Nirmalya Dasgupta
Lab Ay
Paramita Dutta
Lily Martinez
Laura Hinojosa
Kyra Fetter
Ferhat Ay
Jack Cloud
Cemil Can Ali Marandi
Daniela Salgado Figueroa
Dante Bolzan
Emre Unalan
Bolutito Babatunde
Abhijit Chakraborty
Scalable steady state analysis of Boolean biological regulatory networks.
A fast and accurate algorithm for comparative analysis of metabolic pathways
Identification of functional elements and regulatory circuits by Drosophila modENCODE
SubMAP: Aligning metabolic pathways with subnetwork mappings.
Metabolic Network Alignment in Large Scale by Network Compression.
Predictive regulatory models in Drosophila Melanogaster by integrative inference of transcriptional networks.
Genomic interaction profiles in breast cancer reveal altered chromatin architecture.
Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome.
Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
A statistical approach for inferring the 3D structure of the genome.
Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression
Accurate identification of centromere locations in yeast genomes using Hi-C
Comprehensive identification and analysis of human accelerated regulatory DNA
Analysis methods for studying the 3D architecture of the genome
Topologically-associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication timing program
Bipartite structure of the inactive mouse X chromosome
A predictive modeling approach for cell line-specific long-range regulatory interactions
A multitask graph-clustering approach for chomosome conformation capture data sets identifies conserved modules of chromosomal interactions
Neocentromeres provide chromosome segregation accuracy and centromere clustering to multiple loci along a candida albicans chromosome
Form and function of topologically associating genomic domains in budding yeast
Identification of copy number variations and translocations in cancer cells from Hi-C data
Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria
PacBio assembly of a plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family
Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
The Evf2 ultraconserved enhancer lncRNA functionally and spatially organizes megabase distant genes in the developing forebrain
Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Integrative detection and analysis of structural variation in cancer genomes
Identifying cis elements for spatiotemporal control of mammalian DNA replication
Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer
Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies
Measuring the reproducibility and quality of Hi-C data
Comparative 3D genome organization in apicomplexan parasites
The role of 3D genome organization in disease: From compartments to single nucleotides
Selfish: discovery of differential chromatin interactions via a self-similarity measure
Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
Reduced expression of phosphatase PTPN2 promotes pathogenic conversion of Tregs in autoimmunity
Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
Safety and immunogenicity of th tetravalent, live-attenuated dengue vaccine Butantan-DV in adults in Brazil: a two-step, double-blind, randomized placebo-controlled phase 2 trial
Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2
Single-Cell Transcriptomic Analysis of SARS-CoV-2 Reactive CD4 + T Cells
TL1A Promotes Lung Tissue Fibrosis and Airway Remodeling
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants.
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.
Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8+ T cells.
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.
The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway.
Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus.
A comparison of the different anthropometric indices for assessing malnutrition among older people in Turkey: a large population-based screening.
Sox2-Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain.
ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs.
Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy.
Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.
COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types.
Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type–dependent effects of disease-risk variants
Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants
Pluriptency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture
Intermittent PI3Kδ inhibition sustains anti-tumour immunity and curbs irAEs
Human eosinophils express a distinct gene expression program in response to IL-3 compared with common β-chain cytokines IL-5 and GM-CSF
3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma
Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft
MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing.
Brd2 is dispensable for genome compartmentalization and replication timing
17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells.
Integrative Keratinocyte Responses to TWEAK with IL-13 and IL-22 Reveal Pathogenic Transcriptomes Associated with Atopic Dermatitis
Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS
Atypical B cells consist of subsets with distinct functional profiles
LIGHT signaling through LTβR and HVEM in keratinocytes promotes psoriasis and atopic dermatitis-like skin inflammation
Chromatin structure and var2csa – a tango in regulation of var gene expression in the human malaria parasite, Plasmodium falciparum?
LJI scientists develop new method to match genes to their molecular ‘switches’
New research may help scientists hunt down solid tumors and better diagnose disease
No IKAROS, no antibodies
Researchers map the genome to figure out how a protein called IKAROS controls healthy B cell development
LJI kicks off partnership with San Diego’s Fleet Science Center
Fleet's Sharp Minds lecture series to feature immune system experts
Skin diseases are painful enough. They don’t need to be medical mysteries
Local student partners with LJI's Ferhat Ay, Ph.D., to explore skin disease diagnostics
A new window into autoimmune diseases
LJI scientists uncover coordinated immune cell activity as a driver of systemic lupus erythematosus
The Conrad Prebys Foundation grants more than $450,000 for studies into childhood cancer, cardiovascular disease
New funding will support high-risk, high-reward projects led by two early-career scientists
Long days, bus rides and a high schooler’s bioinformatics breakthrough
San Diego high school student Jeffrey Wang spearheads LJI research project, receiving national recognition as Regeneron Science Talent Search finalist
LJI asthma researcher Jermaine Khumalo receives AAI Intersect Fellowship
New fellowship will support data science and immunology cross-training in two pioneering LJI labs
New 3D maps reveal inner workings of immune cell gene expression
LJI scientists track down control elements that govern gene expression from a distance
Genome structure of malaria parasites linked to virulence
Findings could help develop novel therapeutic strategies to combat malaria
