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improved phased assembly software ipa (Pacific Biosciences)

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Pacific Biosciences improved phased assembly software ipa
Improved Phased Assembly Software Ipa, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/ipa+software/application+assembly+microbial+software/pm41507790-102-8-13
Average 86 stars, based on 1 article reviews

improved phased assembly software ipa - by Bioz Stars, 2026-09

86/100 stars

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Article Title: Construction of a reference genome for Starmerella batistae and annotation of Starmerella species reveal an unexpected evolutionary relationship with Schizosaccharomyces pombe and suggest an alternative enzymatic route for sophorolipid production.
Article Snippet: .. CCS reads were assembled using the PacBio assembler 474 algorithm’s Improved Phased Assembly (IPA v1.8.0) method (available at 475 https://github.com/PacificBiosciences/pbipa.git). .. To confirm that our strain is a haploid, 476 pbmm2 v1.10.0 (available at https://github.com/PacificBiosciences/pbmm2), a SMRT C++ 477 wrapper for minimap2’s C API, was used to index the reference genomes and align the se-478 quencing reads to the references.

Article Title: Comparison of whole genome sequencing approaches for Capripox viruses
Article Snippet: .. Alternatively, de-novo assembly was performed directly with the Improved Phased Assembly software IPA ( https://github.com/PacificBiosciences/pbipa ) without host removal or with Canu after removing cattle reads. ..

Article Title: Comparison of whole genome sequencing approaches for Capripox viruses.
Article Snippet: .. Alternatively, de-novo assembly was performed directly with the Improved Phased Assembly software IPA (https://github.com/PacificBiosciences/pbipa) without host removal or with Canu after removing cattle reads. ..

Article Title: Whole-genome sequence of the African Common Reed Frog (Hyperolius viridiflavus viridiflavus) from Ethiopia.
Article Snippet: .. Two other genome assembly pipelines were also used: the Improved 20 Phased Assembler (IPA) from PacBio software (v1.3.1; 21 https://github.com/PacificBiosciences/pbipa) and Canu (Koren, et al., 2017). ..

Article Title: Whole-genome sequence of the African Common Reed Frog ( Hyperolius viridiflavus viridiflavus ) from Ethiopia
Article Snippet: .. Two other genome assembly pipelines were also used: the Improved Phased Assembler (IPA) from PacBio software (v1.3.1; https://github.com/PacificBiosciences/pbipa ) and Canu ( ). ..

Software:

Article Title: First Report of KPC-2-Producing Hafnia paralvei: Evidence of Horizontal Gene Transfer from Klebsiella pneumoniae .
Article Snippet: For molecular epidemiological analysis, genomic DNA was extracted using the Maxwell RSC Tissue DNA Kit (Promega, Madison, WI, USA) and whole-genome sequencing (WGS) was conducted by Macrogen (Seoul, Korea) using the PacBio Sequel IIe platform (Pacific Biosciences, Menlo Park, CA, USA). .. Genome assembly and annotation were performed using the Microbial Genome Analysis pipeline (Pacific Biosciences, Menlo Park, CA, USA) and PROKKA software, respectively. ..

Article Title: Biological and Genomic Characterization of Two Astaxanthin-Producing Paracoccus marcusii Isolates as a Potential Source for Food Additives
Article Snippet: Genomic DNA was extracted from the isolates using the QIAamp DNA Mimi Kit (Qiagen), and the extracted DNA was sequenced using a hybrid approach that combined the PacBio Sequel System (Pacific Biosciences, USA) with a 20-kb SMRTbell template library and the Illumina HiSeq X-10 platform (Illumina, USA).The TruSeq Nano DNA Library Prep Kit (Illumina) was used for library preparation. .. The long-read sequences generated by the PacBio Sequel System were assembled using the Microbial Assembly Application software (Pacific Biosciences), and the resulting assembly was polished using Illumina paired-end reads to improve the accuracy of the genome sequence. ..

Construct:

Article Title: Application of Long-Read Whole-Genome Sequencing to Clarify Genotypic-Phenotypic Discrepancies in Methicillin-Resistant Staphylococcus aureus .
Article Snippet: Whole-genome sequencing was performed using a Revio system (Pacific Biosciences, Menlo Park, CA, USA), a single-molecule real-time (SMRT) sequencing platform, to generate high-fidelity long reads. .. De novo assembly was performed using the Microbial Genome Analysis application (SMRTLINK v25.1; Pacific Biosciences) to construct circularized contiguous sequences. .. To ensure genomic integrity, the assembly was refined using Inspector v1.0.1 (Johns Hopkins University, Baltimore, MD, USA) to detect and correct structural errors.

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GSEA of KEGG pathways and canonical pathways analysis in the DRG tissues post-surgery. Ranked by NES score, the selected six of top 20 enriched KEGG pathways were the Adherens Junction (a), JAK-STAT (d), NOD like receptor (g), Apoptosis (j), WNT (m), and MAPK (p) signaling pathways. The heat maps showing the dynamic expression of the core enrichment genes involved in these signaling pathways (b, e, h, k, n, q). The PPI network shows the interaction of the proteins involved in the above signaling pathways (c, f, i, l, o, r). The enrichment heat-map showing the dynamic activity of canonical pathways at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (s). Each pathway is depicted with a pseudo color (orange for an activated pathway with positive Z-score ≥2, blue for an inhibited pathway with negative Z-score ≤−2, and spot for a non-active pathway with −2 ≤ Z-score ≤2). The canonical pathways were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: GSEA of KEGG pathways and canonical pathways analysis in the DRG tissues post-surgery. Ranked by NES score, the selected six of top 20 enriched KEGG pathways were the Adherens Junction (a), JAK-STAT (d), NOD like receptor (g), Apoptosis (j), WNT (m), and MAPK (p) signaling pathways. The heat maps showing the dynamic expression of the core enrichment genes involved in these signaling pathways (b, e, h, k, n, q). The PPI network shows the interaction of the proteins involved in the above signaling pathways (c, f, i, l, o, r). The enrichment heat-map showing the dynamic activity of canonical pathways at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (s). Each pathway is depicted with a pseudo color (orange for an activated pathway with positive Z-score ≥2, blue for an inhibited pathway with negative Z-score ≤−2, and spot for a non-active pathway with −2 ≤ Z-score ≤2). The canonical pathways were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Protein-Protein interactions, Expressing, Activity Assay

GSEA of GO biological process gene sets in the DRG tissues post-surgery. Ranked by NES score, the selected six of top 20 enriched GO biological process gene sets were nitric oxide mediated transduction (a), central nervous system neuron axongenesis (c), positive regulation of epithelial mesenchymal transition (e), regulation of JNK cascade (j), regulation of cellular response to insulin stimulus (i), and maintenance of blood brain barrier (k). The heatmaps showing the dynamic expression of the core enrichment genes involved in these GO biological process gene sets (b, d, f, h, j, l). The enrichment heat-map showing the dynamic activity of diseases and functions at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (m). Each disease and function are depicted with a pseudo color (orange for an activated disease and function with positive Z-score ≥2, blue for an inhibited disease and function with negative Z-score ≤−2, and spot for a non-active disease and function with −2 ≤ Z-score ≤2). The diseases and functions were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: GSEA of GO biological process gene sets in the DRG tissues post-surgery. Ranked by NES score, the selected six of top 20 enriched GO biological process gene sets were nitric oxide mediated transduction (a), central nervous system neuron axongenesis (c), positive regulation of epithelial mesenchymal transition (e), regulation of JNK cascade (j), regulation of cellular response to insulin stimulus (i), and maintenance of blood brain barrier (k). The heatmaps showing the dynamic expression of the core enrichment genes involved in these GO biological process gene sets (b, d, f, h, j, l). The enrichment heat-map showing the dynamic activity of diseases and functions at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (m). Each disease and function are depicted with a pseudo color (orange for an activated disease and function with positive Z-score ≥2, blue for an inhibited disease and function with negative Z-score ≤−2, and spot for a non-active disease and function with −2 ≤ Z-score ≤2). The diseases and functions were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Transduction, Expressing, Activity Assay

GSEA of GO cellular component, molecular function, and upstream regulators prediction in the DRG tissues post-surgery. Ranked by NES score, the selected three of top 20 enriched GO cellular component gene sets were cytoplasmic stress granule (a), P body (c), actin-based cell projection (e), the selected three of top 20 enriched GO molecular function gene sets were ATPase binding (g), kinase inhibitor activity (i), and Smad binding (k). The heatmaps showing the dynamic expression of the core enrichment genes involved in these GO cellular component (b, d, f) and molecular function (h, j, l) gene sets. The enrichment heatmap showing the predicted upstream regulators at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (m). Each predicted upstream regulator is depicted with a pseudo color (orange for an activated upstream regulator with positive Z-score ≥2, blue for an inhibited upstream regulator with negative Z-score ≤−2, and spot for a non-active upstream regulator with −2 ≤ Z-score ≤2). The predicted upstream regulators were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: GSEA of GO cellular component, molecular function, and upstream regulators prediction in the DRG tissues post-surgery. Ranked by NES score, the selected three of top 20 enriched GO cellular component gene sets were cytoplasmic stress granule (a), P body (c), actin-based cell projection (e), the selected three of top 20 enriched GO molecular function gene sets were ATPase binding (g), kinase inhibitor activity (i), and Smad binding (k). The heatmaps showing the dynamic expression of the core enrichment genes involved in these GO cellular component (b, d, f) and molecular function (h, j, l) gene sets. The enrichment heatmap showing the predicted upstream regulators at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (m). Each predicted upstream regulator is depicted with a pseudo color (orange for an activated upstream regulator with positive Z-score ≥2, blue for an inhibited upstream regulator with negative Z-score ≤−2, and spot for a non-active upstream regulator with −2 ≤ Z-score ≤2). The predicted upstream regulators were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Binding Assay, Activity Assay, Expressing

The impact of DRG neuron axonal promotion via SKP-SCs. (a) Schematic illustration of DRG neurons culture in vitro. The cultured DRG neurons for 20 h and 40 h (b) showed increased neurite outgrowth. Scale bar: 50 μm. (c) The β-Tubulin III cell immunofluorescent staining (red) showed neurites are undergoing a process of growth in length from 48 h to 96 h. Scale bar: 50 μm. Schematic illustration showed the direct (d) and in-direct (Transwell®) (e) co-culture of DRG neurons and SKP-SCs. (h) After direct co-culture 48 h, GFP-SKP-SCs promoted DRGs neurite outgrowth significantly compared to control group (i). (k) After in-direct co-culture 72 h, GFP-SKP-SCs promoted DRGs neurite outgrowth (j) significantly compared to control group (g). Scale bar: 50 μm for f, g, i, j. (l) Morphological changes under phase contrast microscopy in DRG neurons and SKP-SCs direct co-culture, DRG neurons in separate culture, and in-direct (Transwell®) co-culture of DRG neurons and SKP-SCs after 24 h, 48 h, and 72 h. Scale bar: 100 μm. (m) Schematic illustration of LC-MS/MS analysis to identify the secreted proteins from SKP-SCs cultured in serum free basic medium for 4 h. After concentration, the cleared conditioned medium was collected for LC-MS/MS analysis, database search, and protein identification. The enrichment analysis showed top 20 diseases and functions (n) and canonical pathways (o) according to the IPA database. The PPI network shows the interaction of the proteins involved in the functions highly correlated with regeneration (p). Among them, functions as formation of lamellipodia, extension of neurites, extension of cellular protrusions, and related proteins were highlighted (q). Functions as migration of endothelial cells, development of endothelial tissue, vasculogenesis, development of epithelial tissue, endothelial cell development, and related proteins were highlighted (r). Orange nodes stand for a predicted activation state. Blue nodes stand for a predicted inhibition state. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: The impact of DRG neuron axonal promotion via SKP-SCs. (a) Schematic illustration of DRG neurons culture in vitro. The cultured DRG neurons for 20 h and 40 h (b) showed increased neurite outgrowth. Scale bar: 50 μm. (c) The β-Tubulin III cell immunofluorescent staining (red) showed neurites are undergoing a process of growth in length from 48 h to 96 h. Scale bar: 50 μm. Schematic illustration showed the direct (d) and in-direct (Transwell®) (e) co-culture of DRG neurons and SKP-SCs. (h) After direct co-culture 48 h, GFP-SKP-SCs promoted DRGs neurite outgrowth significantly compared to control group (i). (k) After in-direct co-culture 72 h, GFP-SKP-SCs promoted DRGs neurite outgrowth (j) significantly compared to control group (g). Scale bar: 50 μm for f, g, i, j. (l) Morphological changes under phase contrast microscopy in DRG neurons and SKP-SCs direct co-culture, DRG neurons in separate culture, and in-direct (Transwell®) co-culture of DRG neurons and SKP-SCs after 24 h, 48 h, and 72 h. Scale bar: 100 μm. (m) Schematic illustration of LC-MS/MS analysis to identify the secreted proteins from SKP-SCs cultured in serum free basic medium for 4 h. After concentration, the cleared conditioned medium was collected for LC-MS/MS analysis, database search, and protein identification. The enrichment analysis showed top 20 diseases and functions (n) and canonical pathways (o) according to the IPA database. The PPI network shows the interaction of the proteins involved in the functions highly correlated with regeneration (p). Among them, functions as formation of lamellipodia, extension of neurites, extension of cellular protrusions, and related proteins were highlighted (q). Functions as migration of endothelial cells, development of endothelial tissue, vasculogenesis, development of epithelial tissue, endothelial cell development, and related proteins were highlighted (r). Orange nodes stand for a predicted activation state. Blue nodes stand for a predicted inhibition state. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: In Vitro, Cell Culture, Staining, Co-Culture Assay, Control, Microscopy, Liquid Chromatography with Mass Spectroscopy, Concentration Assay, Migration, Activation Assay, Inhibition

The transcriptional alteration of DRG neurons co-cultured with SKP-SCs. (a) Representative images of phase contrast microscopy of SKP-SCs in the upper chamber and lower ventricular DRG neurons after 48 h co-culture. Scale bar: 100 μm. (b) Schematic illustration of transcriptional analysis of lower ventricular DRG neurons for 48 h co-culture, and bioinformatics. The enrichment analysis showed top 20 diseases and functions (c) and canonical pathways (d) according to the IPA database. The PPI network shows the interaction of the key proteins involved in the functions highly correlated with regeneration (e). Up-regulated EGR2 (red) was selected to show multi-functions highly correlated with neuroregeneration (f). The interaction network of downstream regulators of EGR2, its downstream up-regulated (red) genes and down-regulated (green) proteins and their functions (g). Orange nodes stand for a predicted activation state. Blue nodes stand for a predicted inhibition state. Color intensity of the nodes in networks were proportional to differentially expression level. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: The transcriptional alteration of DRG neurons co-cultured with SKP-SCs. (a) Representative images of phase contrast microscopy of SKP-SCs in the upper chamber and lower ventricular DRG neurons after 48 h co-culture. Scale bar: 100 μm. (b) Schematic illustration of transcriptional analysis of lower ventricular DRG neurons for 48 h co-culture, and bioinformatics. The enrichment analysis showed top 20 diseases and functions (c) and canonical pathways (d) according to the IPA database. The PPI network shows the interaction of the key proteins involved in the functions highly correlated with regeneration (e). Up-regulated EGR2 (red) was selected to show multi-functions highly correlated with neuroregeneration (f). The interaction network of downstream regulators of EGR2, its downstream up-regulated (red) genes and down-regulated (green) proteins and their functions (g). Orange nodes stand for a predicted activation state. Blue nodes stand for a predicted inhibition state. Color intensity of the nodes in networks were proportional to differentially expression level. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Cell Culture, Microscopy, Co-Culture Assay, Activation Assay, Inhibition, Expressing

Purified CD4 + T cells from HDs ( n = 3) and patients with acute ATL ( n = 5) were stimulated with anti-CD3 and anti-CD28 in presence of IL-2 for 4 hours at 37°C. The cells were harvested and subjected to scRNA-seq. ( A ) Schematic representation of the experimental setup for ( B to H ). Created in BioRender. S. Roy (2025) https://BioRender.com/9zdi679 . (B) Uniform Manifold Approximation and Projection (UMAP) plot showing all cells split by HD cells (left) and ATL cells (right). (C) Bar plot showing proportion of the cells in each cluster annotated by Azimuth for each HD and ATL sample. (D) UMAP plot showing distribution of T reg cells split by HD cells (left) and ATL cells (right). (E) Violin plot showing PRDM1 expression in T reg cells in HDs and patients with ATL. (F) UMAP plot showing distribution of PRDM1 − versus PRDM1 + T reg populations in HDs and patients with ATL. (G) Pie chart showing percentage of cells in HDs and patients with ATL that express any amount of PRDM1 . (H) Bar plot showing top pathways (by z score) from Qiagen IPA using differentially expressed genes derived from PRDM1 − versus PRDM1 + populations within T reg cells cluster in patients with ATL.

Journal: Science Advances

Article Title: BLIMP1 negatively regulates IL-2 signaling in T cells

doi: 10.1126/sciadv.adx8105

Figure Lengend Snippet: Purified CD4 + T cells from HDs ( n = 3) and patients with acute ATL ( n = 5) were stimulated with anti-CD3 and anti-CD28 in presence of IL-2 for 4 hours at 37°C. The cells were harvested and subjected to scRNA-seq. ( A ) Schematic representation of the experimental setup for ( B to H ). Created in BioRender. S. Roy (2025) https://BioRender.com/9zdi679 . (B) Uniform Manifold Approximation and Projection (UMAP) plot showing all cells split by HD cells (left) and ATL cells (right). (C) Bar plot showing proportion of the cells in each cluster annotated by Azimuth for each HD and ATL sample. (D) UMAP plot showing distribution of T reg cells split by HD cells (left) and ATL cells (right). (E) Violin plot showing PRDM1 expression in T reg cells in HDs and patients with ATL. (F) UMAP plot showing distribution of PRDM1 − versus PRDM1 + T reg populations in HDs and patients with ATL. (G) Pie chart showing percentage of cells in HDs and patients with ATL that express any amount of PRDM1 . (H) Bar plot showing top pathways (by z score) from Qiagen IPA using differentially expressed genes derived from PRDM1 − versus PRDM1 + populations within T reg cells cluster in patients with ATL.

Article Snippet: Pathway enrichment analyses were conducted using Qiagen IPA software (QIAGEN Inc., https://digitalinsights.qiagen.com/IPA ) version 107193442 ( ).

Techniques: Purification, Expressing, Derivative Assay

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