Shibu Yooseph

46.0k total citations · 4 hit papers
100 papers, 6.6k citations indexed

About

Shibu Yooseph is a scholar working on Molecular Biology, Ecology and Artificial Intelligence. According to data from OpenAlex, Shibu Yooseph has authored 100 papers receiving a total of 6.6k indexed citations (citations by other indexed papers that have themselves been cited), including 74 papers in Molecular Biology, 32 papers in Ecology and 10 papers in Artificial Intelligence. Recurrent topics in Shibu Yooseph's work include Genomics and Phylogenetic Studies (40 papers), Microbial Community Ecology and Physiology (25 papers) and Gut microbiota and health (24 papers). Shibu Yooseph is often cited by papers focused on Genomics and Phylogenetic Studies (40 papers), Microbial Community Ecology and Physiology (25 papers) and Gut microbiota and health (24 papers). Shibu Yooseph collaborates with scholars based in United States, Spain and Sweden. Shibu Yooseph's co-authors include Laurie J. Heyer, Semyon Kruglyak, J. Craig Venter, Amir Zarrinpar, Amandine Chaix, Satchidananda Panda, William Nelson, John I. Glass, Christopher L. Dupont and Douglas B. Rusch and has published in prestigious journals such as Nature, Proceedings of the National Academy of Sciences and Nucleic Acids Research.

In The Last Decade

Shibu Yooseph

98 papers receiving 6.5k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Exploring Expression Data: Identification and Analysis of Coexpressed Genes

1999 743 citations Laurie J. Heyer, Semyon Kruglyak et al. Genome Research profile →
Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

2014 653 citations Shibu Yooseph et al. profile →
Essential genes of a minimal bacterium

2006 638 citations Shibu Yooseph, J. Craig Venter et al. Proceedings of the National Academy of Sciences profile →
Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

2014 345 citations Xuesong He, Jeffrey S. McLean et al. Proceedings of the National Academy of Sciences profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Shibu Yooseph United States	40	4.0k	2.0k	727	558	542	100	6.6k
Amnon Amir United States	29	4.1k 1.0×	1.2k 0.6×	751 1.0×	620 1.1×	519 1.0×	67	6.6k
Pengwei Hu China	27	5.8k 1.5×	2.7k 1.3×	668 0.9×	654 1.2×	407 0.8×	120	11.3k
Fangqing Zhao China	49	7.0k 1.8×	950 0.5×	925 1.3×	429 0.8×	707 1.3×	195	9.9k
Luís Pedro Coelho Germany	30	3.4k 0.8×	1.2k 0.6×	388 0.5×	241 0.4×	364 0.7×	53	5.4k
Yoshiki Vázquez‐Baeza United States	33	5.0k 1.3×	998 0.5×	986 1.4×	786 1.4×	669 1.2×	48	7.6k
Zhenjiang Zech Xu China	36	6.5k 1.6×	1.6k 0.8×	1.6k 2.2×	836 1.5×	943 1.7×	94	10.1k
James R. White United States	44	3.7k 0.9×	1.0k 0.5×	642 0.9×	726 1.3×	341 0.6×	145	8.1k
Derrick E. Wood United States	7	3.8k 1.0×	2.0k 1.0×	273 0.4×	861 1.5×	577 1.1×	10	7.1k
Edoardo Pasolli Italy	35	3.8k 0.9×	896 0.4×	780 1.1×	357 0.6×	342 0.6×	80	6.5k
Uri Gophna Israel	45	4.6k 1.1×	1.4k 0.7×	561 0.8×	557 1.0×	1.5k 2.7×	163	7.2k

Countries citing papers authored by Shibu Yooseph

Since Specialization

Citations

This map shows the geographic impact of Shibu Yooseph's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Shibu Yooseph with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Shibu Yooseph more than expected).

Fields of papers citing papers by Shibu Yooseph

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Shibu Yooseph. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Shibu Yooseph. The network helps show where Shibu Yooseph may publish in the future.

Co-authorship network of co-authors of Shibu Yooseph

This figure shows the co-authorship network connecting the top 25 collaborators of Shibu Yooseph. A scholar is included among the top collaborators of Shibu Yooseph based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Shibu Yooseph. Shibu Yooseph is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

Wang, Yuqiu, et al.. (2025). Bidirectional subsethood of shared marker profiles enables accurate virus classification. Microbiome. 13(1). 170–170.

Neal, Craig J., Marco Molinari, Udit Kumar, et al.. (2024). A neoteric antibacterial ceria-silver nanozyme for abiotic surfaces. Biomaterials. 307. 122527–122527. 16 indexed citations

Yooseph, Shibu & Sahar Tavakoli. (2022). Variational Approximation-Based Model Selection for Microbial Network Inference. Journal of Computational Biology. 29(7). 724–737. 1 indexed citations

Rajagopala, Seesandra V., Arash Kamali, Meghan H. Shilts, et al.. (2022). Species-specific transcriptomic changes upon respiratory syncytial virus infection in cotton rats. Scientific Reports. 12(1). 16579–16579. 5 indexed citations

Loftus, Mark, et al.. (2021). Bacterial community structure alterations within the colorectal cancer gut microbiome. BMC Microbiology. 21(1). 98–98. 42 indexed citations

Loftus, Mark, et al.. (2021). Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function. Frontiers in Microbiology. 12. 673632–673632. 10 indexed citations

Hoarfrost, Adrienne, Stephen Nayfach, Joshua Ladau, et al.. (2019). Global ecotypes in the ubiquitous marine clade SAR86. The ISME Journal. 14(1). 178–188. 40 indexed citations

Greenwald, William W., Niels Klitgord, Victor Seguritan, et al.. (2017). Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies. BMC Genomics. 18(1). 296–296. 19 indexed citations

Abeles, Shira R., Marcus B. Jones, Tasha M. Santiago-Rodríguez, et al.. (2016). Microbial diversity in individuals and their household contacts following typical antibiotic courses. Microbiome. 4(1). 39–39. 120 indexed citations

10.

He, Xuesong, Jeffrey S. McLean, Anna Edlund, et al.. (2014). Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences. 112(1). 244–249. 345 indexed citations breakdown →

11.

Williamson, Shannon J., Lisa Zeigler Allen, Hernán Lorenzi, et al.. (2012). Metagenomic Exploration of Viruses throughout the Indian Ocean. PLoS ONE. 7(10). e42047–e42047. 92 indexed citations

12.

Sedghizadeh, Parish P., et al.. (2012). Metagenomic investigation of microbes and viruses in patients with jaw osteonecrosis associated with bisphosphonate therapy. Oral Surgery Oral Medicine Oral Pathology and Oral Radiology. 114(6). 764–770. 31 indexed citations

13.

Goll, Johannes B., Mathangi Thiagarajan, Sahar Abubucker, et al.. (2012). A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP). PLoS ONE. 7(6). e29044–e29044. 7 indexed citations

14.

Wu, Dongying, Martin Wu, Aaron L. Halpern, et al.. (2011). Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS ONE. 6(3). e18011–e18011. 67 indexed citations

15.

Eloe, Emiley A., Douglas Fadrosh, Mark Novotny, et al.. (2011). Going Deeper: Metagenome of a Hadopelagic Microbial Community. PLoS ONE. 6(5). e20388–e20388. 77 indexed citations

16.

Tian, Ying, Xuesong He, Manolito Torralba, et al.. (2010). Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities. Molecular Oral Microbiology. 25(5). 357–367. 103 indexed citations

17.

Kannan, Natarajan, Jian Wu, Ganesh S. Anand, et al.. (2007). Evolution of allostery in the cyclic nucleotide binding module. Genome biology. 8(12). R264–R264. 83 indexed citations

18.

Bartal, Yair, Martı́n Farach-Colton, Shibu Yooseph, & Lisa Zhang. (2002). Fast, Fair and Frugal Bandwidth Allocation in ATM Networks. Algorithmica. 33(3). 272–286. 2 indexed citations

19.

Heyer, Laurie J., Semyon Kruglyak, & Shibu Yooseph. (1999). Exploring Expression Data: Identification and Analysis of Coexpressed Genes. Genome Research. 9(11). 1106–1115. 743 indexed citations breakdown →

20.

Kannan, Sampath, Tandy Warnow, & Shibu Yooseph. (1995). Computing the local consensus of trees. Symposium on Discrete Algorithms. 68–77. 8 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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