Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Ricky S Adkins"'
Autor:
John S. A. Mattick, Robin E. Bromley, Kaylee J. Watson, Ricky S. Adkins, Christopher I. Holt, Jarrett F. Lebov, Benjamin C. Sparklin, Tyonna S. Tyson, David A. Rasko, Julie C. Dunning Hotopp
Publikováno v:
mBio, Vol 15, Iss 10 (2024)
ABSTRACT RNA transcripts are potential therapeutic targets, yet bacterial transcripts have uncharacterized biodiversity. We developed an algorithm for transcript prediction called tp.py using it to predict transcripts (mRNA and other RNAs) in Escheri
Externí odkaz:
https://doaj.org/article/d0edc818c52849dfb46e0614f9812657
Autor:
Gillian Mbambo, Ankit Dwivedi, Olukemi O. Ifeonu, James B. Munro, Biraj Shrestha, Robin E. Bromley, Theresa Hodges, Ricky S. Adkins, Bourema Kouriba, Issa Diarra, Amadou Niangaly, Abdoulaye K. Kone, Drissa Coulibaly, Karim Traore, Amagana Dolo, Mahamadou A. Thera, Matthew B. Laurens, Ogobara K. Doumbo, Christopher V. Plowe, Andrea A. Berry, Mark Travassos, Kirsten E. Lyke, Joana C. Silva
Publikováno v:
Frontiers in Immunology, Vol 14 (2023)
IntroductionHost gene and protein expression impact susceptibility to clinical malaria, but the balance of immune cell populations, cytokines and genes that contributes to protection, remains incompletely understood. Little is known about the determi
Externí odkaz:
https://doaj.org/article/4be637d5b54b4a7cbb6926e457c1deca
Autor:
Matthew Chung, Ricky S. Adkins, John S. A. Mattick, Katie R. Bradwell, Amol C. Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
Publikováno v:
mSystems, Vol 6, Iss 1 (2021)
ABSTRACT Quantification tools for RNA sequencing (RNA-Seq) analyses are often designed and tested using human transcriptomics data sets, in which full-length transcript sequences are well annotated. For prokaryotic transcriptomics experiments, full-l
Externí odkaz:
https://doaj.org/article/b4053ee518834536913a290b2a6553e9
Autor:
Sonia Agrawal, Cesar Arze, Ricky S. Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M. Fraser, Hervé Tettelin, Owen White, Samuel V. Angiuoli, Anup Mahurkar, W. Florian Fricke
Publikováno v:
BMC Genomics, Vol 18, Iss 1, Pp 1-11 (2017)
Abstract Background The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and c
Externí odkaz:
https://doaj.org/article/157a446743d94599a971c4505c4ffbce
Autor:
Seth A Ament, Ricky S Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn A Garden, Michelle Giglio, Brian R Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P Receveur, Mike Schor, Shreyash Sonthalia, Timothy L Tickle, Jessica Way, Ronna Hertzano, Anup A Mahurkar, Owen R White
Publikováno v:
Nucleic acids research.
Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Net
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::851353ed703ce88dd3c65a08f518c94a
https://pubmed.ncbi.nlm.nih.gov/36318260
https://pubmed.ncbi.nlm.nih.gov/36318260
Autor:
Seth A. Ament, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H. Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn A. Garden, Michelle Giglio, Brian R. Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P. Receveur, Mike Schor, Timothy L. Tickle, Jessica Way, Ronna Hertzano, Anup A. Mahurkar, Owen R White
Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell Census Net
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::5a1bd8d457735a1de94211b2653575e8
https://doi.org/10.1101/2022.09.08.505285
https://doi.org/10.1101/2022.09.08.505285
Autor:
Julie C. Dunning Hotopp, Katie R. Bradwell, Lisa Sadzewicz, John S. Mattick, David A. Rasko, Luke J. Tallon, Anup Mahurkar, Claire M. Fraser, Matthew Chung, Amol C. Shetty, Ricky S. Adkins
Publikováno v:
mSystems
mSystems, Vol 6, Iss 1 (2021)
mSystems, Vol 6, Iss 1 (2021)
Most currently available quantification tools for transcriptomics analyses have been designed for human data sets, in which full-length transcript sequences, including the untranslated regions, are well annotated. In most prokaryotic systems, full-le
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e2aa6e10e47f826014eb3611d4b7da8
https://pubmed.ncbi.nlm.nih.gov/33436511
https://pubmed.ncbi.nlm.nih.gov/33436511
Autor:
Cindy T. J. van Velthoven, Eran A. Mukamel, Kanan Lathia, Jeff Goldy, Elizabeth Purdom, Hanqing Liu, Zizhen Yao, Xinxin Wang, Victor Felix, Olivia Fong, Brian R. Herb, Jacinta Lucero, Elizabeth L. Dougherty, Carlo Colantuoni, Thanh Pham, Bing Ren, Valentine Svensson, Sheng-Yong Niu, Rongxin Fang, Davide Risso, Seth A. Ament, Michael Tieu, Christine Rimorin, John Ngai, Ricky S. Adkins, Sandrine Dudoit, Naeem Nadaf, Stephan Fischer, Michael Hawrylycz, Evan Z. Macosko, Anup Mahurkar, Joshua Orvis, Lior Pachter, Thuc Nghi Nguyen, Peter V. Kharchenko, Vasilis Ntranos, Bosiljka Tasic, Joshua D. Welch, Darren Bertagnolli, Charles R. Vanderburg, Yang Eric Li, Eeshit Dhaval Vaishnav, Xiaomeng Hou, Joseph R. Ecker, Delissa McMillen, Kirsten Crichton, Heather Huot Creasy, Antonio Pinto-Duarte, Josef Sulc, A. Sina Booeshaghi, Megan Crow, Chongyuan Luo, Owen White, Kimberly A. Smith, Jayaram Kancherla, Jonathan Crabtree, Herman Tung, Wayne I. Doyle, Angeline Rivkin, M. Margarita Behrens, Hongkui Zeng, Kelly Street, Amy Torkelson, Tommaso Biancalani, Julia K. Osteen, Héctor Corrada Bravo, Aviv Regev, Anna Bartlett, Olivier Poirion, Nick Dee, Qiwen Hu, Michelle G. Giglio, Z. Josh Huang, Andrew Aldridge, Ronna Hertzano, Sebastian Preissl, Matthew Kroll, Koen Van den Berge, Fangming Xie, Jesse Gillis, Joseph R. Nery, Tamara Casper, Hector Roux de Bézieux
Publikováno v:
Nature
Nature, vol 598, iss 7879
NATURE
Nature, vol 598, iss 7879
NATURE
Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1–3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c92cbbd62ebe063cc04fa1e4fb92393a
https://pubmed.ncbi.nlm.nih.gov/34616052
https://pubmed.ncbi.nlm.nih.gov/34616052
Autor:
Z. Josh Huang, Valentine Svensson, Christine Rimorin, Sebastian Preissl, Qiwen Hu, Yang Eric Li, Carlo Colantuoni, Olivier Poirion, Darren Bertagnolli, Vasilis Ntranos, Antonio Pinto-Duarte, Megan Crow, Delissa McMillen, Evan Z. Macosko, Nick Dee, Zizhen Yao, Hongkui Zeng, Hector Roux de Bézieux, Bing Ren, Sheng-Yong Niu, Brian R. Herb, Jacinta Lucero, Ricky S. Adkins, Rongxin Fang, Eeshit Dhaval Vaishnav, Peter V. Kharchenko, Charles R. Vanderburg, Xiaomeng Hou, Joshua D. Welch, Angeline Rivkin, Sandrine Dudoit, Michael Tieu, Michael Hawrylycz, Jayaram Kancherla, Anup Mahurkar, Victor Felix, Lior Pachter, Jonathan Crabtree, Ronna Hertzano, Héctor Corrada Bravo, Aviv Regev, Wayne I. Doyle, Fangming Xie, Owen White, A. Sina Booeshaghi, Chongyuan Luo, Jeff Goldy, Andrew I. Aldrige, Joseph R. Ecker, Naeem Nadaf, Elizabeth Purdom, Hanqing Liu, Eran A. Mukamel, Kanan Lathia, Kelly Street, Michelle G. Giglio, Xinxin Wang, Julia K. Osteen, Olivia Fong, Bosiljka Tasic, Matthew Kroll, Tommaso Biancalani, Thanh Pham, John Ngai, Amy Torkelson, Thuc Nghi Nguyen, Ann Bartlett, Kimberly A. Smith, Kirsten Crichton, Herman Tung, Heather Huot Creasy, Josef Sulc, M. Margarita Behrens, Cindy T. J. van Velthoven, Koen Van den Berge, Jesse Gillis, Joseph R. Nery, Tamara Casper, Elizabeth L. Dougherty, Davide Risso, Seth A. Ament, Stephan Fischer, Joshua Orvis
Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual dat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f7633422e96f93e32198625f13e63944
https://doi.org/10.1101/2020.02.29.970558
https://doi.org/10.1101/2020.02.29.970558
Autor:
Yang Song, Michael C. Kelly, Anup Mahurkar, Kevin Rose, Brian Gottfried, Maggie S. Matern, Matthew W. Kelley, Elena Chrysostomou, Carlo Colantuoni, Owen White, Brian R. Herb, Amiel A. Dror, Robert L. Carter, Ronna Hertzano, Beatrice Milon, Joshua Orvis, Dustin Olley, Ricky S. Adkins, Héctor Corrada Bravo, Jayaram Kancherla, Hela Azaiez, Seth A. Ament
Publikováno v:
Nat Methods
The gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access community-driven tool for multi-omic and multi-species data visualization, analysis and sharing. The gEAR supports visualization of multiple RNA-seq data types (bulk, s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8b134ca3719c465db1356ef5dcfa68fa
https://doi.org/10.1038/s41592-021-01200-9
https://doi.org/10.1038/s41592-021-01200-9