Aaron M Rosenfeld1, Wenzhao Meng2, Eline T Luning Prak2, Uri Hershberg1,3. 1. School of Biomedical Engineering Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA. 2. Department of Pathology and Laboratory Medicine Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104 PA, USA. 3. Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA 19129, USA.
Abstract
As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. AVAILABILITY AND IMPLEMENTATION: ImmuneDB is freely available at http://immunedb.comA demo of the ImmuneDB web interface is available at: http://immunedb.com/demo CONTACT: Uh25@drexel.eduSupplementary information: Supplementary data are available at Bioinformatics online.
As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. AVAILABILITY AND IMPLEMENTATION: ImmuneDB is freely available at http://immunedb.comA demo of the ImmuneDB web interface is available at: http://immunedb.com/demo CONTACT: Uh25@drexel.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Authors: Jason A Vander Heiden; Gur Yaari; Mohamed Uduman; Joel N H Stern; Kevin C O'Connor; David A Hafler; Francois Vigneault; Steven H Kleinstein Journal: Bioinformatics Date: 2014-03-10 Impact factor: 6.937
Authors: Vinodh Pillai; Kavitha Muralidharan; Wenzhao Meng; Asen Bagashev; Derek A Oldridge; Jaclyn Rosenthal; John Van Arnam; Jos J Melenhorst; Diwakar Mohan; Amanda M DiNofia; Minjie Luo; Sindhu Cherian; Jonathan R Fromm; Gerald Wertheim; Andrei Thomas-Tikhonenko; Michele Paessler; Carl H June; Eline T Luning Prak; Vijay G Bhoj; Stephan A Grupp; Shannon L Maude; Susan R Rheingold Journal: Blood Adv Date: 2019-11-26
Authors: Andrea Di Pietro; Jack Polmear; Lucy Cooper; Timon Damelang; Tabinda Hussain; Lauren Hailes; Kristy O'Donnell; Vibha Udupa; Tian Mi; Simon Preston; Areen Shtewe; Uri Hershberg; Stephen J Turner; Nicole L La Gruta; Amy W Chung; David M Tarlinton; Christopher D Scharer; Kim L Good-Jacobson Journal: Nat Immunol Date: 2021-11-29 Impact factor: 25.606
Authors: Rishi R Goel; Mark M Painter; Sokratis A Apostolidis; Divij Mathew; Wenzhao Meng; Aaron M Rosenfeld; Kendall A Lundgreen; Arnold Reynaldi; David S Khoury; Ajinkya Pattekar; Sigrid Gouma; Leticia Kuri-Cervantes; Philip Hicks; Sarah Dysinger; Amanda Hicks; Harsh Sharma; Sarah Herring; Scott Korte; Amy E Baxter; Derek A Oldridge; Josephine R Giles; Madison E Weirick; Christopher M McAllister; Moses Awofolaju; Nicole Tanenbaum; Elizabeth M Drapeau; Jeanette Dougherty; Sherea Long; Kurt D'Andrea; Jacob T Hamilton; Maura McLaughlin; Justine C Williams; Sharon Adamski; Oliva Kuthuru; Ian Frank; Michael R Betts; Laura A Vella; Alba Grifoni; Daniela Weiskopf; Alessandro Sette; Scott E Hensley; Miles P Davenport; Paul Bates; Eline T Luning Prak; Allison R Greenplate; E John Wherry Journal: Science Date: 2021-12-03 Impact factor: 63.714
Authors: Aaron M Rosenfeld; Wenzhao Meng; Dora Y Chen; Bochao Zhang; Tomer Granot; Donna L Farber; Uri Hershberg; Eline T Luning Prak Journal: Front Immunol Date: 2018-06-29 Impact factor: 7.561
Authors: Wenzhao Meng; Bochao Zhang; Gregory W Schwartz; Aaron M Rosenfeld; Daqiu Ren; Joseph J C Thome; Dustin J Carpenter; Nobuhide Matsuoka; Harvey Lerner; Amy L Friedman; Tomer Granot; Donna L Farber; Mark J Shlomchik; Uri Hershberg; Eline T Luning Prak Journal: Nat Biotechnol Date: 2017-08-21 Impact factor: 54.908
Authors: Scott Christley; Walter Scarborough; Eddie Salinas; William H Rounds; Inimary T Toby; John M Fonner; Mikhail K Levin; Min Kim; Stephen A Mock; Christopher Jordan; Jared Ostmeyer; Adam Buntzman; Florian Rubelt; Marco L Davila; Nancy L Monson; Richard H Scheuermann; Lindsay G Cowell Journal: Front Immunol Date: 2018-05-08 Impact factor: 7.561
Authors: Felix Breden; Eline T Luning Prak; Bjoern Peters; Florian Rubelt; Chaim A Schramm; Christian E Busse; Jason A Vander Heiden; Scott Christley; Syed Ahmad Chan Bukhari; Adrian Thorogood; Frederick A Matsen Iv; Yariv Wine; Uri Laserson; David Klatzmann; Daniel C Douek; Marie-Paule Lefranc; Andrew M Collins; Tania Bubela; Steven H Kleinstein; Corey T Watson; Lindsay G Cowell; Jamie K Scott; Thomas B Kepler Journal: Front Immunol Date: 2017-11-01 Impact factor: 8.786
Authors: Michelle Miron; Wenzhao Meng; Aaron M Rosenfeld; Shirit Dvorkin; Maya Meimei Li Poon; Nora Lam; Brahma V Kumar; Yoram Louzoun; Eline T Luning Prak; Donna L Farber Journal: Genome Med Date: 2021-06-14 Impact factor: 11.117