SEPP: SATé-Enabled Phylogenetic Placement

MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies

Minot, S. S., Garb, B. F., Roldan, A., Tang, A., Oskotsky, T., Rosenthal, C. A., Hoffman, N. G., Sirota, M., & Golob, J. L. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100639 · Cited by 16

Intestinal dysbiosis as an intraoperative predictor of septic complications: evidence from human surgical cohorts and preclinical models of peritoneal sepsis

Spari, D., Zwicky, S. N., Yılmaz, B., Salm, L., Candinas, D., & Beldi, G. (2023) · Scientific Reports · doi:10.1038/s41598-023-49034-z · Cited by 15

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel

Alachiotis, N., Berger, S. A., & Stamatakis, A. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-196 · Cited by 15

Microbiome characterization of alpine water springs for human consumption reveals site- and usage-specific microbial signatures

Pedron, R., Esposito, A., Cozza, W., Paolazzi, M., Cristofolini, M., Segata, N., & Jousson, O. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.946460 · Cited by 14

Spatial variation of the gut microbiome in response to long-term metformin treatment in high-fat diet-induced type 2 diabetes mouse model of both sexes

Silamiķele, L., Saksis, R., Silamiķelis, I., Kotoviča, P. P., Brīvība, M., Kalniņa, I., Kalniņa, Z., Frīdmanis, D., & Kloviņš, J. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2188663 · Cited by 15

A Two-Time Point Analysis of Gut Microbiota in the General Population of Buenos Aires and Its Variation Due to Preventive and Compulsory Social Isolation During the COVID-19 Pandemic

Aguilera, P., Mascardi, M. F., Belforte, F. S., Rosso, A. D., Quesada, S., Llovet, I., Iraola, G., Trinks, J., & Steinhardt, A. P. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.803121 · Cited by 15

Chitogel following endoscopic sinus surgery promotes a healthy microbiome and reduces postoperative infections

Megow, A., Alsuliman, Y., Bouras, G. S., Menberu, M. A., Vyskocil, E., Vreugde, S., & Wormald, P. (2022) · International Forum of Allergy & Rhinology · doi:10.1002/alr.23001 · Cited by 13

Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands

Vasco, K. A., Guevara, N., Mosquera, J. M., Zapata, S., & Zhang, L. (2022) · Animal Microbiome · doi:10.1186/s42523-022-00218-4 · Cited by 15

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification

Tsang, C. T. T., Hui, T. K. L., Chung, N. M., Yuen, W. T., & Tsang, L. M. (2024) · Molecular Ecology · doi:10.1111/mec.17377 · Cited by 13

UPP2: fast and accurate alignment of datasets with fragmentary sequences

Park, M., Ivanovic, S. S., Chu, G., Shen, C., & Warnow, T. J. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad007 · Cited by 13

Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal

Bensch, H. M., Lundin, D., Tolf, C., Waldenström, J., & Zöttl, M. (2023) · Journal of Evolutionary Biology · doi:10.1111/jeb.14208 · Cited by 13

Feasibility of Collection and Analysis of Microbiome Data in a Longitudinal Randomized Trial of Community Gardening

Gascón, M., Harrall, K. K., Beavers, A. W., Glueck, D. H., Stanislawski, M. A., Alaimo, K., Villalobos, A., Hébert, J. R., Dexter, K., Li, K., et al. (2020) · Future Microbiology · doi:10.2217/fmb-2019-0195 · Cited by 12

APPLES: Scalable Distance-based Phylogenetic Placement with or without AlignmentsPreprint

Balaban, M., Sarmashghi, S., & Mirarab, S. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/475566 · Cited by 13

Effects of Partially Hydrolyzed Guar Gum Supplementation on the Fecal Microbiotas of Piglets

Inoüe, R., Otabi, H., Yamashita, T., Takizawa, N., Kido, T., Sugiyama, A., Ozeki, M., Abe, A., & Tsukahara, T. (2021) · Pathogens · doi:10.3390/pathogens10111420 · Cited by 12

Constructing phylogenetic trees for microbiome data analysis: A mini-review

Liu, R., Qiao, X., Shi, Y., Peterson, C. B., Bush, W. S., Cominelli, F., Wang, M., & Zhang, L. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.10.032 · Cited by 12

Individuality and stability of the koala ( Phascolarctos cinereus ) faecal microbiota through time

Eisenhofer, R., Brice, K. L., Blyton, M. D. J., Bevins, S. E., Leigh, K. A., Singh, B. K., Helgen, K. M., Hough, I., Daniels, C. B., Speight, N., et al. (2023) · PeerJ · doi:10.7717/peerj.14598 · Cited by 13

Comparison of gut microbiota between immigrant and native populations of the Silver-eared Mesia (Leiothrix argentauris) living in mining area

Zhou, T., Liu, S., & Jiang, A. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1076523 · Cited by 13

SCAMPP+FastTree: improving scalability for likelihood-based phylogenetic placement

Chu, G., & Warnow, T. J. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad008 · Cited by 12

Effects of pair-housing pubertal and adult male and female mice on LPS-induced age-dependent immune responses: A potential role for the gut microbiota

Murray, E., Butcher, J., Kearns, M. M., Lamba, S., Liang, J., Stintzi, A., & Ismail, N. (2023) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2023.03.009 · Cited by 12

Novel Nutraceutical (silymarin, yeast β-glucan, prebiotics, and minerals) shifts gut microbiota and restores large intestine histology of diet-induced metabolic syndrome mice

Filho, V. N., de Freitas, J. A., Franco, L. A. M., Fonseca, J. V. D. S., Martins, R. C. R., Santamarina, A. B., Murata, G. M., Sabino, É. C., Souza, E., Ferreira, M. T., et al. (2023) · Journal of Functional Foods · doi:10.1016/j.jff.2023.105671 · Cited by 11

The core bacteriobiome of Côte d’Ivoire soils across three vegetation zones

Amon, C. E. R., Fossou, R. K., Ebou, A., Koua, D., Kouadjo, C. G., Brou, Y. C., Bi, D. R. R. V., Cowan, D. A., & Zézé, A. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1220655 · Cited by 11

Dietary preservatives alter the gut microbiota in vitro and in vivo with sex-specific consequences for host metabolic development

Schell, L. D., Chadaideh, K. S., Allen‐Blevins, C. R., Venable, E. M., & Carmody, R. N. (2024) · American Journal of Clinical Nutrition · doi:10.1016/j.ajcnut.2025.04.010 · Cited by 11

Variation in bacterial composition, diversity, and activity across different subglacial basal ice types

Doyle, S. M., & Christner, B. C. (2022) · The Cryosphere · doi:10.5194/tc-16-4033-2022 · Cited by 11

Antibiotic Treatment Does Not Ameliorate the Metabolic Changes in Rats Presenting Dysbiosis After Consuming a High Fructose Diet

Bier, A., Khasbab, R., Haberman, Y., Braun, T., Hadar, R., Sosnovski, K. E., Amir, A., Leibowitz, A., & Grossman, E. (2020) · Nutrients · doi:10.3390/nu12010203 · Cited by 11

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic morphine

Sall, I., Foxall, R. L., Felth, L. C., Maret, S., Rosa, Z., Gaur, A., Calawa, J., Pavlik, N., Whistler, J. L., & Whistler, C. A. (2025) · Gut Microbes · doi:10.1080/19490976.2024.2446423 · Cited by 9

Distinct gut microbiome characteristics and dynamics in patients with Parkinson’s disease based on the presence of premotor rapid-eye movement sleep behavior disorders

Lee, J., Jo, S., Lee, J., Choi, M., Kim, K., Lee, S.-J., Kim, H. S., Bae, J., & Chung, S. J. (2025) · Microbiome · doi:10.1186/s40168-025-02095-w · Cited by 11

Phylogenetic double placement of mixed samples

Balaban, M., & Mirarab, S. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa489 · Cited by 11

Scalable and Accurate Phylogenetic Placement Using pplacer-XR

Wedell, E., Cai, Y., & Warnow, T. J. (2021) · Lecture notes in computer science · doi:10.1007/978-3-030-74432-8_7 · Cited by 10

Type 1 diabetes, periodontal health, and a familial history of hyperlipidaemia is associated with oral microbiota in children: a cross-sectional study

Selway, C. A., Jensen, E. D., Peña, A. S., Smart, G., & Weyrich, L. S. (2023) · BMC Oral Health · doi:10.1186/s12903-022-02625-0 · Cited by 12

Optimal Estimation of Wasserstein Distance on a Tree With an Application to Microbiome Studies

Wang, S., Cai, T., & Li, H. (2019) · Journal of the American Statistical Association · doi:10.1080/01621459.2019.1699422 · Cited by 10

Transcript- and annotation-guided genome assembly of the European starlingPreprint

Stuart, K. C., Edwards, R. J., Cheng, Y., Warren, W. C., Burt, D. W., Sherwin, W. B., Hofmeister, N. R., Werner, S. J., Ball, G. F., Melissa Bateson, B., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.07.438753 · Cited by 9

Improving microbial phylogeny with citizen science within a mass-market video game

Sarrazin-Gendron, R., Ghasemloo Gheidari, P., Butyaev, A., Keding, T., Cai, E., Zheng, J., Mutalova, R., Mounthanyvong, J., Zhu, Y., Nazarova, E., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02175-6 · Cited by 9

Endophytic microbial diversity associated with commercial cultivar and crop wild relative banana variety could provide clues for microbial community management

Posada, L. F., Arteaga-Figueroa, L. A., Adarve-Rengifo, I., Cadavid, M., Zapata, S., & Alvarez, J. (2024) · Microbiological Research · doi:10.1016/j.micres.2024.127862 · Cited by 9

Endurance exercise associated with a fructooligosaccharide diet modulates gut microbiota and increases colon absorptive area

Moura, F., Romeiro, C., Petriz, B. A., de Oliveira, N. C., de Almeida, J. A., de Castro, A. P., & Franco, O. L. (2024) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.16563 · Cited by 9

Séance: reference-based phylogenetic analysis for 18S rRNA studies

Medlar, A. J., Aivelo, T., & Löytynoja, A. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0235-7 · Cited by 9

Characterizing the oral and distal gut microbiota of the threatened southern sea otter ( Enhydra lutris nereis ) to enhance conservation practice

Dudek, N. K., Switzer, A. D., Costello, E. K., Murray, M. J., Tomoleoni, J. A., Staedler, M. M., Tinker, M. T., & Relman, D. A. (2022) · Conservation Science and Practice · doi:10.1111/csp2.12640 · Cited by 9

Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy

Smarr, L. L., Hyde, E. R., McDonald, D. T., Sandborn, W. J., & Knight, R. D. (2017) · Methods of Information in Medicine · doi:10.3414/me17-01-0036 · Cited by 9

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: The METS-Microbiome StudyPreprint

Ecklu-Mensah, G., Choo-Kang, C., Maseng, M. G., Donato, S., Bovet, P., Bedu-Addo, K., Plange‐Rhule, J., Forrester, T., Lambert, E. V., Rae, D. E., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.21.533195 · Cited by 10

Influence of polypyrrole-derived nitrogen-doped carbon nanostructure morphology on the microbial composition of anodic biofilms and microbial fuel cell performance

Lascu, I., Gheorghiu, C. C., Bucur, C., Tănase, A., & Dumitru, A. (2024) · Surfaces and Interfaces · doi:10.1016/j.surfin.2024.105586 · Cited by 8

A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis

Panah, F. M., Nielsen, K. D., Simpson, G. L., Schönherz, A. A., Schramm, A., Lauridsen, C., Nielsen, T. S., Højberg, O., Fredborg, M., Purup, S., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1018242 · Cited by 9

Hydrogen peroxide in breast milk is crucial for gut microbiota formation and myelin development in neonatal mice

Kambe, J., Usuda, K., Inoüe, R., Hirayama, K., Ito, M., Suenaga, K., Masukado, S., Liu, H., Miyata, S., Li, C., et al. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2359729 · Cited by 8

Airborne Bacteria over Thawing Permafrost Landscapes in the Arctic

Nieto‐Caballero, M., Barry, K. R., Hill, T. C. J., Douglas, T. A., DeMott, P. J., Kreidenweis, S. M., & Creamean, J. M. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.4c11774 · Cited by 8

Hypothesis testing for phylogenetic composition: a minimum-cost flow perspective

Wang, S., Cai, T., & Li, H. (2020) · Biometrika · doi:10.1093/biomet/asaa061 · Cited by 8

Phylogenetic placement of short reads without sequence alignmentPreprint

Blanke, M., & Morgenstern, B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.19.344986 · Cited by 8

Scalable power analysis and effect size exploration of microbiome community differences with EvidentPreprint

Rahman, G., McDonald, D. T., González, A., Vázquez‐Baeza, Y., Jiang, L., Casals‐Pascual, C., Peddada, S., Hakim, D., Dilmore, A. H., Nowinski, B., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.19.492684 · Cited by 8

Acquisition of an obligate environmental symbiont may be limited in the arboreal environment

Sullivan, L. T., Kelly, S. E., Ravenscraft, A., & Hunter, M. S. (2025) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiaf045 · Cited by 7

Glycomacropeptide as an Efficient Agent to Fight Pathophysiological Mechanisms of Metabolic Syndrome

Sauvé, M. F., Feldman, F., Sané, A. T., Koudoufio, M., Patey, N., Spahis, S., Butcher, J., Duan, H., Figeys, D., Marcil, V., et al. (2024) · Nutrients · doi:10.3390/nu16060871 · Cited by 7

Spatial and Temporal Structure of Environmentally‐Acquired Caballeronia Symbionts of a Leaffooted Bug

Ravenscraft, A., Kelly, S. E., Haviland, D. R., Adamson, J. E., & Hunter, M. S. (2026) · Molecular Ecology · doi:10.1111/mec.70467 · Cited by 8

Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes

Galbraith, J. D., Ludington, A. J., Sanders, K. L., Amos, T. G., Thomson, V. A., Tuipulotu, D. E., Dunstan, N. L., Edwards, R. J., Suh, A., & Adelson, D. L. (2022) · Genes · doi:10.3390/genes13020217 · Cited by 6

ppIacerDC

Koning, E. R., Phillips, M., & Warnow, T. J. (2021) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/3459930.3469516 · Cited by 7

Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention

Orchanian, S. B., Gauglitz, J. M., Wandro, S., Weldon, K. C., Doty, M. M., Stillwell, K., Hansen, S., Jiang, L., Vargas, F., Rhee, K. E., et al. (2022) · Advanced Biology · doi:10.1002/adbi.202101313 · Cited by 7

In vitro metabolic interaction network of a rationally designed nasal microbiota community

Bonillo-Lopez, L., el Khatab, O. R., Obregón-Gutierrez, P., Fernandez-Villacañas, J. A., Florez‐Sarasa, I., Correa‐Fiz, F., Sibila, M., Aragón, V., & Kochanowski, K. (2025) · iScience · doi:10.1016/j.isci.2025.113114 · Cited by 6

Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems

Darriaut, R., Lailheugue, V., Wastin, J., Tran, J., Martins, G., Ballestra, P., Masneuf‐Pomarède, I., Ollat, N., & Lauvergeat, V. (2025) · Scientific Reports · doi:10.1038/s41598-025-12673-5 · Cited by 6

Agrarian diet improves metabolic health in HIV-positive men with Prevotella -rich microbiomes: results from a randomized trial

O'Connor, J. B., Fouquier, J., Neff, C. P., Sterrett, J. D., Marden, T. J., Fiorillo, S. P., Siebert, J., Schneider, J. A., Nusbacher, N. M., Noe, A. T., et al. (2025) · mSystems · doi:10.1128/msystems.01185-25 · Cited by 6

Bacterial community dynamics of spineless cactus silage during fermentation and aerobic stability

Lemos, M. L. P., Leite, G. M., Santana, L. P., Viana, N. B., de Araujo, W. J., Beeck, W. V., Marco, M. L., Zanine, A. D. M., Santos, E. M., & de Oliveira, C. J. B. (2024) · Bioresource Technology Reports · doi:10.1016/j.biteb.2024.101762 · Cited by 8

Conditioner application improves bedding quality and bacterial composition with potential beneficial impacts for dairy cow’s health

Dunière, L., Frayssinet, B., Achard, C. S., Chevaux, E., & Plateau-Gonthier, J. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.04263-23 · Cited by 6

Extremophile hypolithic communities in the Vestfold Hills, East Antarctica

Clarke, L. J., Raes, E. J., Travers, T. D., Virtue, P., & Bergstrom, D. M. (2024) · Antarctic Science · doi:10.1017/s0954102023000408 · Cited by 6

Oh Brother, Where Art Thou? Finding Orthologs in the Twilight and Midnight Zones of Sequence Similarity

Habermann, B. H. (2016) · Springer eBooks · doi:10.1007/978-3-319-41324-2_22 · Cited by 6

Short-Term Dairy Product Elimination and Reintroduction Minimally Perturbs the Gut Microbiota in Self-Reported Lactose-Intolerant Adults

Smith, C. J., Dethlefsen, L., Gardner, C. D., Nguyen, L. A. B., Feldman, M. W., Costello, E. K., Kolodny, O., & Relman, D. A. (2022) · mBio · doi:10.1128/mbio.01051-22 · Cited by 7

Drivers of inter-population variation in the gut microbiomes of sister species of Phanaeus dung beetlesPreprint

Winfrey, C. C., & Sheldon, K. S. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.19.431932 · Cited by 6

Cross-laboratory replication of pseudomyxoma peritonei tumor microbiome reveals reproducible microbial signatures

Nieciecki, V., Blum, F. C., Johnson, R. C., Testerman, T. L., McAvoy, T. J., King, M. C., Gushchin, V., Whitmire, J. M., Frey, K. G., Glang, L. A., et al. (2025) · mSphere · doi:10.1128/msphere.00652-24 · Cited by 6

Maintaining beneficial alga-associated bacterial communities under heat stress: insights from controlled co-culture experiments using antibiotic-resistant bacterial strains

Karimi, E., & Dittami, S. M. (2023) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiad130 · Cited by 5

Discontinuation of HIIT restores diabesity while retraining increases gut microbiota diversity

Ribeiro, F. M., Petriz, B. A., Anderson, M., Assis, V., Rosa, T. D. S., Corrêa, H. D. L., de Oliveira, N. C., Passos, L., Fonseca, A., Arnaldo, L., et al. (2024) · iScience · doi:10.1016/j.isci.2024.110365 · Cited by 5

Interpolation of microbiome composition in longitudinal data sets

Peleg, O., & Borenstein, E. (2024) · mBio · doi:10.1128/mbio.01150-24 · Cited by 5

Changes in permafrost bacterial community composition after thaw across multiple Alaskan locations

Thurston, A. K., Doherty, S. J., Jones, R. M., Douglas, T. A., Baker, C. C. M., Corriveau, E. J., & Barbato, R. A. (2025) · Ecosphere · doi:10.1002/ecs2.70260 · Cited by 5

The genome of Chenopodium ficifolium : developing genetic resources and a diploid model system for allotetraploid quinoa

Ludwig, C., Maughan, P. J., Jellen, E. N., & Davis, T. M. (2025) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkaf162 · Cited by 6

Microbial community dynamics and cycling of plutonium and iron in a seasonally stratified and radiologically contaminated pond

Merino, N., Wasserman, N. L., Coutelot, F. M., Kaplan, D. I., Powell, B. A., Jiao, Y., Kersting, A. B., & Zavarin, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-45182-4 · Cited by 5

SATe-Enabled Phylogenetic Placement

Warnow, T. J. (2013) · Springer eBooks · doi:10.1007/978-1-4614-6418-1_711-1 · Cited by 5

BSCAMPP: Batch-Scaled Phylogenetic Placement on Large Trees

Wedell, E., Shen, C., & Warnow, T. J. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3562281 · Cited by 4

Subspecific variation in gut microbiota of North American bison in a sympatric setting reveals differentially abundant taxa

Grant, M. L., Petri, R. M., Baecklund, T. M., Wilson, G. A., & Kyle, C. J. (2025) · Animal Microbiome · doi:10.1186/s42523-025-00451-7 · Cited by 4

Temperature Thresholds Govern Microbial‐Mediated Dissolved Organic Carbon Dynamics in Coastal Ecosystems

Dong, J., Chen, X., Chen, F., Hu, Z., Tu, Q., Li, G., He, C., Shi, Q., Zheng, Q., Chen, F., et al. (2025) · Advanced Science · doi:10.1002/advs.202511348 · Cited by 4

Comprehensive Phenotyping in Inflammatory Bowel Disease: Search for Biomarker Algorithms in the Transkingdom Interactions Context

Rosso, A. D., Aguilera, P., Quesada, S., Mascardi, M. F., Mascuka, S. N., Cimolai, M. C., Cerezo, J., Spiazzi, R. A., Conlon, M. C., Milano, C., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10112190 · Cited by 4

WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity

Liu, B., & Warnow, T. J. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad024 · Cited by 4

Deconstructing the association between abiotic factors and species assemblages in the global ocean microbiomePreprint

Shan, X., & Cordero, O. X. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.12.989426 · Cited by 4

Therapeutic Potential of Cranberry Proanthocyanidins in Addressing the Pathophysiology of Metabolic Syndrome: A Scrutiny of Select Mechanisms of Action

Feldman, F., Koudoufio, M., Sané, A. T., Marcil, V., Sauvé, M. F., Butcher, J., Patey, N., Martel, C., Spahis, S., Duan, H., et al. (2025) · Antioxidants · doi:10.3390/antiox14030268 · Cited by 5

Absence of gut microbiota restoration following meropenem treatment in a systemic infection model

Ribeiro, F. M., Ribeiro, C. F. A., Cândido, E. D. S., Buccini, D. F., Cardoso, M. H. E. S., Silveira, G. G. D. O. S., de Souza, C. M., Silva, O. N., de Andrade, G. B., da Silva, A. R., et al. (2025) · npj Antimicrobials and Resistance · doi:10.1038/s44259-025-00129-9 · Cited by 4

Oral–gut microbiome axis in a Korean cohort with inflammatory bowel disease and ankylosing spondylitis (INTEGRATE): a prospective and observational study protocol

Kim, H. S., Kim, B., Nam, B., Oh, S. J., Park, S. K., Lee, S. W., Lee, J., Jo, S., Lee, Y.-A., Lee, J., et al. (2025) · BMJ Open · doi:10.1136/bmjopen-2024-092075 · Cited by 3

Autochthonous carbon loading of macroalgae stimulates benthic biological nitrogen fixation rates in shallow coastal marine sediments

Raut, Y., Barr, C. R., Paris, E. R., Kapili, B. J., Dekas, A., & Capone, D. G. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1312843 · Cited by 3

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach

Jiang, Y., McDonald, D. T., Perry, D. S., Knight, R. D., & Mirarab, S. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae361 · Cited by 3

Ultra-Large Alignments Using Ensembles of Hidden Markov Models

Nguyen, N., Mirarab, S., Kumar, K., & Warnow, T. J. (2015) · Lecture notes in computer science · doi:10.1007/978-3-319-16706-0_26 · Cited by 3

Distance-Based Phylogenetic Placement with Statistical Support

Hasan, N. B., Balaban, M., Biswas, A., Bayzid, M. S., & Mirarab, S. (2022) · Biology · doi:10.3390/biology11081212 · Cited by 3

UPP2: Fast and Accurate Alignment Estimation of Datasets with Fragmentary SequencesPreprint

Park, M., Ivanovic, S. S., Chu, G., Shen, C., & Warnow, T. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.26.482099 · Cited by 3

BATCH-SCAMPP: Batch Scaled Phylogenetic Placement Large TreesPreprint

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