Journal Clubs

Seminar

[Journal Club]February/05/2020

Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer / High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells

[Journal Club]January/29/2020

Phenotype molding of stromal cells in the lung tumor microenvironment / APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signalsI'm a news headline

[Journal Club]January/22/2020

Global Positioning System: Understanding Long Noncoding RNAs through Subcellular Localization. / Accurate annotation of human protein-coding small open reading frames

[Journal Club]January/8/2020

Patterns and mechanisms of structural variations in human cancer / Neutrophils escort circulating tumour cells to enable cell cycle progression

[Journal Club]December/18/2019

The biochemical basis of microRNA targeting efficacy / Assembly of long, error-prone reads using repeat graphs.

[Journal Club]December/11/2019

The RNA Atlas, a single nucleotide resolution map of the human transcriptome / RNA modifications detection by comparative Nanopore direct RNA sequencing

[Journal Club]December/04/2019

Search-and-replace genome editing without double-strand breaks or donor DNA / High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

[Journal Club]November/27/2019

Determining cell type abundance and expression from bulk tissues with digital cytometry / Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy

[Journal Club]November/20/2019

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue / An expanded landscape of human long noncoding RNA

[Journal Club]November/6/2019

Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA / Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing

[Journal Club]October/30/2019

A comprehensive examination of Nanopore nativeRNA sequencing for characterization of complextranscriptomes / Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA.

[Journal Club]October/23/2019

The Dynamics of Cytoplasmic mRNA Metabolism / MinCall - MinION end2end convolutional deep learning basecaller

[Journal Club]October/16/2019

scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data / Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning

[Journal Club]October/2/2019

Stem cell differentiation trajectories in Hydra resolved at single-cell resolution.

[Journal Club]September/25/2019

An atlas of human long non-coding RNAs with accurate 5′ ends / Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

[Journal Club]September/18/2019

Neural networks with circular filters enable data efficient inference of sequence motifs / The bone marrow microenvironment at single-cell resolution

[Journal Club]August/28/2019

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution / Accurate detection of complex structural variations using single-molecule sequencing

[Journal Club]August/21/2019

A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation

[Journal Club]August/14/2019

Diversity and dynamics of the Drosophila transcriptome / Synthetic sequence entanglement augments stability and containment of genetic information in cells

[Journal Club]August/07/2019

Polyester: simulating RNA-seq datasets with differential transcript expression / Pervasive, Coordinated Protein-Level ChangesDriven by Transcript Isoform Switching duringMeiosis

[Journal Club] July/31/2019

Comprehensive Integration of Single-Cell Data / CDetection: CRISPR-Cas12b-based DNAdetection with sub-attomolar sensitivityand single-base specificity

[Journal Club] July/24/2019

RNA velocity of single cells

[Journal Club] July/17/2019

Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding / CIRI: an efficient and unbiased algorithm for de novo circular RNA identification

[Journal Club] July/10/2019

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. / A comprehensive catalog of predicted functional upstream open reading frames in humans

[Journal Club] July/03/2019

Fast and accurate genomic analyses using genome graphs / Prediction of potent shRNAs with a sequential classification algorithm.

[Journal Club] June/26/2019

Noncoding deletions reveal a gene that is critical for intestinal function / Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

[Journal Club] June/19/2019

Machine learning meets genome assembly / Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

[Journal Club] June/05/2019

Single-cell transcriptomic analysis of Alzheimer’s disease / Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer

[Journal Club] May/29/2019

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

[Journal Club] May/22/2019

RNA Circularization Diminishes Immunogenicity and Can Extend Translation Duration In Vivo / Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

[Journal Club] May/15/2019

Broad-spectrum enzymatic inhibition of CRISPR-Cas12a / Multi-platform discovery of haplotype-resolved structural variation in human genomes

[Journal Club] May/08/2019

Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice / Deep learning: new computational modelling techniques for genomics

[Journal Club] May/01/2019

Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing / Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

[Journal Club] April/24/2019

Neoantigen-directed immune escape in lung cancer evolution / The bone marrow microenvironment at single-cell resolution

[Journal Club] April/03/2019

Neutrophils escort circulating tumour cells to enable cell cycle progression / Deep-learning augmented RNA-seq analysis of transcript splicing

[Journal Club] March/27/2019

SQUID: transcriptomic structural variationdetection from RNA-seq / Long non-coding RNA ZNFX1-AS1 promotes the tumor progression and metastasis of colorectal cancer by acting as a competing endogenous RNA of miR-144 to regulate EZH2 expression

[Journal Club] March/20/2019

The Landscape of Circular RNA in Cancer / Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

[Journal Club] March/13/2019

The single-cell transcriptional landscape of mammalian organogenesis / CasX enzymes comprise a distinct family of RNA-guided genome editors

[Journal Club] February/27/2019

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing / Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanismsof microRNA regulation

[Journal Club] February/13/2019

Extensive translation of circular RNAs driven by N6-methyladenosine / Stable Intronic Sequence RNAs (sisRNAs): An Expanding Universe

[Journal Club] January/30/2019

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line / The translation of non-canonical open reading frames controls mucosal immunity

[Journal Club] January/23/2019

Simulation of Heterogeneous Tumour Genomes with HeteroGenesis and In Silico Whole Exome Sequencing / Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes

[Journal Club] January/16/2019

Annotation-free quantification of RNA splicing using LeafCutter / Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

[Journal Club] January/9/2019

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma / Evaluation of variability in human kidney organoids

[Journal Club] January/2/2019

A comprehensive analysis of single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer / Bayesian nonparametric discovery of isoforms and individual specific quantification

[Journal Club] December/12/2018

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

[Journal Club] December/5/2018

Structural differences between pri-miRNA paralogs promotes alternative Drosha cleavage and expands target repertoires / Integrative detection and analysis of structural variation in cancer genomes

[Journal Club] November/28/2018

NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing / Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

[Journal Club] November/21/2018

Long Non-coding RNA PVT1 Promotes Cell Proliferation and Migration by Silencing ANGPTL4 Expression in Cholangiocarcinoma / Profiling neuron-autonomous lncRNA changes upon ischemia/reperfusion injury

[Journal Club] November/14/2018

Predictable and precise template-free CRISPR editing of pathogenic variants / Evolutionary pressure against MHC class II Binding Cancer Mutations

[Journal Club] November/7/2018

Classification of DNA sequences using Bloom filters / Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer

[Journal Club] October/24/2018

Deep generative models of genetic variation capture the effects of mutations / Nuclear miR-122 directly regulates the biogenesis of cell survival oncomiR miR-21 at the posttranscriptional level

[Journal Club] October/17/2018

LncRNA CamK-A Regulates Ca2+-SignalingMediated Tumor Microenvironment Remodeling / RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

[Journal Club] October/10/2018

In vivo CRISPR editing with no detectable genomewide off-target mutations / Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

[Journal Club] October/3/2018

Pathway-specific differences between tumor cell lines and normal and tumor tissue cells / MOXI Is a Mitochondrial Micropeptide That Enhances Fatty Acid b-Oxidation

[Journal Club] September/19/2018

SVEngine: an efficient and versatile simulator of clonal evolution genome structural variations with features of cancer

[Journal Club] September/12/2018

Strelka2: fast and accurate calling of germline and somatic variants / Phase Transitions in the Assembly and Function of Human miRISC

[Journal Club] September/5/2018

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19 / Small molecules promote CRISPR-Cpf1-mediated genome editing in human pluripotent stem cells

[Journal Club] August/29/2018

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy / The tiger genome and comparative analysis with lion and snow leopard genomes

[Journal Club] August/22/2018

NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model / Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

[Journal Club] August/15/2018

Prediction of radiosensitive patients with gastric cancer by developing gene signature

[Journal Club] August/8/2018

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain / Resistance Mechanisms to Targeted Therapies in ROS1þ and ALKþ Non–small Cell Lung Cancer

[Journal Club] August/1/2018

Cryo-EM Structure of Human Dicer and Its Complexes with a Pre-miRNA Substrate / Global diversity, population stratification, andselection ofhuman copy-number variation

[Journal Club] July/25/2018

DeepCRISPR: optimized CRISPR guide RNA design by deep learning / Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

[Journal Club] July/18/2018

How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome / Mitoregulin: AlncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency

[Journal Club] July/11/2018

Down-regulation of a pro-apoptotic pathway regulated by PCAF/ADA3 in early stage gastric cancer / Structural variation in the human genome

[Journal Club] July/4/2018

ARCS: scaffolding genome drafts with linked reads / A Biogenesis Step Upstream of Microprocessor Controls miR-17 ~92 Expression

[Journal Club] June/27/2018

DeTiN: overcoming tumor-in-normal contamination / Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

[Journal Club] June/20/2018

Refined sgRNA efficacy prediction improves largeand small-scale CRISPR–Cas9 applications / Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

[Journal Club] June/6/2018

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance / Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

[Journal Club] May/30/2018

Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma / Long noncoding RNA gastric cancerrelated lncRNA1 mediates gastric malignancy through miRNA-885-3p and cyclin-dependent kinase 4

[Journal Club] May/16/2018

Genome-wide analysis of the diversity and ancestry of Korean dogs / The landscape of genomic alterations across childhood cancers

[Journal Club] May/9/2018

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

[Journal Club] May/2/2018

The Immune Landscape of Cancer / N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

[Journal Club] April/18/2018

Sense-antisense lncRNA pair encoded by locus 6p22.3 determines neuroblastoma susceptibility via the USP36-CHD7-SOX9 regulatory Axis / Linear assembly of a human centromere on the Y chromosome

[Journal Club] April/11/2018

Orthologous CRIS PR–Cas9 enzymes for combinatorial genetic screens / Convergent evolution of the genomes of marine mammals

[Journal Club] April/4/2018

Integrated exome and transcriptome sequencing reveals ZAK isoforom uasge in gastric cancer / LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations

[Journal Club] March/28/2018

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus) / Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

[Journal Club] March/21/2018

Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species / Microprocessor Recruitment to Elongating RNA Polymerase II Is Required for Differential Expression of MicroRNAs

[Journal Club] March/7/2018

Universal Alternative Splicing of Noncoding Exons / Clustering huge protein sequence sets in linear time

[Journal Club] February/28/2018

Universal Alternative Splicing of Noncoding Exons / Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

[Journal Club] February/21/2018

Deep learning improves prediction of CRIS PR–Cpf1guide RNA activity / Impediment of Replication Forks by Long Non-coding RNA Provokes Chromosomal Rearrangements by Error-Prone Restart

[Journal Club] January/31/2018

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells

[Journal Club] January/24/2018

Meta-aligner: long-read alignment based on genome statistics / Long Noncoding RNAs in Cancer Pathways

[Journal Club] January/17/2018

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics / Minke whale genome and aquatic adaptation in cetaceans

[Journal Club] January/10/2018

A Seed Mismatch Enhances Argonaute2-Catalyzed Cleavage and Partially Rescues Severely Impaired Cleavage Found in Fish / COSINE: non-seeding method for mapping long noisy sequences

[Journal Club] January/3/2018

Single-cell analysis of long non-coding RNAs in the developing human neocortex / CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR–Cas9 nuclease off-targets

[Journal Club] December/27/2017

confFuse: High-Confidence Fusion Gene Detection across Tumor Entities / Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

[Journal Club] December/20/2017

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations / Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution

[Journal Club] December/13/2017

Comprehensive molecular characterization of gastric adenocarcinoma / Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

[Journal Club] December/6/2017

Predicting off-target effects for end-to-end CRISPR guide design / ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data

[Journal Club] November 15, 2017

xCell: Digitally portraying the tissue cellular heterogeneity landscape / Non-coding Transcriptome Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate

[Journal Club] November/8/2017

The impact of structural variation on human gene expression / Non-coding Transcriptome Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate

[Journal Club] Octoberber/25/2017

Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer / Transposable elements are the primary source of novelty in primate gene regulation

[Journal Club] Octoberber/18/2017

Argonaute CLIP Defines a Deregulated miR-122-Bount Transcriptome that Correlated with Patient Survival in Human Liver Cancer / Alignment-free sequence comparison: benefits, applications, and tools

[Journal Club] Octoberber/11/2017

Changes in the Coding and Non-coding Transcriptome and DNA Methylnome that Define the Schwann Cell Repair Phenotype after Nerve Injury / Alignment-free sequence comparison: benefits, applications, and tools

[Journal Club] September/27/2017

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 / CXCL10/CXCR3 signaling mobilized-regulatory T cells promote liver tumor recurrence after transplantation

[Journal Club] September/20/2017

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms / Lnc-mg is a long non-coding RNA that promotes myogenesis

[Journal Club] September/6/2017

A human microprotein that interacts with the mRNA decapping complex

[Journal Club] August/30/2017

High quality de no vo assembly of the apple genome and methylome dynamics of early fruit development

[Journal Club] August/23/2017

Dietary restriction protects from ageassociated DNA methylation and induces epigenetic reprogramming of lipid metabolism / Multivalent Recruitment of Human Argonaute by GW182

[Journal Club] August/16/2017

Comparison of Cas9 activators in multiple species / A fast approximate algorithm for mapping long reads to large reference databases

[Journal Club] August/9/2017

Integrated genomic characterization of oesophageal carcinoma / Osteoclast Fusion and Fission

[Journal Club] July/26/2017

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics / Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing

[Journal Club] July/19/2017

Next generation mapping reveals novel large genomic rearrangements in prostate cancer

[Journal Club] June/28/2017

Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication / Global landscape of HIV–human protein complexes

[Journal Club] June/21/2017

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes / The Drosophila Dicer-1 Partner Loquacious Enhances miRNA Processing from Hairpins with Unstable Structures at the Dicing Site

[Journal Club] June/14/2017

Flicr, a long noncoding RNA, modulates Foxp3 expression and autoimmunity / Using intron position conservation for homology-based gene prediction

[Journal Club] May/24/2017

Combinatorial CRISCRISCRISCRISPR–Cas9 screens for de novo mapping of genetic interactions / SpatiotemporalDynamicsof IntratumoralImmuneCells Reveal the Immune Landscape in Human Cancer

[Journal Club] May/17/2017

Systematic analysis of telomere length and somatic alterations in 31 cancer types / The role of MicroRNAs in human cancer

[Journal Club] May/10/2017

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk / Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation

[Journal Club] April/26/2017

Genome-wide Mapping of DROSHA Cleavage Sites on Primary MicroRNAs and Noncanonical Substrates / Protein Complex–Based Analysis Framework for High-Throughput Data Sets

[Journal Club] April/19/2017

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq / SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization

[Journal Club] April/05/2017

Evaluation and improvements of clustering algorithms for detecting remote homologous protein families

[Journal Club] March/29/2017

Inactivation of Interferon Receptor Promotes the Establishment of Immune Privileged Tumor Microenvironment / Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

[Journal Club] March/22/2017

Pooled CRISPR screening with single-cell transcriptome read-out / Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

[Journal Club] March/15/2017

Predicting tumor purity from methylation microarray data

[Journal Club] March/08/2017

Translation from unconventional 5′ start sites drives tumour initiation / novoBreak: local assembly for breakpoint detection in cancer genomes, BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers

[Journal Club] March/01/2017

Host gene constraints and genomic context impact the expression and evolution of human microRNAs / Target mimicry provides a new mechanism for regulation of microRNA activity