Garcia-Orozco, Karina D., Chen, Patricia L., Ochoa-Leyva, Adrian, Lopez-Zavala, Alonso A., Carrasco, J. Salvador, Hong, Chris, Brieba, Luis G., Rudiño-Piñera, Enrique, Blood, Philip D., Sawyer, Jason E., Johnson, Charles D., Dindot, Scott V., Sotelo-Mundo, Rogerio R., Criscitiello, Michael F.

“…We present a new transcriptome assembly of the Pacific whiteleg shrimp ( Litopenaeus vannamei ), the species most farmed for human consumption. Its functional…”
Get full text

A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction by Torres, Maria F, Ghaffari, Noushin, Buiate, Ester A S, Moore, Neil, Schwartz, Scott, Johnson, Charles D, Vaillancourt, Lisa J

“…Colletotrichum graminicola is a hemibiotrophic fungal pathogen that causes maize anthracnose disease. It progresses through three recognizable phases of…”
Get full text

State reduction for network intervention in probabilistic Boolean networks by Qian, Xiaoning, Ghaffari, Noushin, Ivanov, Ivan, Dougherty, Edward R.

“…Motivation: A key goal of studying biological systems is to design therapeutic intervention strategies. Probabilistic Boolean networks (PBNs) constitute a…”
Get full text

Modeling the next generation sequencing sample processing pipeline for the purposes of classification by Ghaffari, Noushin, Yousefi, Mohammadmahdi R, Johnson, Charles D, Ivanov, Ivan, Dougherty, Edward R

“…A key goal of systems biology and translational genomics is to utilize high-throughput measurements of cellular states to develop expression-based classifiers…”
Get full text