Biology subjects

Li, J. H.

Publications and source records attributed to Li, J. H..

15 recordsLinked to original sources

bioRxiv2026

GeneBench-Pro: Evaluating Multistage Statistical Reasoning\\in Genomics, Quantitative Biology, and Translational Biomedicine

We introduce GeneBench-Pro, an expanded and improved version of GeneBench that comprises harder problems across a wider breadth of domains. GeneBench-Pro is a benchmark for AI agents performing realistic multi-stage scientific analyses in genomics, quantitative biology, and translational biomedicine which seeks to capture the complexity of real-world problems that computational life scientists face when tasked with producing a conclusion upon which a downstream scientific or translational decision is contingent. The benchmark comprises 129 evaluations targeting quantities of direct practical relevance across 10 primary domains and 21 terminal subdomains, with a genomics-centered core. Similarly to GeneBench, each problem provides the agent with brief context, a target estimand, and minimal guidance otherwise; the agent must then navigate multiple dependent decision points; i.e., substantive inferential forks where a plausible wrong choice changes the downstream analysis, to identify and execute the correct analysis workflow and arrive at the correct answer. Relative to GeneBench, GeneBench-Pro adds 29 new problems, drops three, and introduces significantly redesigned versions of 54 of the remaining 100 overlapping problems. 82 of the 129 problems were reviewed by external domain experts, whose findings led to prompt/data modifications and redesign of those problems whose targets were not sufficiently identifiable. Ten externally reviewed problems are released publicly, 50 held-out problems were provided to Artificial Analysis for independent third-party model benchmarking, and the remainder are retained as an internal holdout. In evaluations over the full 129-problem suite, GPT-5.6 Sol reaches an eval-level pass rate of 28.7% at the max reasoning level, and GPT-5.6 Sol Pro reaches 31.5% in separately reported GPT Pro runs. GPT-5.5 reaches 12.0%, GPT-5.4 reaches 8.9%, and the strongest non-GPT baseline, Claude Opus 4.8, reaches 16.0%. As with GeneBench, models often complete substantial portions of the workflow but exhibit a consistent gap between noticing and acting by identifying local diagnostic signals but failing to propagate the implications to the corresponding analysis decision. As a result, models often select wrong estimators or persist on initially plausible but incorrect analysis paths. GeneBench-Pro therefore measures an emerging capability of long-horizon biological reasoning that remains unreliable. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=46 SRC="FIGDIR/small/735386v4_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@191f09org.highwire.dtl.DTLVardef@144943borg.highwire.dtl.DTLVardef@15fba72org.highwire.dtl.DTLVardef@1c9c65c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Mitochondrial Retrograde Signaling in Arabidopsis thaliana: heterogenous, spatial and polarised aspects

Organelle retrograde signaling studies have exclusively relied on bulk tissues, obscuring cell-type specificity, spatial organization, and heterogeneity within cell types. Here, we use single-nucleus and spatial RNA sequencing to define the cellular and spatial architecture of mitochondrial stress signaling in Arabidopsis thaliana. Inhibition of the mitochondrial electron transport chain by antimycin A and myxothiazol rapidly redistributed nuclei among transcriptional states within epidermal, leaf pavement, and mesophyll lineages, revealing that mitochondrial dysfunction reshapes cell identity trajectories rather than eliciting a uniform response. Stress-associated clusters were already present at low frequency in untreated samples, but the numbers of cells increased following stress treatments, indicating that stress increases the proportion of nuclei occupying pre-existing, primed transcriptional states. Gene-level analyses revealed distinct temporal dynamics and variable cell-state penetrance of the canonical mitochondrial stress markers and identified broadly responsive genes absent from earlier marker sets. Spatial transcriptomics resolved tissue-scale responses, spanning from pan-tissue induction to cell-type- and cluster-restricted activation, and uncovered pronounced adaxial-abaxial polarity in gene expression. Cell identity and spatial inferences were supported by extensive experimental validation using a custom 465-probe 10x Xenium panel and 52 promoter-GFP reporter lines. Together, these data provide a high-resolution framework for organelle-to-nucleus signaling and a resource of cell-type markers and spatial maps to dissect mitochondrial stress signaling and its integration with developmental and environmental pathways.

plant biology↗

bioRxiv2024

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms

BackgroundUnderstanding the genetic causes for variability in chromatin accessibility can shed light on the molecular mechanisms through which genetic variants may affect complex traits. Thousands of ATAC-seq samples have been collected that hold information about chromatin accessibility across diverse cell types and contexts, but most of these are not paired with genetic information and come from diverse distinct projects and laboratories. ResultsWe report here joint genotyping, chromatin accessibility peak calling, and discovery of quantitative trait loci which influence chromatin accessibility (caQTLs), demonstrating the capability of performing caQTL analysis on a large scale in a diverse sample set without pre-existing genotype information. Using 10,293 profiling samples representing 1,454 unique donor individuals across 653 studies from public databases, we catalog 23,381 caQTLs in total. After joint discovery analysis, we cluster samples based on accessible chromatin profiles to identify context-specific caQTLs. We find that caQTLs are strongly enriched for annotations of gene regulatory elements across diverse cell types and tissues and are often strongly linked with genetic variation associated with changes in expression (eQTLs), indicating that caQTLs can mediate genetic effects on gene expression. We demonstrate sharing of causal variants for chromatin accessibility and diverse complex human traits, enabling a more complete picture of the genetic mechanisms underlying complex human phenotypes. ConclusionsOur work provides a proof of principle for caQTL calling from previously ungenotyped samples, and represents one of the largest, most diverse caQTL resources currently available, informing mechanisms of genetic regulation of gene expression and contribution to disease.

genomics↗

bioRxiv2024

A comparison between low-cost library preparation kits for low coverage sequencing

In the fields of human health and agricultural research, low coverage whole-genome sequencing followed by imputation to a large haplotype reference panel has emerged as a cost-effective alternative to genotyping arrays for assaying large numbers of samples. However, a systematic comparison of library preparation methods tailored for low coverage sequencing remains absent in the existing literature. In this study, we evaluated one full sized kit from IDT and miniaturized and evaluated three Illumina-compatible library preparation kits--the KAPA HyperPlus kit (Roche), the DNA Prep kit (Illumina), and an IDT kit--using 96 human DNA samples. Metrics evaluated included imputation concordance with high-depth genotypes, coverage, duplication rates, time for library preparation, and additional optimization requirements. Despite slightly elevated duplication rates in IDT kits, we find that all four kits perform well in terms of imputation accuracy, with IDT kits being only marginally less performant than Illumina and Roche kits. Laboratory handling of the kits was similar: thus, the choice of a kit will largely depend on (1) existing or planned infrastructure, such as liquid handling capabilities, (2) whether a specific characteristic is desired, such as the use of full-length adapters, shorter processing times, or (3) use case, for instance, long vs short read sequencing. Our findings offer a comprehensive resource for both commercial and research workflows of low-cost library preparation methods suitable for high-throughput low coverage whole genome sequencing.

genomics↗

bioRxiv2023

Membrane to cortex attachment determines different mechanical phenotypes in LGR5+ and LGR5- colorectal cancer cells

Colorectal cancer tumors are composed of heterogeneous and plastic cell populations, including a pool of cancer stem cells that express LGR5. Whether these distinct cell populations display different mechanical properties, and how these properties might contribute to metastasis is unknown. Using CRC patient derived organoids (PDOs), we found that compared to LGR5- cells, LGR5+ cancer stem cells are stiffer, adhere better to the extracellular matrix (ECM), move slower both as single cells and clusters, display higher nuclear YAP, show a higher survival rate in response to mechanical confinement, and form larger transendothelial gaps. These differences are largely explained by the downregulation of the membrane to cortex attachment proteins Ezrin/Radixin/Moesin (ERMs) in the LGR5+ cells. By analyzing scRNA-seq expression patterns from a patient cohort, we show that this downregulation is a robust signature of colorectal tumors. Our results show that LGR5- cells display a mechanically dynamic phenotype suitable for dissemination from the primary tumor whereas LGR5+ cells display a mechanically stable and resilient phenotype suitable for extravasation and metastatic growth.

cancer biology↗

bioRxiv2023

The effects of reference panel perturbations on the accuracy of genotype imputation

Reference-based genotype imputation is a standard technique that has become increasingly popular in large-scale studies involving genomic data. The two key elements involved in the process of genotype imputation are (1) the haplotype reference panel to which a target individual is being imputed, and (2) the imputation algorithm used to infer missing genotypes in the target individual. The imputation literature has historically focused mainly on (2), with a typical comparative study investigating the relative performance of various imputation algorithms while holding the reference panel constant. However, the role of the reference panel itself (1) on overall imputation performance is equally, if not more, important than the choice among many high-performing algorithms. Even though it is intuitive that the quality of a reference panel should play a role in the accuracy of imputation, it is nonetheless unclear to what extent common errors during panel creation (e.g., genotyping and phase error) lead to suboptimal imputation performance. In this study, we investigate the effects of applying three distinct modes of perturbations to a widely used haplotype reference panel in human genetics on the resulting imputation accuracy. Specifically, we perturb the reference panel by (1) randomly introducing phase errors, (2) randomly introducing genotype errors, and (3) randomly pruning variants from the panel (all at varying magnitudes). We then impute a set of diverse individuals at various sequencing coverages (0.5x, 1.0x, and 2.0x) to these various perturbed panels and evaluate imputation accuracy using the r2 metric for the entire cohort as well as ancestry-stratified subsets. We observe that both phase- and genotype-perturbations can dramatically affect imputation accuracy, particularly at very low allele frequencies, while pruning variants has a far smaller effect. We then empirically verified that our simulations reliably predict the impact of potential filtering techniques in a real-world dataset. In the context of haplotype reference panels, these results suggest that phasing and genotyping accuracy are far more important than the density of a reference panel used for imputation.

genomics↗

bioRxiv2022

Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates

Low-pass sequencing with genotype imputation has been adopted as a cost-effective method for genotyping. The most widely used method of short-read sequencing uses sequencing by synthesis (SBS). Here we perform a study of a novel sequencing technology -- avidity sequencing. In this short note, we compare the performance of imputation from low-pass libraries sequenced on an Element AVITI system (which utilizes avidity sequencing) to those sequenced on an Illumina NovaSeq 6000 (which utilizes SBS) with an SP flow cell for the same set of biological samples across a range of genetic ancestries. We observed dramatically lower duplication rates in the data deriving from the AVITI system compared to the NovaSeq 6000, resulting in higher effective coverage given a fixed number of sequenced bases, and comparable imputation accuracy performance between sequencing chemistries across ancestries. This study demonstrates that avidity sequencing is a viable alternative to the standard SBS chemistries for applications involving low-pass sequencing plus imputation.

genomics↗

bioRxiv2022

Sex differences in NK cells mediated by the X-linked epigenetic regulator UTX

Viral infection outcomes are sex-biased, with males generally more susceptible than females. Paradoxically, the numbers of anti-viral natural killer (NK) cells are increased in males compared to females. Using samples from mice and humans, we demonstrate that while numbers of male NK cells are increased compared to females, they display impaired production of the anti-viral cytokine IFN-{gamma}. These sex differences were not due solely to divergent levels of gonadal hormones, since these differences persisted in gonadectomized mice. Instead, these differences can be attributed to lower male expression of X-linked Kdm6a (UTX), an epigenetic regulator which escapes X inactivation in female NK cells. NK cell-specific UTX deletion in females phenocopied multiple features of male NK cells, which include increased numbers and reduced IFN-{gamma} production. Integrative ATAC-seq and RNA-seq analysis revealed a critical role for UTX in the regulation of chromatin accessibility and gene expression at loci important in NK cell homeostasis and effector function. Consequently, NK cell-intrinsic UTX levels are critical for optimal anti-viral immunity, since mice with NK cell-intrinsic UTX deficiency show increased lethality to mouse cytomegalovirus (MCMV) challenge. Taken together, these data implicate UTX as a critical molecular determinant of NK cell sex differences and suggest enhancing UTX function as a new strategy to boost endogenous NK cell anti-viral responses.

immunology↗

bioRxiv2020

Relative matching using low coverage sequencing

Finding familial relatives using DNA has multiple applications, in genetic genealogy, population genetics, and forensics. So far, most relative matching algorithms rely on detecting identity-by-descent (IBD) segments with high quality genotype data. Recently, low coverage sequencing (LCS) has received growing attention as a promising cost-effective method to ascertain genomic information. However, with higher error rates, it is unclear whether existing IBD detection can work on LCS datasets. Here, we developed and tested a framework for relative matching using sequencing with 1x coverage (1xLCS). We started by exploring the error characteristics of this method compared to array data. Our results show that after some optimization 1xLCS can exhibit the same genotyping discordance rates as the discordance between two array platforms. Using this observation, we developed a hybrid framework for relative matching and tuned this framework with >2,700 pairs of confirmed genealogical relatives that were genotyped using heterogenous datasets. We then obtained array and 1xLCS on 19 samples and use our framework to find relatives in a database of over 3 million individuals. The total length of shared segments obtained by 1xLCS was virtually indistinguishable to genotyping arrays for matches with a total sharing >200cM (second cousins or closer). For more distant relatives, as long as those were detected by both technologies, the total length obtained by LCS and by genotyping arrays was highly correlated, with no evidence of over- or underestimation. Taken together, our results show that 1xLCS can be a valid alternative to arrays for relative matching, opening the possibility for further democratization of genomic data.

bioinformatics↗

bioRxiv2020

Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

Low-pass sequencing (sequencing a genome to an average depth less than 1 coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5x and 1x) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave-one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ~ 0.5x and higher compared to the Illumina GSA.

genomics↗

bioRxiv2020

Directed manipulation of membrane proteins by fluorescent magnetic nanoparticles

The plasma membrane is the interface through which cells interact with their environment. Membrane proteins are embedded in the lipid bilayer of the plasma membrane and their function in this context is often linked to their specific location and dynamics within the membrane. However, few methods are available for nanoscale manipulation of membrane protein location at the single molecule level. Here, we report the use of fluorescent magnetic nanoparticles (FMNPs) to track membrane molecules and to manipulate their movement. FMNPs allow single-particle tracking (SPT) at 10 nm spatial and 5 ms temporal resolution, and using a magnetic needle, we pull membrane components laterally through the membrane with femtonewton-range forces. In this way, we successfully dragged lipid-anchored and transmembrane proteins over the surface of living cells. Doing so, we detected submembrane barriers and in combination with super-resolution microscopy could localize these barriers to the actin cytoskeleton. We present here a versatile approach to probe membrane processes in live cells via the magnetic control of membrane protein motion.

biophysics↗

bioRxiv2019

Transient Receptor Potential Ankyrin 1 Mediates Afferent Signals in the Inflammatory Reflex

Survival of an organism requires mechanisms to sense damaging factors in the environment. In mammals, bacterial toxins and inflammatory mediators stimulate nociceptive sensory neurons to activate protective reflexes. Whereas the vagus nerve reflex circuit that protects against damaging inflammation, termed the "inflammatory reflex," was described more than twenty years ago1,2, how the vagus nerve detects inflammation to initiate the inflammatory reflex has remained unknown. Here we show that transient receptor potential ankyrin 1 (TRPA1) in sensory vagus neurons is required to sense interleukin-1{beta} (IL-1{beta}), a central cytokine mediator of inflammation and injury. Selective activation of vagus nerve TRPA1 using optopharmacology stimulated the inflammatory reflex to inhibit innate inflammatory responses to bacterial lipopolysaccharide and IL-1{beta}. Proximity ligation assay and immunohistochemistry revealed that IL-1 receptors are co-expressed with TRPA1 in vagus sensory neurons. Whole-cell patch-clamp recordings reveal that TRPA1 is required to mediate IL-1{beta}-dependent depolarization of vagus sensory neurons. Further, TRPA1-deficient mice lack inflammatory reflex attenuation of inflammation, fail to restrain cytokine release, and have significantly enhanced lethality to bacterial sepsis. Therefore, vagus neurons expressing TRPA1 are necessary and sufficient to activate the sensory arc of the inflammatory reflex to protect against harmful inflammation.

physiology↗

bioRxiv2019

Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics

Low pass sequencing has been proposed as a cost-effective alternative to genotyping arrays to identify genetic variants that influence multifactorial traits in humans. For common diseases this typically has required both large sample sizes and comprehensive variant discovery. Genotyping arrays are also routinely used to perform pharmacogenetic (PGx) experiments where sample sizes are likely to be significantly smaller, but clinically relevant effect sizes likely to be larger. To assess how low pass sequencing would compare to array based genotyping for PGx we compared a low-pass assay (in which 1x coverage or less of a target genome is sequenced) along with software for genotype imputation to standard approaches. We sequenced 79 individuals to 1x genome coverage and genotyped the same samples on the Affymetrix Axiom Biobank Precision Medicine Research Array (PMRA). We then down-sampled the sequencing data to 0.8x, 0.6x, and 0.4x coverage, and performed imputation. Both the genotype data and the sequencing data were further used to impute human leukocyte antigen (HLA) genotypes for all samples. We compared the sequencing data and the genotyping array data in terms of four metrics: overall concordance, concordance at single nucleotide polymorphisms in pharmacogenetics-related genes, concordance in imputed HLA genotypes, and imputation r2. Overall concordance between the two assays ranged from 98.2% (for 0.4x coverage sequencing) to 99.2% (for 1x coverage sequencing), with qualitatively similar numbers for the subsets of variants most important in pharmacogenetics. At common single nucleotide polymorphisms (SNPs), the mean imputation r2 from the genotyping array was 90%, which was comparable to the imputation r2 from 0.4x coverage sequencing, while the mean imputation r2 from 1x sequencing data was 96%. These results indicate that low-pass sequencing to a depth above 0.4x coverage attains higher power for trait mapping when compared to the PMRA.

genetics↗

bioRxiv2018

Influence of food and Nosema ceranae infection on the gut microbiota of Apis cerana workers

BackgroundGut microbiota plays an essential role in bees health. To elucidate the effect of food and Nosema ceranae infection on the gut microbiota of honeybee Apis cerana, we used 16S rRNA sequencing to survey the gut microbiota of honeybee workers fed with sugar water or beebread and inoculated with or without N. ceranae.\n\nResultsThe gut microbiota of A. cerana is dominated by Serratia, Snodgrassella, and Lactobacillus genera. The overall gut microbiota diversity was significantly differential by food type. The N. ceranae infection significantly affects the gut microbiota only at bees fed with sugar water. Higher abundance of Lactobacillus, Gluconacetobacter and Snodgrassella and lower abundance of Serratia were found in bees fed with beebread than with sugar water. N. ceranae infection led to higher abundance of Snodgrassella and lower abundance of Serratia in sugar-fed bees. Imputed bacterial KEGG pathways showed the significant metagenomics functional differences by feeding and N. ceranae infections. Furthermore, A. cerana workers fed with sugar water showed lower N. ceranae spore loads but higher mortality than those fed with beebread. The cumulative mortality was strongly positive correlated (rho=0.61) with the changes of overall microbiota dissimilarities by N. ceranae infection.\n\nConclusionsBoth food and N. ceranae infection significantly affect the gut microbiota in A. cerana workers. Beebread feeding not only provide better nutrition but also help establish a more stabled gut microbiota therefore protect bee in response to N. ceranae infection.\n\nAbstract ImportanceGut microbiota plays an essential role in bees health. Scientific evidence suggests the diet and infection can affect the gut microbiota and modulate the gut health, however the interplay between those two factors and bee gut microbiota is not well known. In this study, we used high-throughput sequencing method to monitor the changes of gut microbiota by both food intake and the Nosema ceranae infection. Our result showed that the gut microbiota composition and diversity of Asia Honeybee was significantly associated with both food intake and the N. ceranae infection. More interestingly, bees fed with beebread showed higher microbiota stability and less mortality than those fed with sugar water when infected by N. ceranae. Those data suggest the potential role of beebread, not only providing better nutrition but also helping establish a more stabled gut microbiota to protect bee against N. ceranae infection.

microbiology↗

bioRxiv2018

Comparison of human and murine enteroendocrine cells by transcriptomic and peptidomic profiling

Enteroendocrine cells (EECs) produce hormones that regulate food absorption, insulin secretion and appetite. Both EECs and their peptide products are foci of drug discovery programmes for diabetes and obesity. We compared the human and mouse EEC transcriptome and peptidome to validate mouse as a model of the human enteroendocrine axis. We present the first RNA sequencing analysis of human EECs, and demonstrate strong correlation with mouse, although with outliers including some low abundance G-protein coupled receptors. Liquid chromatography mass spectrometry (LC-MS) identified peptide hormone gradients along the human and mouse gut that should enhance progress in gut physiology and therapeutics.

cell biology↗