Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: Augur
https://packages.ecosyste.ms/registries/pypi.org/packages/Augur
1 version
Latest release: almost 7 years ago
37 downloads last month
Papers Mentioning Augur 37
10.1186/s13073-021-00910-1
Landscape and selection of vaccine epitopes in SARS-CoV-2Cited by: 21
Author(s): Christof C. Smith, Kelly Olsen, Kaylee M. Gentry, Maria J. Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric D. Routh, Julia Kodysh, Timothy J. O’Donnell, Carsten Haber, Kirsten Heiß, Volker Stadler, Erik Garrison, Adam Sandor, Jenny P.-Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark T. Heise, Benjamin G. Vincent, Alex Rubinsteyn
Software Mentions: 27
Published: over 3 years ago
10.3389/fmicb.2020.594928
Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus InfectivityCited by: 45
Author(s): Sunil K. Raghav, Arup Ghosh, Jyotirmayee Turuk, Satish Kumar, Atimukta Jha, Swati Madhulika, Manasi Priyadarshini, Viplov Kumar Biswas, P. Sushree Shyamli, Balveer Singh, Neha Singh, Deepika Singh, Ankita Datey, Kiran Avula, Shuchi Smita, Jyotsnamayee Sabat, Debdutta Bhattacharya, Jaya Singh Kshatri, Dileep Vasudevan, Amol Ratnakar Suryawanshi, Rupesh Dash, Shantibhusan Senapati, Tushar Kant Beuria, Roy Swain, Soma Chattopadhyay, Gulam Hussain Syed, Anshuman Dixit, Punit Prasad, Sanghamitra Pati, Ajay Parida
Software Mentions: 8
Published: about 4 years ago
10.1038/s41392-021-00703-3
Differential immune responses in pregnant patients recovered from COVID-19Cited by: 21
Author(s): Ge Chen, Yiming Zhang, Yaoyao Zhang, Jihui Ai, Bin Yang, Mengge Cui, Qiande Liao, Hanxiao Chen, Hualin Bai, Dashing Shang, Jing Chen, Chaoyang Sun, Haiyi Liu, Fengyuan Liu, Biming Mao, Guoqiang Sun, Lu Chen, Jing-wen Lin, Kezhen Li
Software Mentions: 7
Published: over 3 years ago
10.7717/peerj-cs.601
GrimoireLab: A toolset for software development analyticsCited by: 16
Author(s): Santiago Dueñas, Valerio Cosentino, Jesús M. González-Barahona, Alvaro del Castillo San Félix, Daniel Izquierdo-Cortázar, Luis Cañas-Díaz, Alberto Pérez García-Plaza
Software Mentions: 6
Published: over 3 years ago
10.1186/1751-0473-8-9
Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomesCited by: 11
Author(s): Andrew Perry, Bosco Ho
Software Mentions: 4
Published: almost 12 years ago
10.3390/vaccines9060616
A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in IsraelCited by: 20
Author(s): Neta S. Zuckerman, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Itay Bar-Or, Victoria Indenbaum, Merav Weil, Yaniv Lustig, Ella Mendelson, Michal Mandelboim, Orna Mor, Neta S. Zuckerman
Software Mentions: 3
Published: over 3 years ago
10.21105/joss.02906
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogensCited by: 101
Author(s): John Huddleston, James Hadfield, Thomas H. Sibley, Jover Lee, Kairsten Fay, Misja Ilcisin, Elias Harkins, Trevor Bedford, Richard A. Neher, Emma B. Hodcroft
Software Mentions: 3
Published: almost 4 years ago
10.3906/biy-2005-35
Phylogenetic analysis of SARS-CoV-2 genomes in TurkeyCited by: 13
Author(s): Ogün Adebali, Aylin Bircan, Defne Circi, Burak İŞlek, Zeynep Kilinc, Berkay Selçuk, Berk Turhan
Software Mentions: 3
Published: over 4 years ago
10.3389/fgene.2021.586569
Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease EpidemiologyCited by: 27
Author(s): Madhvi Joshi, Apurvasinh Puvar, Dinesh Kumar, Afzal Ansari, Maharshi Pandya, Janvi Raval, Zarna Patel, Pinal Trivedi, Monika Gandhi, Labdhi Pandya, Komal Patel, Nitin Savaliya, S. B. Bagatharia, Sachin Kumar, Chaitanya Joshi
Software Mentions: 3
Published: almost 4 years ago
10.3390/v13050836
Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain)Cited by: 12
Author(s): Carlos S. Casimiro-Soriguer, Javier Pérez-Florido, Jose L. Fernández-Rueda, Irene Pedrosa-Corral, Vicente Guillot-Sulay, Nicola Lorusso, Luis Javier Martínez-González, José María Navarro-Marí, Joaquı́n Dopazo, Sara Sanbonmatsu‐Gámez
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0193562
TeamWATCH: Visualizing development activities using a 3-D city metaphor to improve conflict detection and team awarenessCited by: 3
Author(s): En Ye, Xin Ye, Chang Liu
Software Mentions: 3
Published: almost 7 years ago
10.1186/s12879-019-4566-2
Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in ColombiaCited by: 12
Author(s): Allison Black, Louise H. Moncla, Katherine Laiton‐Donato, Barney Potter, Lissethe Pardo, Angélica Rico, Catalina Tovar, Diana Patricia Rojas, Ira M. Longini, M. Elizabeth Halloran, Dioselina Peláez-Carvajal, Juan David Ramírez, Marcela Mercado-Reyes, Trevor Bedford
Software Mentions: 3
Published: about 5 years ago
10.1186/1471-2180-8-20
Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e σB regulonCited by: 135
Author(s): Torsten Hain, Hamid Hossain, Som Subhra Chatterjee, Silke Machata, Ute Volk, Sandra Wagner, Benedikt Brors, Stefan A. Haas, Carsten Kuenne, André Billion, Sonja Otten, Jan Pané‐Farré, Susanne Engelmann, Trinad Chakraborty
Software Mentions: 3
Published: almost 17 years ago
10.1371/journal.pone.0018783
Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic FeaturesCited by: 154
Author(s): Delphine M. Saulnier, F.D. Santos, Stefan Roos, Toni Ann Mistretta, Jennifer K. Spinler, Douwe Molenaar, Bas Teusink, James Versalovic
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2105-9-173
LocateP: Genome-scale subcellular-location predictor for bacterial proteinsCited by: 133
Author(s): Miaomiao Zhou, Jos Boekhorst, Christof Francke, Roland J. Siezen
Software Mentions: 2
Published: over 16 years ago
10.3390/vaccines9080937
The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452RCited by: 11
Author(s): Orna Mor, Michal Mandelboim, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Ital Nemet, Limor Kliker, Yaniv Lustig, Ella Mendelson, Neta S. Zuckerman
Software Mentions: 2
Published: over 3 years ago
10.3390/v13030394
The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral DefenseCited by: 25
Author(s): Cem Azgari, Zeynep Kilinc, Berk Turhan, Defne Circi, Ogün Adebali
Software Mentions: 2
Published: almost 4 years ago
10.1186/1471-2105-11-39
An automatic method for identifying surface proteins in bacteria: SLEPCited by: 19
Author(s): Emanuela Giombini, Massimiliano Orsini, Danilo Carrabino, Anna Tramontano
Software Mentions: 2
Published: almost 15 years ago
10.1371/journal.pone.0234671
Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using NextstrainCited by: 29
Author(s): Bart van de Vossenberg, M. Visser, Maaike Bruinsma, H. Koenraadt, Marcel Westenberg, Marleen Botermans
Software Mentions: 2
Published: about 4 years ago
10.1080/22221751.2020.1773745
Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countriesCited by: 45
Author(s): Xuemei Yang, Ning Dong, Edward Wai Chi Chan, Sheng Chen
Software Mentions: 2
Published: almost 5 years ago
10.3390/e22091043
Complexity in Economic and Social Systems: Cryptocurrency Market at around COVID-19Cited by: 56
Author(s): S. Dróżdż, Jarosław Kwapień, Paweł Oświęcimka, Tomasz Stanisz, Marcin Wątorek
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-021-84891-6
Bioinformatics-based prediction of conformational epitopes for Enterovirus A71 and Coxsackievirus A16Cited by: 7
Author(s): Liping Wang, Miao Zhu, Yulu Fang, Hao Rong, Liuying Gao, Qi Liao, Lina Zhang, Dong Chen
Software Mentions: 2
Published: almost 4 years ago
10.3390/ijms21124546
Betacoronavirus Genomes: How Genomic Information has been Used to Deal with Past Outbreaks and the COVID-19 PandemicCited by: 35
Author(s): Alejandro Llanes, Carlos M. Restrepo, Zuleima Caballero, Sreekumari Rajeev, Melissa Kennedy, Ricardo Lleonart
Software Mentions: 2
Published: over 4 years ago
10.2807/1560-7917.ES.2021.26.26.2100557
Neutralising capacity against Delta (B.1.617.2) and other variants of concern following Comirnaty (BNT162b2, BioNTech/Pfizer) vaccination in health care workers, IsraelCited by: 119
Author(s): Yaniv Lustig, Neta S. Zuckerman, Ital Nemet, Nofar Atari, Limor Kliker, Gili Regev‐Yochay, Einav Sapir, Orna Mor, Sharon Alroy‐Preis, Ella Mendelson, Michal Mandelboim
Software Mentions: 1
Published: over 3 years ago
10.1177/1535370220975351
Genomic analysis of SARS-CoV-2 reveals local viral evolution in GhanaCited by: 18
Author(s): Joyce M. Ngoi, Peter K. Quashie, Collins M. Morang’a, Joseph Humphrey Kofi Bonney, Dominic Selorm Yao Amuzu, Selassie Kumordjie, Ivy A. Asante, Evelyn Yayra Bonney, Miriam Eshun, Linda Boatemaa, Vanessa Magnusen, Erasmus Nikoi Kotey, Nicaise Tuikue Ndam, Frederick Tei-Maya, Augustina Arjarquah, Evangeline Obodai, Isaac Darko Otchere, Yaw Bediako, Joe Kimanthi Mutungi, Lucas Amenga-Etego, John Kofi Odoom, Abraham K. Anang, George B. Kyei, Bright Adu, William Ampofo, Gordon A. Awandare
Software Mentions: 1
Published: about 4 years ago
10.1007/s11262-021-01866-5
A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020Cited by: 25
Author(s): Broňa Brejová, Kristína Boršová, Viktória Hodorová, Viktória Čabanová, Lenka Reizigová, Evan D. Paul, Pavol Čekan, Boris Klempa, Jozef Nosek, Tomáš Vinař
Software Mentions: 1
Published: over 3 years ago
10.1128/MRA.00016-21
Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G MutationCited by: 2
Author(s): Ishwar Singh, Umashankar Vetrivel, Darasaguppe R. Harish, Debprasad Chattophadhyay
Software Mentions: 1
Published: almost 4 years ago
10.1128/MRA.00677-20
Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Early Manifestations of COVID-19 in IsraelCited by: 2
Author(s): Inbar Cohen-Gihon, Ofir Israeli, Ohad Shifman, Dana Stein, Hagit Achdout, Shay Weiss, Michal Mandelboim, Oran Erster, Gili Regev‐Yochay, Gad Segal, Shmuel Yitzhaki, Shmuel C. Shapira, Adi Beth-Din, Anat Zvi
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-020-74666-w
Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle EastCited by: 26
Author(s): Ahmad Abou Tayoun, Tom Loney, Hamda Khansaheb, Sathishkumar Ramaswamy, Divinlal Harilal, Zulfa Deesi, Rupa Varghese, Hanan Al Suwaidi, Abdulmajeed Alkhajeh, Laila AlDabal, Mohammed Uddin, Rifat Hamoudi, Rabih Halwani, Abiola Senok, Qutayba Hamid, Norbert Nowotny, Alawi A. Alsheikh‐Ali
Software Mentions: 1
Published: about 4 years ago
10.1186/1471-2164-13-144
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenesCited by: 75
Author(s): Torsten Hain, Rohit Ghai, André Billion, Carsten Kuenne, Christiane Steinweg, Benjamin Izar, Walid Mohamed, Mobarak Abu Mraheil, Eugen Domann, S Schaffrath, Uwe Kärst, Alexander Goesmann, Sebastian Oehm, Alfred Pühler, Rainer Merkl, Sonja Vorwerk, Philippe Glaser, Patricia Garrido, Christophe Rusniok, Carmen Buchrieser, Werner Goebel, Trinad Chakraborty
Software Mentions: 1
Published: over 12 years ago
10.1038/s41598-021-92851-3
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune responseCited by: 19
Author(s): Rong Liu, Pei‐Ju Wu, Pauline Ogrodzki, S. A. Mahmoud, Ke Liang, Pengjuan Liu, Stephen Francis, Hanif Khalak, Denghui Liu, Junhua Li, Tao Ma, Fang Chen, Weibin Liu, Xinyu Huang, Wenjun He, Zhaorong Yuan, Nan Qiao, Xin Meng, Budoor Alqarni, Javier Quilez, Vinay Kusuma, Li Lin, Xin Jin, Chongguang Yang, Xavier Anton, Ashish Koshy, Huanming Yang, Xun Xu, Jian Wang, Peng Xiao, Nawal Al Kaabi, Mohammed Saifuddin Fasihuddin, Francis Amirtharaj Selvaraj, Stefan Weber, Farida Ismail Al Hosani, Siyang Liu, Walid Zaher
Software Mentions: 1
Published: over 3 years ago
10.3390/v13091806
High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021Cited by: 8
Author(s): Ueric José Borges de Souza, Raíssa Nunes dos Santos, Fabrício Souza Campos, Karine Lima Lourenço, Flávio Guimarães da Fonseca, Fernando Rosado Spilki, Corona-ômica.BR
Software Mentions: 1
Published: over 3 years ago
10.1126/scitranslmed.abe2555
Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2Cited by: 185
Author(s): Alexandra Popa, Jakob-Wendelin Genger, Michael D. Nicholson, Thomas Penz, Daniela Schmid, Stephan W. Aberle, Benedikt Agerer, Alexander Lercher, Lukas Endler, Henrique G. Colaço, Mark J. Smyth, Michael Schuster, Miguel L. Grau, Francisco Martínez-Jiménez, Oriol Pich, Wegene Borena, Erich Pawelka, Zsofia Keszei, Martin Senekowitsch, Jan Laine, Judith H. Aberle, Monika Redlberger‐Fritz, Mario Karolyi, Alexander Zoufaly, Sabine Maritschnik, Martin Borkovec, Peter Hufnagl, Manfred Nairz, Günter Weiß, Michael T. Wolfinger, Dorotheé von Laer, Giulio Superti‐Furga, Núria López‐Bigas, Elisabeth Puchhammer‐Stöckl, Franz Allerberger, Franziska Michor, Christoph Bock, Andréas Bergthaler
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0042982
Subcellular Localization of Extracytoplasmic Proteins in Monoderm Bacteria: Rational Secretomics-Based Strategy for Genomic and Proteomic AnalysesCited by: 39
Author(s): Sandra Rénier, Pierre Micheau, Régine Talon, Michel Hébraud, Mickaël Desvaux
Software Mentions: 1
Published: over 12 years ago
10.1128/MRA.01109-20
Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore SequencingCited by: 8
Author(s): Piroon Jenjaroenpun, Visanu Wanchai, Kikumi D. Ono‐Moore, Jennifer Laudadio, Laura P. James, Sean H. Adams, Fred Prior, Intawat Nookaew, David W. Ussery, Thidathip Wongsurawat
Software Mentions: 1
Published: almost 4 years ago
10.1128/MRA.00231-21
Genome Sequences of Five SARS-CoV-2 Variants from Mumbai, India, Obtained by Nanopore SequencingCited by: 3
Author(s): Kayzad Nilgiriwala, Ayan Mandal, Grishma Patel, Tejal Mestry, Smriti Vaswani, Ambreen Shaikh, Kalpana Sriraman, Swapneil Parikh, Shreevatsa Udupa, Nirjhar Chatterjee, Jayanthi Shastri, Nerges Mistry
Software Mentions: 1
Published: over 3 years ago
10.1186/1471-2164-14-47
Reassessment of the Listeria monocytogenespan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genomeCited by: 171
Author(s): Carsten Kuenne, André Billion, Mobarak Abu Mraheil, Axel Strittmatter, Rolf Daniel, Alexander Goesmann, Sukhadeo B. Barbuddhe, Torsten Hain, Trinad Chakraborty
Software Mentions: 1
Published: almost 12 years ago