https://www.minot.bio/home daily 1.0 2025-02-11 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1498005626277-RHNGTY2E2S2CYDNMPU5U/IMG_20170527_132148.jpg Home https://www.minot.bio/home/2025/2/11/publish-interactive-data-visualizations-for-free-with-python-and-marimo monthly 0.5 2025-02-14 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/b9e5d3b5-f24a-4b98-b7c4-9eb4fd71b875/screenshot2.gif Home - Publish Interactive Data Visualizations for Free with Python and Marimo - Make it stand out Click on the image to open the app for yourself https://www.minot.bio/home/2023/4/19/specific-host-metabolite-and-gut-microbiome-alterations-are-associated-with-bone-loss-during-spaceflight monthly 0.5 2023-04-19 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/d6a69367-210c-4f2b-a205-134992a17ac7/Screen+Shot+2023-04-19+at+8.31.13+AM.png Home - Specific host metabolite and gut microbiome alterations are associated with bone loss during spaceflight - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.minot.bio/home/2023/3/29/practical-reproducibility-in-bioinformatics monthly 0.5 2023-03-29 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/f68c36bb-1090-4363-a235-00b55c94ecc3/Practical+reproducibility+in+bioinformatics+%28link Home - Practical Reproducibility in Bioinformatics - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.minot.bio/home/2022/9/15/python-based-data-viz-with-no-installation-required monthly 0.5 2022-09-15 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/f7879f9c-7e66-406a-9551-84410a4a2d54/demo-screenshot.png Home - Python-Based Data Viz (With No Installation Required) - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.minot.bio/home/2022/7/15/dispatches-from-the-microbial-frontier-of-cancer-research monthly 0.5 2022-07-15 https://www.minot.bio/home/2021/12/14/microbial-pan-genome-cartography monthly 0.5 2021-12-18 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1eaab25d-f1be-4c3c-b6f9-f38958fa95b2/image-asset.png Home - Microbial Pan-Genome Cartography - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.minot.bio/home/2021/4/17/looking-under-the-lamppost-reference-genomes-in-metagenomics monthly 0.5 2021-04-19 https://www.minot.bio/home/2021/3/1/whats-big-about-small-proteins monthly 0.5 2021-03-01 https://www.minot.bio/home/2021/1/9/whats-the-matter-with-recombination monthly 0.5 2021-01-09 https://www.minot.bio/home/2020/10/16/geneshot-identifying-microbial-genes-associated-with-human-health-and-disease monthly 0.5 2020-10-16 https://www.minot.bio/home/2020/8/5/zarr-taking-the-headache-out-of-massive-datasets monthly 0.5 2020-08-05 https://www.minot.bio/home/2020/3/25/automating-your-code monthly 0.5 2020-03-25 https://www.minot.bio/home/2019/11/25/quality-and-insights-nbspthe-human-gut-virome-in-2019 monthly 0.5 2019-11-25 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1574708476058-2VNFV3YMC74P6IEDLRTA/1-s2.0-S1931312819305335-fx1_lrg.jpg Home - Quality and Insights – The Human Gut Virome in 2019 https://www.minot.bio/home/2019/10/4/shiny-microbiome-analysis monthly 0.5 2019-10-05 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1570209550530-S79IRCKJP3SUCKO3BS0S/Screen+Shot+2019-10-04+at+10.18.37+AM.png Home - Shiny Microbiome Analysis https://www.minot.bio/home/microbiomesurveys monthly 0.5 2019-09-18 https://www.minot.bio/home/2019/7/9/3d-structures-of-gut-bacteria-and-the-human-immune-system monthly 0.5 2019-07-09 https://www.minot.bio/home/2019/5/14/brown-2019-bacteroides-sphingolipids monthly 0.5 2019-05-14 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1557834090953-FXNTSR34PPA7TI8VBVQR/1-s2.0-S1931312819302057-fx1_lrg.jpg Home - Molecules Mediating Microbial Manipulation of Mouse (and Human) Maladies https://www.minot.bio/home/2019/5/7/working-with-nextflow-at-fred-hutch monthly 0.5 2019-05-07 https://www.minot.bio/home/2019/4/14/public-posting-for-slides monthly 0.5 2019-04-14 https://www.minot.bio/home/2019/3/4/minot-willis-cags-2019 monthly 0.5 2019-03-06 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1551745601347-OPKRYLZOJ0C7DB2IQ5RK/Fig2a.png Home - Preprint: Identifying genes in the human microbiome that are reproducibly associated with human disease Figure 2A: Association of microbial CAGs with host CRC across two independent cohorts. https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1551745733950-QJ5XOJPMMTKPWO3ZSEHN/Fig3c.png Home - Preprint: Identifying genes in the human microbiome that are reproducibly associated with human disease Figure 3C: Presence of CRC-associated genes across a subset of microbial isolates in RefSeq. Color bar shows coefficient of correlation with CRC. https://www.minot.bio/home/2019/2/25/bioinformatics-reproducibility-portability-transparency-and-technical-debt monthly 0.5 2019-02-25 https://www.minot.bio/home/2019/1/18/massive-unexplored-genetic-diversity-of-the-human-microbiome monthly 0.5 2019-01-18 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1547831287501-L3VURYANPEHIEVSD8N9G/graphical_abstract.jpg Home - Massive unexplored genetic diversity of the human microbiome https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1547831386423-G7L3QP56ARTCODZPF0JG/gr1.jpg Home - Massive unexplored genetic diversity of the human microbiome https://www.minot.bio/home/2018/12/13/quick-note-on-workflow-managers monthly 0.5 2018-12-13 https://www.minot.bio/home/2018/11/6/the-blessing-and-the-curse-of-dimensionality monthly 0.5 2018-11-06 https://www.minot.bio/home/2018/9/22/the-rise-of-the-machines-workflow-managers-for-bioinformatics monthly 0.5 2018-09-25 https://www.minot.bio/home/2018/9/20/niche-theory-and-the-human-gut-microbiome monthly 0.5 2018-09-20 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1537480495560-9PMH1VXRRC1LQ12AXOJI/1-s2.0-S0092867418311024-fx1_lrg.jpg Home - Niche Theory and the Human Gut Microbiome https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1537480535663-ZWMFZRZIK9IZ000KGPPS/1-s2.0-S0092867418311085-fx1_lrg.jpg Home - Niche Theory and the Human Gut Microbiome https://www.minot.bio/home/2018/8/21/microbiome-research-hope-over-hype monthly 0.5 2018-08-21 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1534876811722-EQZVE54EH1QULDIKG4HK/Screen+Shot+2018-08-21+at+11.39.53+AM.png Home - Microbiome Research: Hope over Hype Fig. 5: A microbial choline TMA lyase inhibitor reverses diet-induced changes in cecal microbial community composition associated with plasma TMAO levels, platelet responsiveness, and in vivo thrombosis potential. Schematic of the relationship between human gut commensal choline TMA lyase activity, TMA and TMAO generation, and enhanced platelet responsiveness and thrombosis risk in the host https://www.minot.bio/home/2018/7/6/update-on-making-cags-or-the-importance-of-good-software monthly 0.5 2018-07-07 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1530922245478-9ZJ71HMFWD2SQLS8V18A/68747470733a2f2f7261772e6769746875622e636f6d2f73706f746966792f616e6e6f792f6d61737465722f616e6e2e706e67.png Home - Update on Making CAGs, or The Importance of Good Software Annoy (Approximate Nearest Neighbors Oh Yeah) https://www.minot.bio/home/2018/5/25/hybrid-approach-to-microbiome-research-to-culture-and-not-to-culture monthly 0.5 2018-05-25 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1527275849713-98DTE8ZDIYRLQMIUVIUJ/13073_2017_490_Fig3.gif Home - Hybrid Approach to Microbiome Research (to Culture, and Not to Culture) Fig. 3: R. gnavus metagenomic strain phylogeny. https://www.minot.bio/home/2018/5/17/notes-on-identifying-co-abundant-genes monthly 0.5 2018-05-17 https://www.minot.bio/home/2018/4/12/tracking-outbreaks-with-whole-genome-sequencing monthly 0.5 2018-04-13 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1523637146184-VAAU9Y5U1KDFZ530PSA8/Screen+Shot+2018-04-13+at+9.28.06+AM.png Home - Tracking outbreaks with whole-genome sequencing Overall view of 1262 isolates collected over 1 year in an ICU (Roach, et al. 2015) https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1523637236492-WF2V0UH0BKG37D440MYP/Screen+Shot+2018-04-13+at+9.31.47+AM.png Home - Tracking outbreaks with whole-genome sequencing Zoomed-in view of a clade including Acinetobacter (red), Haemophillus (green), Moraxella (teal), and Neisseria (blue). The rollover text shows metadata for sample 583, which was sampled from the same patient as its closest neighbor in the tree, sample 595. https://www.minot.bio/home/2018/4/4/famli monthly 0.5 2018-04-05 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1522877951837-APC8TYR28BEE6PE3JUGV/Fig+01+Schematic.png Home - Functional Analysis of Metagenomes by Likelihood Inference: FAMLI Illustration of the FAMLI algorithm https://www.minot.bio/home/2018/3/28/journal-club-graftm monthly 0.5 2018-03-28 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1522265804197-XUCF7HMTLBVKNWNN94C2/Screen+Shot+2018-03-28+at+12.36.25+PM.png Home - Journal Club: GraftM, a tool for scalable, phylogenetically informed classification of genes within metagenomes https://www.minot.bio/home/2018/2/15/detecting-viruses-from-short-read-metagenomic-data monthly 0.5 2018-02-16 https://www.minot.bio/home/slay-antimicrobial-peptides monthly 0.5 2018-01-26 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1517004041152-4HYF28LNPWXH39OFU7P2/fx1.jpg Home - Journal Club: Discovering new antibiotics with SLAY https://www.minot.bio/home/epigenetic-binning monthly 0.5 2018-01-03 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1515021746326-HAEQT2JZ9OUJS46HGLRS/Screen+Shot+2018-01-03+at+3.22.07+PM.png Home - Journal Club: Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation Figure 2c shows the binning of genome fragments in a sample containing a known mixture of bacteria. https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1515021800673-4K3CT5QOP37U3ZTCACE4/Screen+Shot+2018-01-03+at+3.23.05+PM.png Home - Journal Club: Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation Figure 2e shows the binning of genome fragments in a gut microbiome sample containing a mixture of unknown bacteria (and viruses, fungi, etc.). https://www.minot.bio/home/2017/11/20/bacterial-urease-in-crohns-disease monthly 0.5 2017-11-20 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1511218285822-BZKRLD2R46BAM4WDV8Q7/Screen+Shot+2017-11-20+at+2.51.12+PM.png Home - Journal Club: A role for bacterial urease in gut dysbiosis and Crohn’s disease Fig. 2. Associations between bacterial taxa abundance ascertained by fecal shotgun metagenomic sequencing and the fecal metabolome in healthy pediatric subjects and those with Crohn’s disease. https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1511218820841-BXU2KX2L8MYO7OVWWYN3/Screen+Shot+2017-11-20+at+2.59.43+PM.png Home - Journal Club: A role for bacterial urease in gut dysbiosis and Crohn’s disease Fig. 3. In vivo heavy isotope assays using 15N-labeled urea to determine the effect of bacterial urease on nitrogen flux in the murine gut microbiota. https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1511219229804-62B4342PPCF37SI7VARO/image-asset.png Home - Journal Club: A role for bacterial urease in gut dysbiosis and Crohn’s disease Fig. 6. Effect of E. coli urease on colitis in a T cell adoptive transfer mouse model of colitis https://www.minot.bio/home/2017/10/26/making-sparse-dataframes-efficiently monthly 0.5 2017-10-26 https://www.minot.bio/home/hmp-strain-variation monthly 0.5 2017-10-30 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1507310288892-4AM8ZLK89C2H1EBIJ15S/Fig1a Home - Journal Club: Strains, functions and dynamics in the expanded Human Microbiome Project Figure 1a: Personalization, niche association, and reference genome coverage in strain-level metagenomic profiles. a, Mean phylogenetic divergences17 between strains of species with sufficient coverage at each targeted body site (minimum 2 strain pairs) https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1507310987773-ZK5TMLU8MG2MTFC2BO0G/Fig1bde Home - Journal Club: Strains, functions and dynamics in the expanded Human Microbiome Project Figure 1, continued. b, Individuals tended to retain personalized strains, as visualized by a principal coordinates analysis (PCoA) plot for Actinomyces sp. oral taxon 448, in which lines connect samples from the same individual. d, PCoA showing niche association of Haemophilus parainfluenzae, showing subspecies specialization to three different body sites. e, PCoA for Eubacterium siraeum. https://www.minot.bio/home/gemcitabine-resistance monthly 0.5 2017-09-19 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1505766485781-LRHUXX151SFC37F72KU0/Geller2017.fig4.png Home - Journal Club: Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine Fig. 4. Characterization of bacteria in human pancreatic ductal adenocarcinomas. https://www.minot.bio/home/2017/7/21/joining-the-hutch monthly 0.5 2017-09-07 https://www.minot.bio/home/2017/8/28/journal-club-long-term-taxonomic-and-functional-divergence-from-donor-bacterial-strains-following-fecal-microbiota-transplantation-in-immunocompromised-patients monthly 0.5 2017-08-28 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1503938851484-O5EFXD58MXOIK1CL4IC5/journal.pone.0182585.g003.PNG Home - Journal Club: Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients Fig 3. The total gene complement of E. coli in Subject A experiences large-scale remodeling in association with FMT, resulting in broad reductions in genes significantly enriched for virulence factors. https://www.minot.bio/home/2017/7/21/journal-club-revised-computational-metagenomic-processing-uncovers-hidden-and-biologically-meaningful-functional-variation-in-the-human-microbiome monthly 0.5 2017-07-21 https://www.minot.bio/home/2017/7/20/journal-club-two-dynamic-regimes-in-the-human-gut-microbiome monthly 0.5 2017-07-20 https://www.minot.bio/home/category/Musings monthly 0.5 https://www.minot.bio/home/category/Journal+Club monthly 0.5 https://www.minot.bio/home/category/Publication monthly 0.5 https://www.minot.bio/home/category/Code+Discussion monthly 0.5 https://www.minot.bio/home/tag/visualization monthly 0.5 https://www.minot.bio/home/tag/software monthly 0.5 https://www.minot.bio/home/tag/methods monthly 0.5 https://www.minot.bio/home/tag/taxonomy monthly 0.5 https://www.minot.bio/home/tag/virome monthly 0.5 https://www.minot.bio/home/tag/pangenomes monthly 0.5 https://www.minot.bio/home/tag/diversity monthly 0.5 https://www.minot.bio/home/tag/metabolomics monthly 0.5 https://www.minot.bio/home/tag/phylogenetics monthly 0.5 https://www.minot.bio/home/tag/phage monthly 0.5 https://www.minot.bio/home/tag/cloud+computing monthly 0.5 https://www.minot.bio/home/tag/workflow+managers monthly 0.5 https://www.minot.bio/home/tag/marimo monthly 0.5 https://www.minot.bio/home/tag/python monthly 0.5 https://www.minot.bio/home/tag/viruses monthly 0.5 https://www.minot.bio/home/tag/metaproteomics monthly 0.5 https://www.minot.bio/home/tag/data+analysis monthly 0.5 https://www.minot.bio/home/tag/FMT monthly 0.5 https://www.minot.bio/home/tag/microbiome monthly 0.5 https://www.minot.bio/home/tag/inflammatory+bowel+disease monthly 0.5 https://www.minot.bio/home/tag/pandas monthly 0.5 https://www.minot.bio/home/tag/culture monthly 0.5 https://www.minot.bio/home/tag/metagenomics monthly 0.5 https://www.minot.bio/home/tag/bioinformatics monthly 0.5 https://www.minot.bio/home/tag/cancer monthly 0.5 https://www.minot.bio/home/tag/antibiotics monthly 0.5 https://www.minot.bio/home/tag/publications monthly 0.5 https://www.minot.bio/slides daily 0.75 2019-12-11 https://www.minot.bio/slides/2019/12/11/cmist-microbiome-club-dec-2019 monthly 0.5 2019-12-11 https://www.minot.bio/slides/2019/11/26/video-recording-of-nextflow-camp-2019 monthly 0.5 2019-11-26 https://www.minot.bio/slides/2019/9/18/nextflow-camp-2019 monthly 0.5 2019-09-18 https://www.minot.bio/slides/2019/5/7/may-7th-2019-nbspusing-nextflow-for-cloud-computing-at-fred-hutch monthly 0.5 2019-05-07 https://www.minot.bio/slides/2019/4/23/april-24th-2019-workflows-to-enable-scientific-cloud-computing monthly 0.5 2019-04-23 https://www.minot.bio/slides/2019/4/14/april-16th-2019-nbspfred-hutch-translational-data-science-irc monthly 0.5 2019-04-14 https://www.minot.bio/slides/category/Presentations monthly 0.5 https://www.minot.bio/slides/tag/cloud+computing monthly 0.5 https://www.minot.bio/slides/tag/nextflow monthly 0.5 https://www.minot.bio/slides/tag/workflow+managers monthly 0.5 https://www.minot.bio/about daily 0.75 2018-05-04 https://images.squarespace-cdn.com/content/v1/592c49ea15cf7dec0ae78267/1498002609220-R15IC2UG9K8KJXK9L3HA/image-asset.jpeg About https://www.minot.bio/publications daily 0.75 2020-10-21