Exploring coronavirus research papers

This repository explores a graph of research papers released during COVID-19 Open Research Dataset Challenge (CORD-19)

This repository does not participate in the challenge, but aims to help researchers and scientists find top papers in the data set.

Below are

• 100 most cited papers
• 100 papers with the highest PageRank

Most cited

1. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia - 422
2. Identification of a novel coronavirus in patients with severe acute respiratory syndrome - 246
3. A novel coronavirus associated with severe acute respiratory syndrome - 232
4. Global trends in emerging infectious diseases - 208
5. Bats are natural reservoirs of SARS-like coronaviruses - 189
6. Coronavirus as a possible cause of severe acute respiratory syndrome - 164
7. Characterization of a novel coronavirus associated with severe acute respiratory syndrome - 153
8. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats - 148
9. Identification of a new human coronavirus - 143
10. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC - 142
11. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans - 130
12. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China - 130
13. Basic local alignment search tool - 129
14. Transmission dynamics and control of severe acute respiratory syndrome - 126
15. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia - 126
16. MUSCLE: multiple sequence alignment with high accuracy and high throughput - 125
17. Cloning of a human parvovirus by molecular screening of respiratory tract samples - 123
18. Hospital outbreak of Middle East respiratory syndrome coronavirus - 122
19. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor - 118
20. World Health Organization - 113
21. A new coronavirus-like particle associated with diarrhea in swine - 109
22. A major outbreak of severe acute respiratory syndrome in Hong Kong - 108
23. Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures - 106
24. Middle East respiratory syndrome - 105
25. Fruit bats as reservoirs of Ebola virus - 105
26. The molecular biology of coronaviruses - 104
27. Severe acute respiratory syndrome - 103
28. Clinical features of patients infected with 2019 novel coronavirus in Wuhan - 102
29. Superspreading and the effect of individual variation on disease emergence - 101
30. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study - 101
31. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study - 101
32. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study - 99
33. Bats: important reservoir hosts of emerging viruses - 98
34. Evidence for camel-to-human transmission of MERS coronavirus - 95
35. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation - 95
36. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus - 95
37. Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong - 94
38. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia - 93
39. Risk factors for human disease emergence - 92
40. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods - 92
41. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus - 88
42. Evolution and ecology of influenza A viruses - 88
43. Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines - 88
44. Coronavirus avian infectious bronchitis virus - 86
45. Strategies for containing an emerging influenza pandemic in Southeast Asia - 85
46. Human infection with a novel avian-origin influenza A (H7N9) virus - 82
47. Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction - 81
48. A newly discovered human pneumovirus isolated from young children with respiratory tract disease - 81
49. Distinct patterns of IFITM-mediated restriction of filoviruses, SARS coronavirus, and influenza A virus - 80
50. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster - 79
51. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia - 79
52. Identification of severe acute respiratory syndrome in Canada - 79
53. Pandemic potential of a strain of influenza A (H1N1): early findings - 78
54. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study - 77
55. A diverse range of gene products are effectors of the type I interferon antiviral response - 77
56. Middle East respiratory syndrome coronavirus in bats, Saudi Arabia - 77
57. Antibodies against MERS coronavirus in dromedary camels - 76
58. A pneumonia outbreak associated with a new coronavirus of probable bat origin - 75
59. Coronaviruses post-SARS: update on replication and pathogenesis - 75
60. Family cluster of Middle East respiratory syndrome coronavirus infections - 75
61. The severe acute respiratory syndrome - 74
62. Viral pneumonia - 74
63. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage - 73
64. Molecular basis of binding between novel human coronavirus MERS-CoV and its receptor CD26 - 73
65. Loop-mediated isothermal amplification of DNA - 72
66. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum - 72
67. How generation intervals shape the relationship between growth rates and reproductive numbers - 71
68. A simple method of estimating fifty per cent endpoints - 71
69. Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States - 71
70. Mfold web server for nucleic acid folding and hybridization prediction - 70
71. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs - 70
72. A simple method of estimating fifty percent endpoints - 70
73. Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt - 70
74. Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group - 69
75. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder - 68
76. Fields Virology - 67
77. An efficient method to make human monoclonal antibodies from memory B cells: potent neutralization of SARS coronavirus - 67
78. IFITM3 restricts the morbidity and mortality associated with influenza - 67
79. Host range and emerging and reemerging pathogens - 66
80. Severe respiratory illness caused by a novel coronavirus - 66
81. Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4 - 65
82. A Novel Coronavirus from Patients with Pneumonia in China - 64
83. Strategies for mitigating an influenza pandemic - 64
84. Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis - 63
85. Coot: model-building tools for molecular graphics - 63
86. The global distribution and burden of dengue - 63
87. Factors that make an infectious disease outbreak controllable - 62
88. Fast gapped-read alignment with Bowtie 2 - 61
89. Clustal W and Clustal X version 2.0 - 61
90. Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections - 61
91. A cluster of cases of severe acute respiratory syndrome in Hong Kong - 60
92. Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection - 60
93. Coronavirus diversity, phylogeny and interspecies jumping - 60
94. Transmission of MERS-coronavirus in household contacts - 60
95. MEGA6: molecular evolutionary genetics analysis version 6.0 - 59
96. Emergence of a novel swine-origin influenza A (H1N1) virus in humans - 59
97. Endosomal proteolysis of the Ebola virus glycoprotein is necessary for infection - 59
98. The genome sequence of the SARS-associated coronavirus - 58
99. Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States - 58
100. Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study - 57

Highest PageRank

1. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia - 0.000030214273580887554
2. A novel coronavirus associated with severe acute respiratory syndrome - 0.000017851516003512185
3. Identification of a novel coronavirus in patients with severe acute respiratory syndrome - 0.00001778469801970066
4. Coronavirus as a possible cause of severe acute respiratory syndrome - 0.000013696721148887258
5. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia - 0.000013634041139832885
6. Clinical features of patients infected with 2019 novel coronavirus in Wuhan - 0.000012842491017243939
7. Global trends in emerging infectious diseases - 0.00001182368859219638
8. Bats are natural reservoirs of SARS-like coronaviruses - 0.000011819467230975972
9. A Novel Coronavirus from Patients with Pneumonia in China - 0.000011757534664161738
10. Transmission dynamics and control of severe acute respiratory syndrome - 0.000011519771727110827
11. A major outbreak of severe acute respiratory syndrome in Hong Kong - 0.000011342285012659375
12. World Health Organization - 0.00001104666096924675
13. Hospital outbreak of Middle East respiratory syndrome coronavirus - 0.000010981291080537561
14. A new coronavirus-like particle associated with diarrhea in swine - 0.00001077198725204711
15. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study - 0.00001074176644367653
16. Middle East respiratory syndrome - 0.000010585742112134148
17. Characterization of a novel coronavirus associated with severe acute respiratory syndrome - 0.000010554979635345487
18. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster - 0.000010351237167486713
19. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study - 0.000009957987891039725
20. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study - 0.00000991905869482425
21. Cloning of a human parvovirus by molecular screening of respiratory tract samples - 0.000009858613809020958
22. A pneumonia outbreak associated with a new coronavirus of probable bat origin - 0.000009769927957405335
23. Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines - 0.000009678630222204843
24. Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong - 0.000009636481211101517
25. Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction - 0.000009530182643695209
26. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China - 0.00000951707628096151
27. Identification of a new human coronavirus - 0.00000936263247963982
28. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation - 0.00000925037192813049
29. Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans - 0.000009245242954069329
30. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study - 0.00000906832747661447
31. Identification of severe acute respiratory syndrome in Canada - 0.000008997075541369225
32. Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures - 0.000008974560331460351
33. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats - 0.000008947824534547954
34. Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-EMC - 0.000008880872935326923
35. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia - 0.000008873571873919721
36. MUSCLE: multiple sequence alignment with high accuracy and high throughput - 0.000008645760841476574
37. Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study - 0.000008624439877568346
38. Superspreading and the effect of individual variation on disease emergence - 0.000008611447270746965
39. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China - 0.000008547843027717236
40. Basic local alignment search tool - 0.000008227838940488223
41. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor - 0.000007903328147367947
42. A novel coronavirus from patients with pneumonia in China - 0.000007796454578505519
43. Factors that make an infectious disease outbreak controllable - 0.000007584831675029194
44. Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections - 0.000007536467730729938
45. No reuse allowed without permission. The copyright holder for this preprint (which was not peer-reviewed) is the - 0.00000749193057354163
46. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding - 0.000007456373525659563
47. Evidence for camel-to-human transmission of MERS coronavirus - 0.00000744971136441726
48. Seroepidemiology for MERS coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in Egypt - 0.000007419974056741979
49. Family cluster of Middle East respiratory syndrome coronavirus infections - 0.000007413875852229176
50. A novel coronavirus outbreak of global health concern - 0.0000074055758714005645
51. Bats: important reservoir hosts of emerging viruses - 0.0000073470214154087844
52. Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States - 0.000007344909703336689
53. Severe acute respiratory syndrome - 0.000007273972424495137
54. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods - 0.000007256752860092913
55. A cluster of cases of severe acute respiratory syndrome in Hong Kong - 0.00000722833124375235
56. Transmission of MERS-coronavirus in household contacts - 0.0000071810619117285815
57. Antibodies against MERS coronavirus in dromedary camels - 0.000007160449132517955
58. MERS outbreak in Korea: hospital-to-hospital transmission - 0.000007064667911333143
59. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia - 0.000007028691985167885
60. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia - 0.000006976024301505739
61. Pandemic potential of a strain of influenza A (H1N1): early findings - 0.0000068848028647450815
62. How generation intervals shape the relationship between growth rates and reproductive numbers - 0.000006847368756742034
63. Emergence of porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences - 0.000006767342733403059
64. Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States - 0.000006725233762989542
65. Human infection with a novel avian-origin influenza A (H7N9) virus - 0.0000066450909351996185
66. Coronavirus avian infectious bronchitis virus - 0.000006625072292783845
67. Risk factors for human disease emergence - 0.000006615979322983559
68. A newly discovered human pneumovirus isolated from young children with respiratory tract disease - 0.000006538503882594968
69. Proc. Natl. Acad. Sci - 0.0000065370681680189255
70. Strategies for containing an emerging influenza pandemic in Southeast Asia - 0.000006516995307023328
71. The severe acute respiratory syndrome - 0.000006512961554483116
72. Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group - 0.000006512166415418912
73. MERS coronaviruses in dromedary camels - 0.000006507620398347028
74. Clinical features and short-term outcomes of 144 patients with SARS in the greater Toronto area - 0.000006421905408260493
75. The molecular biology of coronaviruses - 0.000006326788211471908
76. Proc. Natl Acad. Sci. USA - 0.0000062823861275022985
77. Fruit bats as reservoirs of Ebola virus - 0.000006228691692423214
78. Loop-mediated isothermal amplification of DNA - 0.000006217201167025759
79. MEGA6: molecular evolutionary genetics analysis version 6.0 - 0.000006197643458896986
80. Outbreak of porcine epidemic diarrhea in suckling piglets - 0.000006185916941482974
81. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus - 0.000006155203733440755
82. Clinical characteristics of 2019 novel coronavirus infection in China - 0.000006105420038098192
83. Middle East respiratory syndrome coronavirus in bats, Saudi Arabia - 0.000006033628556917748
84. Severe respiratory illness caused by a novel coronavirus - 0.0000060248395698908535
85. Evidence of human coronavirus HKU1 and human bocavirus in Australian children - 0.000005978414011847801
86. Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions - 0.000005921730074933322
87. Distinct characteristics and complex evolution of PEDV strains - 0.0000059081228759718215
88. The genome sequence of the SARS-associated coronavirus - 0.000005817842731262006
89. Viral pneumonia - 0.000005730198017290083
90. Effectiveness of precautions against droplets and contact in prevention of nosocomial transmission of severe acute respiratory syndrome (SARS) - 0.00000572998627863784
91. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus - 0.0000056940635906927955
92. License statement: This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes - 0.0000056806211589341725
93. Preliminary epidemiological assessment of MERS-CoV outbreak in South Korea - 0.000005642895169745001
94. Interhuman transmissibility of Middle East respiratory syndrome coronavirus: estimation of pandemic risk - 0.000005622208427863623
95. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs - 0.0000056187397882373115
96. Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences - 0.0000055994227189676705
97. Infectious diseases of humans - 0.000005547080507808995
98. Evolution and ecology of influenza A viruses - 0.000005528221342988328
99. Global burden of childhood pneumonia and diarrhoea - 0.00000552404759957462
100. Structure of MERS-CoV spike receptor-binding domain complexed with human receptor DPP4 - 0.000005518633891110089

local development

1. Download the dataset.
2. Install node

And then perform one-time initialization

git clone https://github.com/anvaka/cord-19
cd cord-19
npm install

Once all modules are installed, run the command to collect stats:

node print-stats.js path_to_kaggle_data_set

Here path_to_kaggle_data_set is the root folder with json_schema.txt file in it. E.g.:

node print-stats.js ~/Downloads/2020-03-13

License

Code in this repository is licensed under MIT license.

COVID DATASET LICENSE AGREEMENT

By accessing, downloading or otherwise using any Journals, Articles, Metadata, Abstracts, Full-Texts or any other content types provided in the COVID-19 Open Research Dataset (CORD-19) Database (the “Data”), You expressly acknowledge and agree to the following:

• AI2 grants to You a worldwide, perpetual, non-exclusive, non-transferable license to use and make derivatives of the Data for text and data mining only.
• AI2 warrants that it has the right to make the Data available to You as provided for in and subject to this Agreement and in accordance with applicable law. EXCEPT FOR THE LIMITED WARRANTY IN THIS SECTION, THE DATA IS PROVIDED “AS IS”, WITHOUT ANY WARRANTIES OF ANY KIND.
• You agree to comply with all applicable local, state, national, and international laws and regulations with respect to AI2’s license and Your use of the Data.
• Data provided by AI2 is from copyrighted sources of the respective copyright holders. You are solely responsible for Your and Your users’ compliance with any copyright, patent or trademark restrictions and are referred to the copyright, patent or trademark notices appearing in the original sources, all of which are hereby incorporated by reference.