Biology subjects

Deshpande, D.

Publications and source records attributed to Deshpande, D..

8 recordsLinked to original sources

bioRxiv2025

Robust software development practices improve citations of RNA-seq tools

RNA sequencing (RNA-seq) has emerged as an exemplary technology in biology and clinical applications, offering a crucial complement to other transcriptomic profiling protocols due to its high sensitivity, precision, and accuracy in characterizing transcriptomes. However, the rapid proliferation of RNA-seq tools necessitates the adoption of robust software development practices. Such development underscores the critical need to examine how RNA-seq tools are developed, maintained, and distributed; and whether the data they generate is reproducible as all of these factors are essential for ensuring software reliability, transparency, and trust in scientific findings. We conducted a comprehensive assessment of 434 RNA-seq tools developed between 2008 and 2024, categorizing them based on the type of analysis they perform. Our evaluation encompassed their software development and distribution methodologies, as well as the attributes contributing to their widespread adoption and dependability within the biomedical community, which were quantified by factors such as package manager availability, containerization, multithreading support, documentation quality, and inclusion of example datasets. Our findings establish the first documented positive association between rigorous software development practices and their adoption of published RNA-seq tools as measured by citations (Mann-Whitney U test, p-value = 4.9 x 10-26). By identifying key characteristics of widely adopted software, our findings guide developing robust and user-friendly RNA-seq tools, thereby reinforcing the call for rigorous community-wide standards.

bioinformatics↗

bioRxiv2025

Tigecycline pharmacodynamics in the hollow fiber system of Mycobacterium avium-complex lung disease, and the utility of MICs and time-kill studies in drug development

BackgroundGuideline-based therapy (GBT) drugs for Mycobacterium avium-complex (MAC) lung disease (LD) were chosen in part because they have low MICs. Despite these low MICs, GBT achieves six-month sustained sputum culture conversion in only 43% of patients. MethodsFirst, we co-incubated tigecycline with MAC for seven days in time-kill studies and calculated the exposure mediating 50% of maximal effect (Emax) or EC50. Next, we performed tigecycline exposure-effect studies in the hollow fiber system of MAC (HFS-MAC) inoculated with the reference ATCC#700898 isolate. Third, we performed an exposure-effect study in the HFS-MAC inoculated with 5 different isolates. Finally, the target exposure (EC80) was used to identify a clinical dose of inhaled tigecycline for MAC-LD in 10,000 subject Monte Carlo experiments (MCE). ResultsIn time-kill studies the EC50 was 0-24h area under the concentration-time curve-to-MIC (AUC0-24/MIC) of 62.24 for extracellular and 0.14 for intracellular MAC (p<0.001). In the HFS-MAC inoculated with ATCC#700898, the EC50 statistically differed between sampling days by 2,370.7%. However, studies with five different isolates demonstrated a stable and robust day-to-day EC50 (%CV=18.18%), with an EC80 AUC0-24/MIC of 33.65. The Emax was 4.84 log10 CFU/mL. In MCE, tigecycline inhalational doses of 35-40 mg/day achieved the EC80 target in >90% of virtual patients, with and an MIC breakpoint of 256 mg/L. ConclusionTime-kill studies do not inform on PK/PD target exposures or extent of kill. Inclusion of multiple MAC isolates in HFS-MAC studies improves precision of pharmacokinetic/pharmacodynamic parameter estimates. Tigecycline via the inhalational route could contribute to treatment of MAC-LD.

pharmacology and toxicology↗

bioRxiv2025

Systematic and quantitative analyses of pre-clinical Mycobacterium avium Lung Disease Tools for Drug Development and Transition from Animal Models to New Approach Methodologies

Animal and new approach methodologies such as the hollow fiber system model [HFS] are used for Mycobacterium avium-complex [MAC] lung disease [LD] preclinical drug development. Our objective was to perform a systematic review to benchmark these pre-clinical tools. We performed a literature search to identify preclinical pharmacokinetics/pharmacodynamics [PK/PD] studies for MAC-LD. Preferred Reporting Items for Systematic Reviews and Meta-analyses was used for bias minimization. Twenty HFS-MAC and 3 mouse studies met PK/PD inclusion criteria. We created a novel quality score tool based on predictors of clinical response, design optimization, and information theory. The quality score was judged high in 10%, good in 50%, adequate in 30%, and poor in 10% of studies. Monte Carlo experiments for PK/PD target attainment were reported in 61% of studies. On repetitive sampling, the PK/PD target exposure estimate varied significantly between sampling days in 76% of studies. The solution was ordinary differential equations with parameter outputs such as {gamma} [nonlinear kill-slope] and time-to-extinction applied to both HFS-MAC and patients sputa CFU/mL output. Next, we ranked the antibiotics by extent of microbial kill as fold-improvement over guideline-based therapy. The three top ranked drugs for microbial kill were omadacycline [69-fold], tedizolid [19-fold], and ceftriaxone [8-fold]. We recommend the HFS-MAC as tractable for exposure-effect and dose-fractionation studies, ranking antibiotics effect, and for translation to clinical doses. The analyses inform us of HFS-MAC recommendations for regulatory authorities and drug developers, including quality scores for optimal PK/PD design for target identification, resistance suppression, and choice of the best novel regimen.

pharmacology and toxicology↗

bioRxiv2025

Assessing genomic reproducibility of read alignment tools

Genomic research relies on accurate and reproducible computational analyses of DNA sequencing data to draw reliable biological conclusions. Read mapping, the process of aligning reads to a reference genome, is central to many applications, including variant detection and comparative genomics. While several tools have been developed for this task, genomic reproducibility1, defined as the consistency of results across replicates, remains underexplored. Here, we address this question by introducing a methodology based on synthetic replicates of sequencing data, generated by perturbing the original reads through shuffling, reverse complementing, or combined shuffling and reverse complementing. Our approach is able to simulate variability observed across sequencing runs due to differences in library preparation techniques. We evaluated the reproducibility of eight alignment tools (BWA-MEM22, Bowtie23, HISAT24, minimap25, NextGenMap6, SNAP7, SMALT7,8 and Subread9) under these perturbations using whole-genome sequencing (WGS) data. Synthetic replicates were aligned and compared to the original sample to quantify discrepancies. Mapping accuracy changes ranged from 0.0001% to 4.4% for primary reads, which are alignments not marked as secondary, supplementary, or duplicates, and up to 12.2% for high-quality primary reads. For primary reads, the percentage of reads commonly mapped in both the original and synthetic replicate ranged from 91.66% to 100% relative to the total number of mapped reads in the original dataset. High-quality filtering improved consistency, though some tools still failed to recover more than 70% of the original alignments. Within the set of common reads, the incidence of inconsistent mappings was as high as 13.53% for primary reads and 6.73% for high-quality primary reads. Bowtie 2 was fully reproducible under the shuffling replicate, Subread was fully reproducible under the reverse-complement replicate, whereas NextGenMap exhibited only minor inconsistencies. By contrast, SNAP and minimap2 displayed the most significant variability under reverse complementing. We further demonstrate that alignment inconsistencies propagate to the downstream task of calling structural genomic variants. Using Manta for structural-variant (SV) calling, we observed that Bowtie 2, HISAT2, and minimap2 maintained perfect SV concordance between original and replicate alignments, whereas other tools exhibited lower concordance, with Subread scoring only 87% concordance. In conclusion, our comprehensive evaluation demonstrates that synthetic perturbations reveal critical differences in how alignment tools handle technical variability and how these differences propagate to downstream variant analyses, underscoring the necessity of incorporating reproducibility benchmarks into the selection and validation of read mappers to ensure robust and reliable genomic interpretations.

bioinformatics↗

bioRxiv2023

Analytical code sharing practices in biomedical research

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71x10-9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10-07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

scientific communication and education↗

bioRxiv2022

CLARITY increases sensitivity and specificity of fluorescence immunostaining in long-term archived human brain tissue

Immunohistochemistry on archival human brains is often limited because several conditions arise that complicate the use for high-resolution fluorescence microscopy. In this study, we developed a novel clearing approach for immunofluorescence-based analysis of perfusion- and immersion-fixed post mortem human brain tissue, termed hCLARITY. hCLARITY is optimized for specificity by reducing off-target labeling and yields very sensitive stainings in human brain sections allowing for super-resolution microscopy with unprecedented imaging of pre- and postsynaptic compartments. Moreover, hallmarks of the Alzheimers disease were preserved with hCLARITY, and importantly classical DAB or Nissl stainings are compatible with this protocol. hCLARITY is extremely versatile as demonstrated by the use of more than 30 well performing antibodies and allows for de- and subsequent re-staining of the same tissue section, which is important for multi-labelling approaches, e.g., in super-resolution microscopy. Taken together, hCLARITY enables research of the human brain with highest sensitivity and down to sub-diffraction resolution and therefore has enormous potential for the investigation of local morphological changes, e.g., in neurodegenerative diseases. Striking Image / Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/489700v1_ufig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@1732df2org.highwire.dtl.DTLVardef@cda615org.highwire.dtl.DTLVardef@152b44aorg.highwire.dtl.DTLVardef@ba972a_HPS_FORMAT_FIGEXP M_FIG Summary of the main advantages of hCLARITY. CLARITY was applied on human post mortem brain tissue in direct comparison to untreated sections (minus CLARITY). Owing to removal of lipids during the clearing with SDS and the resulting reduction in light scattering, cleared sections were less opaque. The denaturing effect of the detergent SDS most likely results in better accessibility of certain epitopes. The major benefits of hCLARITY were found in an increased sensitivity and specificity of antibodies for neuronal cells. The adapted hCLARITY protocol is compatible with staining techniques for confocal microscopy, super-resolution microscopy, and light microscopy. C_FIG

neuroscience↗

bioRxiv2022

Novel tuberculosis combination regimens of two and three-months therapy duration

The tuberculosis treatment duration is 4-6 months, but can be 18-20 months with multidrug resistance. Ultrashort regimens that cure regardless of resistance status ["pan-tuberculosis regimens"] would be a major step towards global tuberculosis control. Starting with seven drugs [bedaquiline, delamanid, pretomanid, OPC-167832, sutezolid, moxifloxacin, and pyrazinamide] in clinical testing, we calculated that there were thousands of possible novel combinations to evaluate. We used mathematical and pharmacokinetics/pharmacodynamic-based hollow fiber modeling to reduce this complexity to nine combinations, which we tested. Each regimens fast and slow growth bacteria kill-slope trajectories and times-to-extinction were estimated and translated to minimum required therapy duration in patients. Sputum microbial kill trajectories of two combination regimens that have undergone clinical testing were correctly predicted by this approach. Four pan-tuberculosis regimens were predicted to achieve relapse-free cure after 2-3 months therapy in patients. The kill-slopes were used to design expedited clinical trials that minimize patients risks.

pharmacology and toxicology↗

bioRxiv2020

Shank2 expression identifies a subpopulation of glycinergic interneurons involved in nociception and altered in an autism mouse model

Patients suffering from Autism Spectrum Disorders (ASD) experience disturbed nociception in form of either hyposensitivity to pain or hypersensitivity and allodynia. We have determined that Shank2-KO mice, which recapitulate the genetic and behavioural disturbances of ASD, display increased sensitivity to formalin pain and thermal, but not mechanical allodynia. We demonstrate that high levels of Shank2 expression identifies a subpopulation of neurons in murine and human dorsal spinal cord, composed mainly by glycinergic interneurons and that loss of Shank2 causes the decrease in NMDAR in excitatory synapses on these inhibitory interneurons. In fact, in the subacute phase of the formalin test, glycinergic interneurons are strongly activated in WT mice but not in Shank2-KO mice. As consequence, nociception projection neurons in lamina I are activated in larger numbers in Shank2-KO mice. Our findings prove that Shank2 expression identifies a new subset of inhibitory interneurons involved in reducing the transmission of nociceptive stimuli and whose unchecked activation is associated with pain hypersensitivity. Thus, we provide evidence that dysfunction of spinal cord pain processing circuits may underlie the nociceptive phenotypes in ASD patients and mouse models.

neuroscience↗