A citation-based method for searching scientific literature

Muhammad Tahir Ul Qamar, Xitong Zhu, Muhammad Sarwar Khan, Feng Xing, Ling-Ling Chen. Plant Genome 2020
Times Cited: 11







List of co-cited articles
108 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".
Hervé Tettelin, Vega Masignani, Michael J Cieslewicz, Claudio Donati, Duccio Medini, Naomi L Ward, Samuel V Angiuoli, Jonathan Crabtree, Amanda L Jones, A Scott Durkin,[...]. Proc Natl Acad Sci U S A 2005
36

How the pan-genome is changing crop genomics and improvement.
Rafael Della Coletta, Yinjie Qiu, Shujun Ou, Matthew B Hufford, Candice N Hirsch. Genome Biol 2021
69
36

The immune epitope database (IEDB) 3.0.
Randi Vita, James A Overton, Jason A Greenbaum, Julia Ponomarenko, Jason D Clark, Jason R Cantrell, Daniel K Wheeler, Joseph L Gabbard, Deborah Hix, Alessandro Sette,[...]. Nucleic Acids Res 2015
652
27

GalaxyRefine: Protein structure refinement driven by side-chain repacking.
Lim Heo, Hahnbeom Park, Chaok Seok. Nucleic Acids Res 2013
441
27

PatchDock and SymmDock: servers for rigid and symmetric docking.
Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J Wolfson. Nucleic Acids Res 2005
27

BPGA- an ultra-fast pan-genome analysis pipeline.
Narendrakumar M Chaudhari, Vinod Kumar Gupta, Chitra Dutta. Sci Rep 2016
420
27

Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins.
Douglas B Craig, Alan A Dombkowski. BMC Bioinformatics 2013
237
27

SCRATCH: a protein structure and structural feature prediction server.
J Cheng, A Z Randall, M J Sweredoski, P Baldi. Nucleic Acids Res 2005
633
27

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.
Andreas Grote, Karsten Hiller, Maurice Scheer, Richard Münch, Bernd Nörtemann, Dietmar C Hempel, Dieter Jahn. Nucleic Acids Res 2005
651
27


Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations.
Peng Qin, Hongwei Lu, Huilong Du, Hao Wang, Weilan Chen, Zhuo Chen, Qiang He, Shujun Ou, Hongyu Zhang, Xuanzhao Li,[...]. Cell 2021
92
27

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement.
Aamir W Khan, Vanika Garg, Manish Roorkiwal, Agnieszka A Golicz, David Edwards, Rajeev K Varshney. Trends Plant Sci 2020
91
27

The barley pan-genome reveals the hidden legacy of mutation breeding.
Murukarthick Jayakodi, Sudharsan Padmarasu, Georg Haberer, Venkata Suresh Bonthala, Heidrun Gundlach, Cécile Monat, Thomas Lux, Nadia Kamal, Daniel Lang, Axel Himmelbach,[...]. Nature 2020
126
27

Towards plant pangenomics.
Agnieszka A Golicz, Jacqueline Batley, David Edwards. Plant Biotechnol J 2016
112
27

Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus.
Jia-Ming Song, Zhilin Guan, Jianlin Hu, Chaocheng Guo, Zhiquan Yang, Shuo Wang, Dongxu Liu, Bo Wang, Shaoping Lu, Run Zhou,[...]. Nat Plants 2020
223
27

Pan-Genome of Wild and Cultivated Soybeans.
Yucheng Liu, Huilong Du, Pengcheng Li, Yanting Shen, Hua Peng, Shulin Liu, Guo-An Zhou, Haikuan Zhang, Zhi Liu, Miao Shi,[...]. Cell 2020
226
27

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.
Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M Tieman, Elizabeth A Burzynski-Chang, Tara L Fish, Kaitlin A Stromberg, Gavin L Sacks,[...]. Nat Genet 2019
229
27

Exploring and Exploiting Pan-genomics for Crop Improvement.
Yongfu Tao, Xianrong Zhao, Emma Mace, Robert Henry, David Jordan. Mol Plant 2019
88
27

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice.
Qiang Zhao, Qi Feng, Hengyun Lu, Yan Li, Ahong Wang, Qilin Tian, Qilin Zhan, Yiqi Lu, Lei Zhang, Tao Huang,[...]. Nat Genet 2018
260
27

The pangenome of an agronomically important crop plant Brassica oleracea.
Agnieszka A Golicz, Philipp E Bayer, Guy C Barker, Patrick P Edger, HyeRan Kim, Paula A Martinez, Chon Kit Kenneth Chan, Anita Severn-Ellis, W Richard McCombie, Isobel A P Parkin,[...]. Nat Commun 2016
195
27

ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline.
Muhammad Tahir Ul Qamar, Xitong Zhu, Feng Xing, Ling-Ling Chen. Bioinformatics 2019
13
27

Molecular docking.
Garrett M Morris, Marguerita Lim-Wilby. Methods Mol Biol 2008
247
18

Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches.
Muhammad Tahir Ul Qamar, Sajjad Ahmad, Israr Fatima, Faisal Ahmad, Farah Shahid, Anam Naz, Sumra Wajid Abbasi, Abbas Khan, Muhammad Usman Mirza, Usman Ali Ashfaq,[...]. Comput Biol Med 2021
43
18

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
18



Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT.
Yunjia Chen, Peng Yu, Jingchu Luo, Ying Jiang. Mamm Genome 2003
121
18

Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches.
Zulkar Nain, Faruq Abdulla, M Mizanur Rahman, Mohammad Minnatul Karim, Md Shakil Ahmed Khan, Sifat Bin Sayed, Shafi Mahmud, S M Raihan Rahman, Md Moinuddin Sheam, Zahurul Haque,[...]. J Biomol Struct Dyn 2020
50
18

Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: a reverse vaccinology based approach.
Anam Naz, Faryal Mehwish Awan, Ayesha Obaid, Syed Aun Muhammad, Rehan Zafar Paracha, Jamil Ahmad, Amjad Ali. Infect Genet Evol 2015
123
18

Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae.
Hamza Arshad Dar, Tahreem Zaheer, Muhammad Shehroz, Nimat Ullah, Kanwal Naz, Syed Aun Muhammad, Tianyu Zhang, Amjad Ali. Vaccines (Basel) 2019
55
18

In silico approach for predicting toxicity of peptides and proteins.
Sudheer Gupta, Pallavi Kapoor, Kumardeep Chaudhary, Ankur Gautam, Rahul Kumar, Gajendra P S Raghava. PLoS One 2013
586
18

Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets.
Amjad Ali, Anam Naz, Siomar C Soares, Marriam Bakhtiar, Sandeep Tiwari, Syed S Hassan, Fazal Hanan, Rommel Ramos, Ulisses Pereira, Debmalya Barh,[...]. Biomed Res Int 2015
37
18

Global Contributors to Antibiotic Resistance.
Aastha Chokshi, Ziad Sifri, David Cennimo, Helen Horng. J Glob Infect Dis 2019
162
18

Reverse vaccinology.
Marirosa Mora, Daniele Veggi, Laura Santini, Mariagrazia Pizza, Rino Rappuoli. Drug Discov Today 2003
71
18


PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
Nancy Y Yu, James R Wagner, Matthew R Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S Cenk Sahinalp, Martin Ester, Leonard J Foster,[...]. Bioinformatics 2010
18


MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R Miller, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, Adrian E Roitberg. J Chem Theory Comput 2012
18


Genome-based vaccine development: a short cut for the future.
Danilo Gomes Moriel, Maria Scarselli, Laura Serino, Marirosa Mora, Rino Rappuoli, Vega Masignani. Hum Vaccin 2008
29
18

Peptide Vaccine: Progress and Challenges.
Weidang Li, Medha D Joshi, Smita Singhania, Kyle H Ramsey, Ashlesh K Murthy. Vaccines (Basel) 2014
347
18


Towards a peptide-based vaccine against Shigella sonnei: A subtractive reverse vaccinology based approach.
Shehneela Baseer, Sajjad Ahmad, Kara E Ranaghan, Syed Sikander Azam. Biologicals 2017
52
18

PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome.
Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach, Amjad Ali. BMC Bioinformatics 2019
46
18

Pan-vaccinomics approach towards a universal vaccine candidate against WHO priority pathogens to address growing global antibiotic resistance.
Saba Ismail, Farah Shahid, Abbas Khan, Sadia Bhatti, Sajjad Ahmad, Anam Naz, Ahmad Almatroudi, Muhammad Tahir Ul Qamar. Comput Biol Med 2021
27
18

Two years into reverse vaccinology.
Jeannette Adu-Bobie, Barbara Capecchi, Davide Serruto, Rino Rappuoli, Mariagrazia Pizza. Vaccine 2003
83
18

Galaxy: a platform for interactive large-scale genome analysis.
Belinda Giardine, Cathy Riemer, Ross C Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, James Taylor,[...]. Genome Res 2005
18

Subtractive genome analysis for in silico identification and characterization of novel drug targets in Streptococcus pneumonia strain JJA.
Abdul Wadood, Alam Jamal, Muhammad Riaz, Ajmal Khan, Reaz Uddin, Musharraf Jelani, Syed Sikander Azam. Microb Pathog 2018
27
18

Metabolomics for Plant Improvement: Status and Prospects.
Rakesh Kumar, Abhishek Bohra, Arun K Pandey, Manish K Pandey, Anirudh Kumar. Front Plant Sci 2017
102
18

Transposable elements contribute to activation of maize genes in response to abiotic stress.
Irina Makarevitch, Amanda J Waters, Patrick T West, Michelle Stitzer, Candice N Hirsch, Jeffrey Ross-Ibarra, Nathan M Springer. PLoS Genet 2015
217
18


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.