Search Results - "Kocher, Jean‐Pierre A."

Linnorm: improved statistical analysis for single cell RNA-seq expression data by Yip, Shun H, Wang, Panwen, Kocher, Jean-Pierre A, Sham, Pak Chung, Wang, Junwen

“…Linnorm is a novel normalization and transformation method for the analysis of single cell RNA sequencing (scRNA-seq) data. Linnorm is developed to remove…”
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Measure transcript integrity using RNA-seq data by Wang, Liguo, Nie, Jinfu, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette E, Dasari, Surendra, Vedell, Peter T, Barman, Poulami, Wang, Liewei, Weinshiboum, Richard, Jen, Jin, Huang, Haojie, Kohli, Manish, Kocher, Jean-Pierre A

“…Stored biological samples with pathology information and medical records are invaluable resources for translational medical research. However, RNAs extracted…”
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CRISPR/Cas9-mediated excision of ALS/FTD-causing hexanucleotide repeat expansion in C9ORF72 rescues major disease mechanisms in vivo and in vitro by Meijboom, Katharina E., Abdallah, Abbas, Fordham, Nicholas P., Nagase, Hiroko, Rodriguez, Tomás, Kraus, Carolyn, Gendron, Tania F., Krishnan, Gopinath, Esanov, Rustam, Andrade, Nadja S., Rybin, Matthew J., Ramic, Melina, Stephens, Zachary D., Edraki, Alireza, Blackwood, Meghan T., Kahriman, Aydan, Henninger, Nils, Kocher, Jean-Pierre A., Benatar, Michael, Brodsky, Michael H., Petrucelli, Leonard, Gao, Fen-Biao, Sontheimer, Erik J., Brown, Robert H., Zeier, Zane, Mueller, Christian

“…A GGGGCC 24+ hexanucleotide repeat expansion (HRE) in the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and…”
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Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection by Sangtani, Ajleeta, Wang, Chen, Weaver, Amy, Hoppman, Nicole L., Kerr, Sarah E., Abyzov, Alexej, Shridhar, Viji, Staub, Julie, Kocher, Jean-Pierre A., Voss, Jesse S., Podratz, Karl C., Wentzensen, Nicolas, Kisiel, John B., Sherman, Mark E., Bakkum-Gamez, Jamie N.

“…We aimed to assess whether endometrial cancer (EC) can be detected in shed DNA collected with vaginal tampon by analyzing copy number, methylation markers, and…”
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Early genetic aberrations in patients with sporadic colorectal cancer by Druliner, Brooke R., Ruan, Xiaoyang, Sicotte, Hugues, O'Brien, Daniel, Liu, Hongfang, Kocher, Jean‐Pierre A., Boardman, Lisa

“…Chromosome instability (CIN) is widely observed in both sporadic and hereditary colorectal cancer (CRC). Defects in APC and WNT signaling are primarily…”
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The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation by Kocher, Jean-Pierre A, Quest, Daniel J, Duffy, Patrick, Meiners, Michael A, Moore, Raymond M, Rider, David, Hossain, Asif, Hart, Steven N, Dinu, Valentin

“…The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed…”
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PB-Motif—A Method for Identifying Gene/Pseudogene Rearrangements With Long Reads: An Application to CYP21A2 Genotyping by Stephens, Zachary, Milosevic, Dragana, Kipp, Benjamin, Grebe, Stefan, Iyer, Ravishankar K., Kocher, Jean-Pierre A.

“…Long read sequencing technologies have the potential to accurately detect and phase variation in genomic regions that are difficult to fully characterize with…”
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3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer by Asmann, Yan W, Klee, Eric W, Thompson, E Aubrey, Perez, Edith A, Middha, Sumit, Oberg, Ann L, Therneau, Terry M, Smith, David I, Poland, Gregory A, Wieben, Eric D, Kocher, Jean-Pierre A

“…Massive parallel sequencing has the potential to replace microarrays as the method for transcriptome profiling. Currently there are two protocols: full-length…”
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HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data by Yan, Huihuang, Evans, Jared, Kalmbach, Mike, Moore, Raymond, Middha, Sumit, Luban, Stanislav, Wang, Liguo, Bhagwate, Aditya, Li, Ying, Sun, Zhifu, Chen, Xianfeng, Kocher, Jean-Pierre A

“…Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-Seq) has been widely used to identify genomic loci of transcription factor…”
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Transcriptional atlas of cardiogenesis maps congenital heart disease interactome by Li, Xing, Martinez-Fernandez, Almudena, Hartjes, Katherine A, Kocher, Jean-Pierre A, Olson, Timothy M, Terzic, Andre, Nelson, Timothy J

“…Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart…”
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SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations by Hart, Steven N, Sarangi, Vivekananda, Moore, Raymond, Baheti, Saurabh, Bhavsar, Jaysheel D, Couch, Fergus J, Kocher, Jean-Pierre A

“…Structural variation (SV) represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing…”
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A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines by Asmann, Yan W, Hossain, Asif, Necela, Brian M, Middha, Sumit, Kalari, Krishna R, Sun, Zhifu, Chai, High-Seng, Williamson, David W, Radisky, Derek, Schroth, Gary P, Kocher, Jean-Pierre A, Perez, Edith A, Thompson, E Aubrey

“…SnowShoes-FTD, developed for fusion transcript detection in paired-end mRNA-Seq data, employs multiple steps of false positive filtering to nominate fusion…”
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Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags by Chen, Xianfeng, Johnson, Stephen, Jeraldo, Patricio, Wang, Junwen, Chia, Nicholas, Kocher, Jean-Pierre A, Chen, Jun

“…Illumina paired-end sequencing has been increasingly popular for 16S rRNA gene-based microbiota profiling. It provides higher phylogenetic resolution than…”
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HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data by Baheti, Saurabh, Tang, Xiaojia, O'Brien, Daniel R, Chia, Nicholas, Roberts, Lewis R, Nelson, Heidi, Boughey, Judy C, Wang, Liewei, Goetz, Matthew P, Kocher, Jean-Pierre A, Kalari, Krishna R

“…Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the…”
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CircularLogo: A lightweight web application to visualize intra-motif dependencies by Ye, Zhenqing, Ma, Tao, Kalmbach, Michael T, Dasari, Surendra, Kocher, Jean-Pierre A, Wang, Liguo

“…The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the…”
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Multilevel Parallelization of AutoDock 4.2 by Norgan, Andrew P, Coffman, Paul K, Kocher, Jean-Pierre A, Katzmann, David J, Sosa, Carlos P

“…Background Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing…”
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The impact of pharmacokinetic gene profiles across human cancers by Zimmermann, Michael T, Therneau, Terry M, Kocher, Jean-Pierre A

“…The right drug to the right patient at the right time is one of the ideals of Individualized Medicine (IM) and remains one of the most compelling promises of…”
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Murine leukemia virus uses NXF1 for nuclear export of spliced and unspliced viral transcripts by Sakuma, Toshie, Davila, Jaime I, Malcolm, Jessica A, Kocher, Jean-Pierre A, Tonne, Jason M, Ikeda, Yasuhiro

“…Intron-containing mRNAs are subject to restricted nuclear export in higher eukaryotes. Retroviral replication requires the nucleocytoplasmic transport of both…”
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Aberrant immunohistochemical expression of CD4 as a rare finding in metastatic melanoma by Chatzopoulos, Kyriakos, O'Brien, Daniel R., Sotiriou, Sotiris, Khazaie, Khashayarsha, Jen, Jin, Kocher, Jean‐Pierre A., Markovic, Svetomir N., Flotte, Thomas J.

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A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas by Lin, Sangdi, Wang, Chen, Zarei, Shabnam, Bell, Debra A, Kerr, Sarah E, Runger, George C, Kocher, Jean-Pierre A

“…Copy Number Alternations (CNAs) is defined as somatic gain or loss of DNA regions. The profiles of CNAs may provide a fingerprint specific to a tumor type or…”
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