cran: SoDA | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2021.616956

Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean
Cited by: 9
Author(s): Liuyang Li, Laxman Pujari, Chao Wu, Dongyang Huang, Yuqiu Wei, Congcong Guo, Guicheng Zhang, Wenzhe Xu, Haijiao Liu, Xingzhou Wang, Min Wang, Jun Sun
Software Mentions: 9
Published: over 3 years ago

10.1111/eva.12932

Fine‐scale seascape genomics of an exploited marine species, the common cockle <i>Cerastoderma edule</i>, using a multimodelling approach
Cited by: 25
Author(s): Ilaria Coscia, Sophie B. Wilmes, Joseph E. Ironside, Alice Goward‐Brown, Enda O’Dea, Shelagh K. Malham, Allan D. McDevitt, Peter Robins
Software Mentions: 8
Published: over 4 years ago

10.1128/AEM.02220-20

Influence of Spatial Scale on Structure of Soil Bacterial Communities across an Arctic Landscape
Cited by: 5
Author(s): Lucie Malard, Muhammad Zohaib Anwar, Carsten Suhr Jacobsen, David A. Pearce
Software Mentions: 6
Published: almost 4 years ago

10.3390/microorganisms9020208

Aquatic Bacterial Diversity, Community Composition and Assembly in the Semi-Arid Inner Mongolia Plateau: Combined Effects of Salinity and Nutrient Levels
Cited by: 29
Author(s): Xiangming Tang, Guobo Xie, Kwang‐Tsao Shao, Wei Tian, Guang Gao, Boqiang Qin
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-018-19939-1

Acute effects of air pollution on respiratory disease mortalities and outpatients in Southeastern China
Cited by: 46
Author(s): Zhe Mo, Qiang Fu, Lifang Zhang, Danni Lyu, Guangming Mao, Lizhi Wu, Pingwei Xu, Zhifang Wang, Xuejiao Pan, Zhijian Chen, Xiaofeng Wang, Xiaoming Lou
Software Mentions: 5
Published: over 6 years ago

10.1098/rstb.2014.0240

Assigning and visualizing germline genes in antibody repertoires
Cited by: 19
Author(s): Simon D. W. Frost, Ben Murrell, Alamgir Hossain, Gregg J. Silverman, Sergei L. Kosakovsky Pond
Software Mentions: 5
Published: about 9 years ago

10.1093/femsec/fiz128

Biogeographical patterns in soil bacterial communities across the Arctic region
Cited by: 49
Author(s): Lucie Malard, Muhammad Zohaib Anwar, Carsten Suhr Jacobsen, David A. Pearce
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.2-103.v1

Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors
Cited by: 139
Author(s): Thomas B. Kepler
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0037648

Isolation of HIV-1-Neutralizing Mucosal Monoclonal Antibodies from Human Colostrum
Cited by: 29
Author(s): James Friedman, S. Munir Alam, Xiaoying Shen, Shi-Mao Xia, Shelley Stewart, Kara Anasti, Justin Pollara, Genevieve G. Fouda, Guang Yang, Garnett Kelsoe, Guido Ferrari, Georgia D. Tomaras, Barton F. Haynes, Hua‐Xin Liao, M. Anthony Moody, Sallie R. Permar
Software Mentions: 3
Published: over 12 years ago

10.7717/peerj.3997

Indicators for the use of robotic labs in basic biomedical research: a literature analysis
Cited by: 9
Author(s): Paul Groth, Jessica Cox
Software Mentions: 3
Published: about 7 years ago

10.3389/fimmu.2012.00386

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing
Cited by: 13
Author(s): Miri Michaeli, Hila Noga, Hilla Tabibian‐Keissar, Iris Barshack, Ramit Mehr
Software Mentions: 3
Published: almost 13 years ago

10.3389/fimmu.2016.00681

BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires
Cited by: 16
Author(s): Donald W. Lee, Ilja V. Khavrutskii, Anders Wallqvist, Sina Bavari, Christopher L. Cooper, Sidhartha Chaudhury
Software Mentions: 3
Published: almost 8 years ago

10.1002/ece3.1522

Environmental factors prevail over dispersal constraints in determining the distribution and assembly of Trichoptera species in mountain lakes
Cited by: 8
Author(s): Guillermo de Mendoza, Marc Ventura, Jordi Catalan
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-9-S12-S20

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies
Cited by: 16
Author(s): Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Tao Lin, Yixue Li, Zhiwei Cao
Software Mentions: 2
Published: almost 16 years ago

10.7717/peerj.6230

Serverless OpenHealth at data commons scale—traversing the 20 million patient records of New York’s SPARCS dataset in real-time
Cited by: 5
Author(s): Jonas S. Almeida, Janos Hajagos, Joel Saltz, Mary Saltz
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0159396

Phylogeographic Analysis of Blastomyces dermatitidis and Blastomyces gilchristii Reveals an Association with North American Freshwater Drainage Basins
Cited by: 35
Author(s): Lisa R. McTaggart, Elizabeth M. Brown, Susan E. Richardson
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0118192

VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool
Cited by: 12
Author(s): Giulia Paciello, Andrea Acquaviva, Chiara Pighi, Alberto Ferrarini, Enrico Macii, Alberto Zamò, Elisa Ficarra
Software Mentions: 2
Published: over 9 years ago

10.1016/j.cell.2019.04.036

Longitudinal Analysis of the Human B Cell Response to Ebola Virus Infection
Cited by: 138
Author(s): Carl W. Davis, Katherine Jackson, Anita K. McElroy, Peter Halfmann, Jessica Huang, Chakravarthy Chennareddy, Ashley E. Piper, Yvonne Leung, César G. Albariño, Ian Crozier, Ali H. Ellebedy, John Sidney, Alessandro Sette, Tianwei Yu, Sandra C. A. Nielsen, Arthur J. Goff, Christina F. Spiropoulou, Erica Ollman Saphire, Guy Cavet, Yoshihiro Kawaoka, Aneesh K. Mehta, Pamela J. Glass, Scott D. Boyd, Rafi Ahmed
Software Mentions: 2
Published: over 5 years ago

10.1093/aobpla/plv149

Genetic delineation of local provenance defines seed collection zones along a climate gradient
Cited by: 6
Author(s): Kristina M. Hufford, Erik J. Veneklaas, Hans Lambers, Siegfried L. Krauss
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.ppat.1003173

Viral Escape from Neutralizing Antibodies in Early Subtype A HIV-1 Infection Drives an Increase in Autologous Neutralization Breadth
Cited by: 48
Author(s): Megan K. Murphy, Ling Yue, Ruimin Pan, Saikat Boliar, Anurag Sethi, Jiang Tian, Katja Pfafferot, Etienne Karita, Susan Allen, Emmanuel Cormier, Paul Goepfert, Persephone Borrow, James E. Robinson, S. Gnanakaran, Eric Hunter, Xiang‐Peng Kong, Cynthia A. Derdeyn
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0045931

Early Postnatal B Cell Ontogeny and Antibody Repertoire Maturation in the Opossum, Monodelphis domestica
Cited by: 12
Author(s): Xinxin Wang, Alana Sharp, Robert D. Miller
Software Mentions: 1
Published: about 12 years ago

10.3389/fimmu.2014.00264

Immunoglobulin Gene Repertoire Diversification and Selection in the Stomach â€“ From Gastritis to Gastric Lymphomas
Cited by: 20
Author(s): Miri Michaeli, Hilla Tabibian‐Keissar, Ginette Schiby, Gitit Shahaf, Yishai Pickman, Lena Hazanov, Kinneret Rosenblatt, Deborah K. Dunn-Walters, Iris Barshack, Ramit Mehr
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0023532

Isolation of a Human Anti-HIV gp41 Membrane Proximal Region Neutralizing Antibody by Antigen-Specific Single B Cell Sorting
Cited by: 138
Author(s): Lynn Morris, Xi Chen, Munir Alam, Georgia D. Tomaras, Ruijun Zhang, Dawn J. Marshall, Bing Chen, Robert Parks, Andrew Foulger, Frederick H. Jaeger, Michele. Donathan, Mira. Bilska, Elin S. Gray, Salim Safurdeen. Abdool Karim, Thomas B. Kepler, John F. Whitesides, David C. Montefiori, M. Anthony Moody, Hua‐Xin Liao, Barton F. Haynes
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0025797

H3N2 Influenza Infection Elicits More Cross-Reactive and Less Clonally Expanded Anti-Hemagglutinin Antibodies Than Influenza Vaccination
Cited by: 156
Author(s): M. Anthony Moody, Ruijun Zhang, Emmanuel B. Walter, Christopher W. Woods, Geoffrey S. Ginsburg, Micah T. McClain, Thomas N. Denny, Xi Chen, Supriya Munshaw, Dawn J. Marshall, John F. Whitesides, Mark Drinker, Joshua D. Amos, Thaddeus C. Gurley, Joshua Eudailey, Andrew Foulger, K Derosa, Robert Parks, Robert Meyerhoff, Jia Yu, Daniel M. Kozink, Brice E. Barefoot, Elizabeth Ramsburg, Surender Khurana, Hana Golding, Nathan Vandergrift, S. Munir Alam, Georgia D. Tomaras, Thomas B. Kepler, Garnett Kelsoe, Hua‐Xin Liao, Barton F. Haynes
Software Mentions: 1
Published: about 13 years ago

10.1186/1745-7580-4-3

Large-scale analysis of human heavy chain V(D)J recombination patterns
Cited by: 43
Author(s): Joseph M. Volpe, Thomas B. Kepler
Software Mentions: 1
Published: almost 17 years ago

10.1186/1745-7580-5-1

Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains
Cited by: 6
Author(s): Joseph M. Volpe, Thomas B. Kepler
Software Mentions: 1
Published: almost 16 years ago

10.1186/1745-7580-6-S1-S4

Clustering-based identification of clonally-related immunoglobulin gene sequence sets
Cited by: 32
Author(s): Zhiliang Chen, Andrew M. Collins, Yan Wang, Bruno Gaëta
Software Mentions: 1
Published: almost 15 years ago

10.1186/2043-9113-3-15

Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template
Cited by: 10
Author(s): Miri Michaeli, Michal Barák, Lena Hazanov, Hila Noga, Ramit Mehr
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-213X-9-51

A tamoxifen inducible knock-in allele for investigation of E2A function
Cited by: 10
Author(s): Mark T. Jones, Motonari Kondo, Yuan Zhuang
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.ppat.1004403

Ontogeny of Recognition Specificity and Functionality for the Broadly Neutralizing Anti-HIV Antibody 4E10
Cited by: 27
Author(s): Kathryn Finton, Della Friend, James Jaffe, Mesfin Gewe, Michael Holmes, H. Benjamin Larman, Andrew B. Stuart, Kevin Larimore, Philip D. Greenberg, Stephen J. Elledge, Leonidas Stamatatos, Roland K. Strong
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.ppat.1008373

Structure and mechanism of monoclonal antibody binding to the junctional epitope of Plasmodium falciparum circumsporozoite protein
Cited by: 30
Author(s): David Oyen, Jonathan L. Torres, Phillip C. Aoto, Yevel Flores-García, Špela Binter, Tossapol Pholcharee, Sean M. Carroll, Sini Reponen, R. Wash, Qi Liang, Franck Lemiale, Emily Locke, Allan Bradley, C. Richter King, Daniel Emerling, Paul Kellam, Fidel Zavala, Andrew B. Ward, Ian A. Wilson
Software Mentions: 1
Published: over 4 years ago

10.1016/j.ebiom.2019.02.060

Longitudinal analysis of acute and convalescent B cell responses in a human primary dengue serotype 2 infection model
Cited by: 24
Author(s): Usha K. Nivarthi, Huy A. Tu, Matthew J. Delacruz, Jesica Swanstrom, Bhumi Patel, Anna P. Durbin, Stephen S. Whitehead, Kristen K. Pierce, Beth D. Kirkpatrick, Ralph S. Baric, Ngan Thi Kim Nguyen, Daniel Emerling, Aravinda M. de Silva, Sean A. Diehl
Software Mentions: 1
Published: over 5 years ago

Ecosyste.ms: Papers

Projects: cran: SoDA

Papers Mentioning SoDA 32