| Systemic Health Implications of the Leaky Barriers within the Oral-Gut-Brain Axis and its Pathways of Communication. |
Kim RY, Kuraji R, Kapila YL |
European Medical Journal (Chelmsford, England) |
41404120 |
Eur Med J (Chelmsf) |
2025 Mar |
https://www.ncbi.nlm.nih.gov/pubmed/41404120 |
| Oral virome in health and disease. |
Hernandez-Kapila YL, Kim RY, Gokhale SS, Lin YL, Dommisch H, Slots J, Weisenberger DJ |
Journal of the American Dental Association (1939) |
42012437 |
J Am Dent Assoc |
2026 Apr 21 |
https://www.ncbi.nlm.nih.gov/pubmed/42012437 |
| The FDA's plan to phase out animal testing. |
Gerke S, Balamut J, Wagner JK |
Trends in biotechnology |
41571550 |
Trends Biotechnol |
2026 Jan 21 |
https://www.ncbi.nlm.nih.gov/pubmed/41571550 |
| Single cell transcriptomic analysis reveals dynamic cellular composition changes at acupuncture point BL23 (Shenshu) in low back pain. |
Zhao G, Wu X, Huang S, Huang S, Zhang G, Zhou X, Cao S, Lim HJ, Duhon MII, Li R, Boström KI, Li X |
Molecular pain |
41312958 |
Mol Pain |
2025 Jan-Dec |
https://www.ncbi.nlm.nih.gov/pubmed/41312958 |
| Of mice and men-The emerging oral-gut-brain axis of health and disease. |
Hernandez-Kapila YL, Weisenberger DJ |
Periodontology 2000 |
42394275 |
Periodontol 2000 |
2026 Jul 2 |
https://www.ncbi.nlm.nih.gov/pubmed/42394275 |
| To boldly go where no microRNAs have gone before: spaceflight impact on risk for small-for-gestational-age infants. |
Corti G, Kim J, Enguita FJ, Guarnieri JW, Grossman LI, Costes SV, Fuentealba M, Scott RT, Magrini A, Sanders LM, Singh K, Sen CK, Juran CM, Paul AM, Furman D, Calleja-Agius J, Mason CE, Galeano D, Bottini M, Beheshti A |
Communications biology |
39369042 |
Commun Biol |
2024 Oct 5 |
https://www.ncbi.nlm.nih.gov/pubmed/39369042 |
| Multi-Omics Profiling of Individuals Sustaining Extreme Physical Stressors. |
Sakharkar A, Chen R, LeRoy E, Nelson TM, Proszynski J, Kim J, Park J, Arikatla MR, Mathyk B, Mason CE |
Life (Basel, Switzerland) |
41010319 |
Life (Basel) |
2025 Sep 1 |
https://www.ncbi.nlm.nih.gov/pubmed/41010319 |
| Long-read metagenomics reveals phage dynamics in the human gut microbiome. |
Wirbel J, Hickey AS, Chang D, Enright NJ, Dvorak M, Chanin RB, Schmidtke DT, Bhatt AS |
Nature |
41299176 |
Nature |
2026 Jan |
https://www.ncbi.nlm.nih.gov/pubmed/41299176 |
| CAMP: a modular metagenomics analysis system for integrated multistep data exploration. |
Mak L, Tierney B, Wei W, Ronkowski C, Toscan RB, Turhan B, Toomey M, Andrade-Martínez JS, Fu C, Lucaci AG, Solano AHB, Setubal JC, Henriksen JR, Zimmerman S, Kopbayeva M, Noyvert A, Iwan Z, Kar S, Nakazawa N, Meleshko D, Horyslavets D, Kantsypa V, Frolova A, Kahles A, Danko D, Elhaik E, Labaj P, Mangul S, International MetaSUB Consortium, Mason CE, Hajirasouliha I |
NAR genomics and bioinformatics |
41551931 |
NAR Genom Bioinform |
2026 Mar |
https://www.ncbi.nlm.nih.gov/pubmed/41551931 |
| The Microbe Directory: a centralized database for biological interpretation of microbiome data. |
Sierra MA, Ryon K, Arikatla MR, Elshafey R, Bhaskar H, Proszynski J, Bhattacharya C, Shaaban H, Danko DC, Ambrose P, Spaulding SA, Zambrano MM, Consortium TMD, Mason CE |
Database : the journal of biological databases and curation |
40996703 |
Database (Oxford) |
2025 Jan 18 |
https://www.ncbi.nlm.nih.gov/pubmed/40996703 |
| The prototypic crAssphage is a linear phage-plasmid. |
Schmidtke DT, Hickey AS, Wirbel J, Lin JD, Liachko I, Sherlock G, Bhatt AS |
Cell host & microbe |
40730160 |
Cell Host Microbe |
2025 Aug 13 |
https://www.ncbi.nlm.nih.gov/pubmed/40730160 |
| A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material. |
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bioRxiv : the preprint server for biology |
39677813 |
bioRxiv |
2024 Dec 5 |
https://www.ncbi.nlm.nih.gov/pubmed/39677813 |
| A second space age spanning omics, platforms and medicine across orbits. |
Mason CE, Green J, Adamopoulos KI, Afshin EE, Baechle JJ, Basner M, Bailey SM, Bielski L, Borg J, Borg J, Broddrick JT, Burke M, Caicedo A, Castañeda V, Chatterjee S, Chin CR, Church G, Costes SV, De Vlaminck I, Desai RI, Dhir R, Diaz JE, Etlin SM, Feinstein Z, Furman D, Garcia-Medina JS, Garrett-Bakelman F, Giacomello S, Gupta A, Hassanin A, Houerbi N, Irby I, Javorsky E, Jirak P, Jones CW, Kamal KY, Kangas BD, Karouia F, Kim J, Kim JH, Kleinman AS, Lam T, Lawler JM, Lee JA, Limoli CL, Lucaci A, MacKay M, McDonald JT, Melnick AM, Meydan C, Mieczkowski J, Muratani M, Najjar D, Othman MA, Overbey EG, Paar V, Park J, Paul AM, Perdyan A, Proszynski J, Reynolds RJ, Ronca AE, Rubins K, Ryon KA, Sanders LM, Glowe PS, Shevde Y, Schmidt MA, Scott RT, Shirah B, Sienkiewicz K, Sierra MA, Siew K, Theriot CA, Tierney BT, Venkateswaran K, Hirschberg JW, Walsh SB, Walter C, Winer DA, Yu M, Zea L, Mateus J, Beheshti A |
Nature |
38862027 |
Nature |
2024 Aug |
https://www.ncbi.nlm.nih.gov/pubmed/38862027 |
| Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair. |
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Scientific data |
40670386 |
Sci Data |
2025 Jul 16 |
https://www.ncbi.nlm.nih.gov/pubmed/40670386 |
| Molecular and physiological changes in the SpaceX Inspiration4 civilian crew. |
Jones CW, Overbey EG, Lacombe J, Ecker AJ, Meydan C, Ryon K, Tierney B, Damle N, MacKay M, Afshin EE, Foox J, Park J, Nelson TM, Suhail Mohamad M, Byhaqui SGA, Aslam B, Tali UA, Nisa L, Menon PV, Patel CO, Khan SA, Ebert DJ, Everson A, Schubert MC, Ali NN, Sarma MS, Kim J, Houerbi N, Grigorev K, Garcia Medina JS, Summers AJ, Gu J, Altin JA, Fattahi A, Hirzallah MI, Wu JH, Stahn AC, Beheshti A, Klotz R, Ortiz V, Yu M, Patras L, Matei I, Lyden D, Melnick A, Banerjee N, Mullane S, Kleinman AS, Loesche M, Menon AS, Donoviel DB, Urquieta E, Mateus J, Sargsyan AE, Shelhamer M, Zenhausern F, Bershad EM, Basner M, Mason CE |
Nature |
38862026 |
Nature |
2024 Aug |
https://www.ncbi.nlm.nih.gov/pubmed/38862026 |
| Astroimmunology: the effects of spaceflight and its associated stressors on the immune system. |
Winer DA, Du H, Kim J, Chang V, Burke M, Winer S, Costes SV, Frippiat JP, Sams C, Paul AM, Wu H, Ullrich O, Baatout S, Beheshti A, Mason CE, Choukér A, Crucian BE |
Nature reviews. Immunology |
41102553 |
Nat Rev Immunol |
2026 Mar |
https://www.ncbi.nlm.nih.gov/pubmed/41102553 |
| Analysis of metagenomic data. |
Liu S, Rodriguez JS, Munteanu V, Ronkowski C, Sharma NK, Alser M, Andreace F, Blekhman R, Błaszczyk D, Chikhi R, Crandall KA, Della Libera K, Francis D, Frolova A, Gancz AS, Huntley NE, Jaiswal P, Kosciolek T, Łabaj PP, Łabaj W, Luan T, Mason C, Moustafa AM, Muralidharan HS, Mutlu O, Mansouri Ghiasi N, Rahnavard A, Sun F, Tian S, Tierney BT, Van Syoc E, Vicedomini R, Zackular JP, Zelikovsky A, Zielińska K, Ganda E, Davenport ER, Pop M, Koslicki D, Mangul S |
Nature reviews. Methods primers |
40688383 |
Nat Rev Methods Primers |
2025 |
https://www.ncbi.nlm.nih.gov/pubmed/40688383 |
| Co-evolved Partners of Immunity: A Trait-Based Map of Human Keystone Organisms. |
Asiaee A, Mallal N, Phillips E, Mallal S |
bioRxiv : the preprint server for biology |
41502936 |
bioRxiv |
2026 Feb 11 |
https://www.ncbi.nlm.nih.gov/pubmed/41502936 |
| Interplay of genetic predisposition, plasma metabolome and Mediterranean diet in dementia risk and cognitive function. |
Liu Y, Gu X, Li Y, Wang F, Vyas CM, Peng C, Dong D, Li Y, Zhang Y, Zhang Y, Zeleznik OA, Kang JH, Wang M, Hu FB, Willett WC, Okereke OI, Eliassen AH, Kraft P, Stampfer MJ, Wang DD |
Nature medicine |
40855194 |
Nat Med |
2025 Nov |
https://www.ncbi.nlm.nih.gov/pubmed/40855194 |
| Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions. |
Zhang Y, Wang DD |
Gut microbes |
41845564 |
Gut Microbes |
2026 Dec 31 |
https://www.ncbi.nlm.nih.gov/pubmed/41845564 |
| Optimizing methods for virome analysis based on studies of a synthetic viral community. |
Duan J, Marques AD, Hogenauer M, Hwang Y, Zhang Y, Timperman A, Higgins S, Wilson NG, Fitts EA, Lim HK, Bittinger K, Moustafa AM, Collman RG, Bushman FD |
bioRxiv : the preprint server for biology |
41278782 |
bioRxiv |
2025 Oct 23 |
https://www.ncbi.nlm.nih.gov/pubmed/41278782 |
| Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction. |
Merenstein C, Litichevskiy L, Thaiss C, Collman RG, Bushman FD |
Microbiome |
41772715 |
Microbiome |
2026 Mar 3 |
https://www.ncbi.nlm.nih.gov/pubmed/41772715 |
| Optimizing methods for virome analysis based on studies of a synthetic viral community. |
Duan J, Marques AD, Hogenauer M, Hwang Y, Zhang Y, Timperman A, Higgins S, Wilson NG, Fitts EA, Lim HK, Bittinger K, Moustafa AM, Collman RG, Bushman FD |
mSystems |
42227741 |
mSystems |
2026 Jun 23 |
https://www.ncbi.nlm.nih.gov/pubmed/42227741 |
| DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics. |
Hillary LS, Knotts TA, Adams SH, Ali MR, Olm MR, Emerson JB |
bioRxiv : the preprint server for biology |
41394752 |
bioRxiv |
2025 Nov 26 |
https://www.ncbi.nlm.nih.gov/pubmed/41394752 |
| DNA Viral Size Fraction Metagenomics for Human Stool Samples. |
Denison ER, Hillary LS, Bolanos HA, Anagu HI, Emerson JB |
Journal of visualized experiments : JoVE |
41973723 |
J Vis Exp |
2026 Mar 24 |
https://www.ncbi.nlm.nih.gov/pubmed/41973723 |
| A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions. |
Camargo AP, Baltoumas FA, Ndela EO, Fiamenghi MB, Merrill BD, Carter MM, Pinto Y, Chakraborty M, Andreeva A, Ghiotto G, Shaw J, Proal AD, Sonnenburg JL, Bhatt AS, Roux S, Pavlopoulos GA, Nayfach S, Kyrpides NC |
bioRxiv : the preprint server for biology |
41279291 |
bioRxiv |
2025 Nov 2 |
https://www.ncbi.nlm.nih.gov/pubmed/41279291 |
| Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes. |
Fiamenghi MB, Camargo AP, Chasapi IN, Baltoumas FA, Roux S, Egorov AA, Aplakidou E, Ndela EO, Vasquez YM, Chen IA, Palaniappan K, Reddy TBK, Mukherjee S, Ivanova NN, Schulz F, Woyke T, Eloe-Fadrosh EA, Pavlopoulos GA, Kyrpides NC |
Nucleic acids research |
41312645 |
Nucleic Acids Res |
2026 Jan 6 |
https://www.ncbi.nlm.nih.gov/pubmed/41312645 |
| Viral Load Measurements for Kaposi Sarcoma Herpesvirus (KSHV/HHV8): Review and an Updated Assay. |
Cano P, Seltzer T, Seltzer J, Peng A, Landis J, Pluta L, Dittmer DP |
Journal of medical virology |
39648698 |
J Med Virol |
2024 Dec |
https://www.ncbi.nlm.nih.gov/pubmed/39648698 |
| Protocol for large-scale, high-yield, high-purity extracellular vesicle purification from human plasma. |
Zanganeh S, Arias GF, Cone AS, Yuan R, Dittmer DP |
STAR protocols |
41818236 |
STAR Protoc |
2026 Mar 20 |
https://www.ncbi.nlm.nih.gov/pubmed/41818236 |
| Session Introduction: Biological molecular function: methods and benchmarks for finding function in biological dark matter. |
McDermott JE, Bromberg Y, Carter H, Wheeler T |
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing |
41758157 |
Pac Symp Biocomput |
2026 |
https://www.ncbi.nlm.nih.gov/pubmed/41758157 |
| Differential microbial community assembly following co-housing versus microbiota transplant. |
Weagley JS, Chica Cárdenas LA, Romani A, Sullender ME, Aggarwal S, Makimaa H, Hogarty MP, Rodgers R, Kennedy EA, Foster L, Schriefer LA, Baldridge MT |
The ISME journal |
41247324 |
ISME J |
2025 Jan 2 |
https://www.ncbi.nlm.nih.gov/pubmed/41247324 |
| Dynamics of Bacterial and Viral Transmission in Experimental Microbiota Transplantation. |
Weagley JS, Cárdenas LAC, Romani A, Sullender ME, Aggarwal S, Makimaa H, Hogarty MP, Rodgers R, Kennedy EA, Foster L, Schriefer LA, Baldridge MT |
bioRxiv : the preprint server for biology |
39868290 |
bioRxiv |
2025 May 7 |
https://www.ncbi.nlm.nih.gov/pubmed/39868290 |
| Single cell viral tagging of Faecalibacterium prausnitzii reveals rare bacteriophages omitted by other techniques. |
Campbell DE, Wu X, Hall LR, Lawrence D, Molleston JM, Schriefer LA, Droit L, Weagley JS, Olson BS, Rimmer J, Parkes M, Handley SA, Baldridge MT |
Gut microbes |
40754853 |
Gut Microbes |
2025 Dec |
https://www.ncbi.nlm.nih.gov/pubmed/40754853 |
| Dietary fat disrupts a commensal-host lipid network that promotes metabolic health. |
Klag K, Ott D, Tippetts TS, Nicolson RJ, Tatum SM, Bauer KM, Stephen-Victor E, Weis AM, Bell R, Weagley J, Maschek JA, Vu DL, Heaver S, Ley R, O'Connell R, Holland WL, Summers SA, Stephens WZ, Round JL |
Cell metabolism |
41197631 |
Cell Metab |
2026 Jan 6 |
https://www.ncbi.nlm.nih.gov/pubmed/41197631 |
| Clec12a controls colitis by tempering inflammation and restricting expansion of specific commensals. |
Chiaro TR, Greenewood M, Bauer KM, Ost KS, Stephen-Victor E, Murphy M, Weis AM, Nelson MC, Hill JH, Bell R, Voth W, Jackson T, Klag KA, O'Connell RM, Zac Stephens W, Round JL |
Cell host & microbe |
39788099 |
Cell Host Microbe |
2025 Jan 8 |
https://www.ncbi.nlm.nih.gov/pubmed/39788099 |
| Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing. |
Abay T, Stickels RR, Takizawa MT, Nalbant BN, Hsieh YH, Hwang S, Snopkowski C, Yu KKH, Abou-Mrad Z, Tabar V, Howitt BE, Ludwig LS, Chaligné R, Satpathy AT, Lareau CA |
Nature genetics |
39779958 |
Nat Genet |
2025 Feb |
https://www.ncbi.nlm.nih.gov/pubmed/39779958 |
| Cell type-specific purifying selection of synonymous mitochondrial DNA variation. |
Lareau CA, Maschmeyer P, Yin Y, Gutierrez JC, Dhindsa RS, Gribling-Burrer AS, Zielinski S, Hsieh YH, Nitsch L, Dimitrova V, Nalbant B, Buquicchio FA, Abay T, Stickels RR, Ulirsch JC, Yan P, Wang F, Miao Z, Sandor K, Daniel B, Liu V, Mendez PL, Knaus P, Meyer M, Greenleaf WJ, Kundaje A, Smyth RP, Munschauer M, Ludwig LS, Satpathy AT |
Proceedings of the National Academy of Sciences of the United States of America |
40705423 |
Proc Natl Acad Sci U S A |
2025 Jul 29 |
https://www.ncbi.nlm.nih.gov/pubmed/40705423 |
| Clonal lineage tracing of innate immune cells in human cancer. |
Liu V, Sandor K, Yan PK, Miao M, Yin Y, Stickels RR, Chen AY, Hiam-Galvez K, Gutierrez J, Zhang W, Sajjath SM, Valbuena R, Wang S, Dániel B, Ludwig LS, Howitt BE, Lareau C, Satpathy AT |
bioRxiv : the preprint server for biology |
40777278 |
bioRxiv |
2025 Jul 21 |
https://www.ncbi.nlm.nih.gov/pubmed/40777278 |
| Population-scale sequencing resolves determinants of persistent EBV DNA. |
Nyeo SS, Cumming EM, Burren OS, Pagadala MS, Gutierrez JC, Ali TA, Kida LC, Chen Y, Chu H, Hu F, Zou XZ, Hollis B, Fabre MA, MacArthur S, Wang Q, Ludwig LS, Dey KK, Petrovski S, Dhindsa RS, Lareau CA |
Nature |
41606327 |
Nature |
2026 Feb |
https://www.ncbi.nlm.nih.gov/pubmed/41606327 |
| Functionally dominant hotspot mutations of mitochondrial ribosomal RNA genes in cancer. |
Boscenco S, Tait-Mulder J, Kim M, Tang C, Park T, McNulty F, Lilla S, Zanivan S, Huerta-Uribe A, Nalbant B, Zucker M, Sumpton D, Monteuuis G, Jackson CB, Wei W, Chinnery PF, Chaligne R, Lareau CA, Reznik E, Gammage PA |
Nature genetics |
41184543 |
Nat Genet |
2025 Nov |
https://www.ncbi.nlm.nih.gov/pubmed/41184543 |
| CAR-engineered lymphocyte persistence is governed by a FAS ligand-FAS autoregulatory circuit. |
Yi F, Cohen T, Zimmerman N, Dündar F, Zumbo P, Eltilib R, Brophy EJ, Arkin H, Feucht J, Gormally MV, Hackett CS, Kropp KN, Etxeberria I, Chandran SS, Zhao Z, Cai W, Daniyan AF, Park JH, Lareau CA, Hsu KC, Sadelain M, Betel D, Klebanoff CA |
Nature cancer |
40696154 |
Nat Cancer |
2025 Oct |
https://www.ncbi.nlm.nih.gov/pubmed/40696154 |
| Population-scale sequencing resolves correlates and determinants of latent Epstein-Barr Virus infection. |
Nyeo SS, Cumming EM, Burren OS, Pagadala MS, Gutierrez JC, Ali TA, Kida LC, Chen Y, Hu F, Hollis B, Fabre M, MacArthur S, Wang Q, Ludwig LS, Dey KK, Petrovski S, Dhindsa RS, Lareau CA |
bioRxiv : the preprint server for biology |
40791404 |
bioRxiv |
2025 Jul 18 |
https://www.ncbi.nlm.nih.gov/pubmed/40791404 |
