Nicholas M. Luscombe

The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.

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How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.

Assessed papers (3)

• A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3' UTR structure to RNA metabolism.
  2023 L1 72/100
• <i>N6</i>-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in y⚑
  2022 L1 55/100 ⚑
• RNA modifications detection by comparative Nanopore direct RNA sequencing.
  2021 L1 50/100

3 assessed by us (0 reproduced) · 260 not yet assessed — every PubMed paper on record, linked below.

• The impact of visual-auditory interactions on well-being: colour and soundscapes in urban spaces ↗

  npj Acoustics · 2026
  not yet assessed
• nf-core/cutandrun: A Nextflow pipeline for the analysis of CUT&RUN, CUT&Tag and TIP-seq datasets ↗

  The Journal of Open Source Software · 2026
  not yet assessed
• A single-cell atlas of the bobtail squid visual and nervous system highlights molecular principles of convergent evolution ↗

  Nature Ecology & Evolution · 2025 · PMID 40481147
  not yet assessed
• Genomic insights and the conservation potential of captive breeding: The case of Chinese alligator ↗

  Science Advances · 2025 · PMID 40173227
  not yet assessed
• Integrative profiling of condensation-prone RNAs during early development ↗

  Cell Genomics · 2025 · PMID 41265448
  not yet assessed
• Transcriptomes of a fast-developing chordate uncover drastic differences in transcription factors and localized maternal RNA composition compared with those of ascidians ↗

  Development · 2025 · PMID 40099490
  not yet assessed
• Unlocking the full potential of Oxford Nanopore reads with NOVOLoci ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• Integrative Profiling of Condensation-Prone RNAs During Early Development ↗

  SSRN Electronic Journal · 2025
  not yet assessed
• The complete mitogenome of an unidentified Oikopleura species ↗

  F1000Research · 2025 · PMID 40248647
  not yet assessed
• The complete mitogenome of an unidentified Oikopleura species ↗

  F1000Research · 2025
  not yet assessed
• Peer Review Report For: The complete mitogenome of an unidentified Oikopleura species [version 3; peer review: 3 approved, 1 approved with reservations] ↗

  2025
  not yet assessed
• Peer Review Report For: The complete mitogenome of an unidentified Oikopleura species [version 1; peer review: 1 approved, 1 approved with reservations] ↗

  2025
  not yet assessed
• Peer Review Report For: The complete mitogenome of an unidentified Oikopleura species [version 2; peer review: 2 approved, 2 approved with reservations] ↗

  2025
  not yet assessed
• Peer Review Report For: The complete mitogenome of an unidentified Oikopleura species [version 2; peer review: 2 approved, 2 approved with reservations] ↗

  2025
  not yet assessed
• Peer Review Report For: The complete mitogenome of an unidentified Oikopleura species [version 1; peer review: 1 approved, 1 approved with reservations] ↗

  2025
  not yet assessed
• Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles

  Dipòsit Digital de la Universitat de Barcelona (Universitat de Barcelona) · 2025
  not yet assessed
• Pathogenic Keratinocyte States and Fibroblast Niches Define the Tissue Microenvironment in Severe Hidradenitis Suppurativa ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles ↗

  Molecular Biology and Evolution · 2024 · PMID 39686543
  not yet assessed
• Poised PABP–RNA hubs implement signal-dependent mRNA decay in development ↗

  Nature Structural & Molecular Biology · 2024 · PMID 39054355
  not yet assessed
• Tracing Homopolymers in Oikopleura dioica 's Mitogenome ↗

  Genome Biology and Evolution · 2024 · PMID 39162185
  not yet assessed
• Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species ↗

  Genome Research · 2024 · PMID 38621828
  not yet assessed
• Tracing Homopolymers in Oikopleura dioica ’s mitogenome ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Integrative profiling of condensation-prone RNAs during early development ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Cross-tissue isoform switches by human transcription factors suggest a widespread regulatory mechanism ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• The complete mitogenome of an unidentified Oikopleura species ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Less, but more: new insights from appendicularians on chordate Fgf evolution and the divergence of tunicate lifestyles ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Subtype-specific Patterns of Evolution and Clinically Relevant Genomic Instability in Wilms Tumour ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• The complete mitogenome of an unidentified Oikopleura species ↗

  F1000Research · 2024
  not yet assessed
• Annelid functional genomics reveal the origins of bilaterian life cycles ↗

  Nature · 2023 · PMID 36697830
  not yet assessed
• scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border ↗

  eLife · 2023 · PMID 37530410
  not yet assessed
• A gene regulatory network for neural induction ↗

  eLife · 2023 · PMID 36867045
  not yet assessed
• nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis ↗

  Wellcome Open Research · 2023 · PMID 37829674
  not yet assessed
• clipplotr —a comparative visualization and analysis tool for CLIP data ↗

  RNA · 2023 · PMID 36894192
  not yet assessed
• A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism

  Nucleic Acids Research · 2023 · PMID 37013995
  L1 72/100
• Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells ↗

  Wellcome Open Research · 2023 · PMID 38074197
  not yet assessed
• RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis ↗

  Brain · 2023 · PMID 36789492
  not yet assessed
• Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells ↗

  Wellcome Open Research · 2023
  not yet assessed
• Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Extreme genome scrambling in cryptic Oikopleura dioica species ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Poised PABP-RNA hubs implement signal-dependent mRNA decay in development ↗

  Research Square · 2023
  not yet assessed
• Author response: scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border ↗

  2023
  not yet assessed
• Underlying data for: nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2023
  not yet assessed
• Underlying data for: nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2023
  not yet assessed
• Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells ↗

  Figshare · 2023
  not yet assessed
• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast⚑

  eLife · 2022 · PMID 36422864
  L1 55/100 ⚑
• Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing ↗

  F1000Research · 2022 · PMID 35350547
  not yet assessed
• The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe ↗

  Marine Biology · 2022
  not yet assessed
• A single-cell atlas of bobtail squid visual and nervous system highlights molecular principles of convergent evolution ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Annelid functional genomics reveal the origins of bilaterian life cycles ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• A gradient border model for cell fate decisions at the neural plate border ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Annelid functional genomics reveal the origins of bilaterian life cycles ↗

  Research Square · 2022
  not yet assessed
• Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• A computationally-enhanced hiCLIP atlas reveals Staufen1 RNA binding features and links 3’ UTR structure to RNA metabolism ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• Development of the Research Data Archive at OIST ↗

  Lecture notes in computer science · 2022
  not yet assessed
• A Moonlighting Function of Aldh18a1 Supports Pausing RNA Polymerase II in Promoter-Proximal Regions ↗

  SSRN Electronic Journal · 2022
  not yet assessed
• The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2022
  not yet assessed
• ESDR048 - The transcriptional landscape of hidradenitis suppurativa at single-cell and spatial resolution ↗

  2022
  not yet assessed
• Author response: N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast ↗

  2022
  not yet assessed
• Author response: A gene regulatory network for neural induction ↗

  2022
  not yet assessed
• Peer Review Report For: Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing [version 1; peer review: 2 approved] ↗

  2022
  not yet assessed
• Peer Review Report For: Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing [version 1; peer review: 2 approved] ↗

  2022
  not yet assessed
• RNA modifications detection by comparative Nanopore direct RNA sequencing

  Nature Communications · 2021 · PMID 34893601
  L1 50/100
• TDP-43 condensation properties specify its RNA-binding and regulatory repertoire ↗

  Cell · 2021 · PMID 34380047
  not yet assessed
• High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Genome biology · 2021 · PMID 33446241
  not yet assessed
• Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing ↗

  BMC Genomics · 2021 · PMID 33781200
  not yet assessed
• Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer ↗

  Wellcome Open Research · 2021 · PMID 34286104
  not yet assessed
• Cytoplasmic cleavage of IMPA1 3′ UTR is necessary for maintaining axon integrity ↗

  Cell Reports · 2021 · PMID 33626357
  not yet assessed
• Intergenic RNA mainly derives from nascent transcripts of known genes ↗

  Genome biology · 2021 · PMID 33952325
  not yet assessed
• Reactive astrocytes in ALS display diminished intron retention ↗

  Nucleic Acids Research · 2021 · PMID 33684213
  not yet assessed
• Aberrant cytoplasmic intron retention is a blueprint for RNA binding protein mislocalization in VCP-related amyotrophic lateral sclerosis ↗

  Brain · 2021 · PMID 33693641
  not yet assessed
• psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation ↗

  Nature Communications · 2021 · PMID 33674615
  not yet assessed
• Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs ↗

  Nucleic Acids Research · 2021 · PMID 34871434
  not yet assessed
• RGS4 RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons ↗

  International Journal of Molecular Sciences · 2021 · PMID 34884825
  not yet assessed
• Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast ↗

  Cell Reports · 2021 · PMID 33472063
  not yet assessed
• Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. ↗

  Institutional Repositories DataBase (IRDB) · 2021
  not yet assessed
• H3S28P Antibody Staining of Okinawan Oikopleura dioica Suggests the Presence of Three Chromosomes ↗

  F1000Research · 2021
  not yet assessed
• Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states ↗

  Genome Research · 2021 · PMID 34963663
  not yet assessed
• clipplotr - a comparative visualisation and analysis tool for CLIP data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions ↗

  Nature Communications · 2021 · PMID 34011993
  not yet assessed
• Author Correction: High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Genome biology · 2021 · PMID 33494761
  not yet assessed
• A gene regulatory network for neural induction ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Comparative transcriptomics reveals unique patterns of convergence in the evolution of eusociality ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Chromwave: Deciphering the DNA-Encoded Competition between Transcription Factors and Nucleosomes with Deep Neural Networks ↗

  SSRN Electronic Journal · 2021
  not yet assessed
• Epiblast morphogenesis is controlled by selective mRNA decay triggered by LIN28A relocation ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Publisher Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP ↗

  Nature Structural & Molecular Biology · 2021
  not yet assessed
• Ultraplex- A rapid, flexible, all-in-one fastq demultiplexer [version 1; peer review- 1 approved]

  UCL Discovery (University College London) · 2021
  not yet assessed
• Additional file 4 of High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Figshare · 2021
  not yet assessed
• Additional file 8 of High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Figshare · 2021
  not yet assessed
• Additional file 2 of High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Figshare · 2021
  not yet assessed
• Additional file 3 of High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Figshare · 2021
  not yet assessed
• Additional file 1 of Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing ↗

  Figshare · 2021
  not yet assessed
• Additional file 6 of High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Figshare · 2021
  not yet assessed
• Additional file 5 of High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts ↗

  Figshare · 2021
  not yet assessed
• ChromWave: Deciphering the DNA-encoded competition between transcription factors and nucleosomes with deep neural networks ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Pervasive chromosomal instability and karyotype order in tumour evolution ↗

  Nature · 2020 · PMID 32879494
  not yet assessed
• What is AI? Applications of artificial intelligence to dermatology ↗

  British Journal of Dermatology · 2020 · PMID 31960407
  not yet assessed
• RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions ↗

  Nature Communications · 2020 · PMID 32094342
  not yet assessed
• Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome ↗

  Nature Communications · 2020 · PMID 32170069
  not yet assessed
• How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets ↗

  Frontiers in Genetics · 2020 · PMID 32508872
  not yet assessed
• Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq ↗

  Scientific Reports · 2020 · PMID 32188910
  not yet assessed
• A genome database for a Japanese population of the larvacean Oikopleura dioica ↗

  Development Growth & Differentiation · 2020 · PMID 32677034
  not yet assessed
• Widespread use of the “ascidian” mitochondrial genetic code in tunicates ↗

  F1000Research · 2020 · PMID 32148763
  not yet assessed
• Clinically Relevant Vulnerabilities of Deep Machine Learning Systems for Skin Cancer Diagnosis ↗

  Journal of Investigative Dermatology · 2020 · PMID 32931808
  not yet assessed
• Paraspeckle components NONO and PSPC1 are not mislocalized from motor neuron nuclei in sporadic ALS ↗

  Brain · 2020 · PMID 32844195
  not yet assessed
• Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica ↗

  Journal of Visualized Experiments · 2020 · PMID 32628172
  not yet assessed
• Centromere-specific antibody-mediated karyotyping of Okinawan Oikopleura dioica suggests the presence of three chromosomes ↗

  F1000Research · 2020 · PMID 33728042
  not yet assessed
• Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica ↗

  Journal of Visualized Experiments · 2020
  not yet assessed
• CD147 ( BSG ) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• PsiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Intergenic RNA mainly derives from nascent transcripts of known genes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Centromere-specific antibody-mediated karyotyping of Okinawan Oikopleura dioica suggests the presence of three chromosomes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Author Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP ↗

  Nature Structural & Molecular Biology · 2020 · PMID 32641771
  not yet assessed
• H3S28P Antibody Staining of Okinawan Oikopleura dioica Suggests the Presence of Three Chromosomes [version 2; peer review: 2 approved]

  F1000Research · 2020
  not yet assessed
• Peer Review Report For: Widespread use of the “ascidian” mitochondrial genetic code in tunicates [version 1; peer review: 2 approved] ↗

  2020
  not yet assessed
• Peer Review Report For: Widespread use of the “ascidian” mitochondrial genetic code in tunicates [version 1; peer review: 2 approved] ↗

  2020
  not yet assessed
• A genome database for a Japanese population of the larvacean Oikopleura dioica

  Institutional Repositories DataBase (IRDB) · 2020
  not yet assessed
• How Do You Identify m⁶A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets

  Institutional Repositories DataBase (IRDB) · 2020
  not yet assessed
• Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis ↗

  Brain · 2019 · PMID 31368485
  not yet assessed
• A systems view of spliceosomal assembly and branchpoints with iCLIP ↗

  Nature Structural & Molecular Biology · 2019 · PMID 31570875
  not yet assessed
• Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors ↗

  Cell Reports · 2019 · PMID 30784590
  not yet assessed
• Widespread use of the “ascidian” mitochondrial genetic code in tunicates ↗

  F1000Research · 2019
  not yet assessed
• RNA modifications detection by comparative Nanopore direct RNA sequencing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes ↗

  Genome Research · 2019 · PMID 31097474
  not yet assessed
• RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Widespread FUS mislocalization is a molecular hallmark of ALS ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Publisher Correction: c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells ↗

  Nature Immunology · 2019 · PMID 30733606
  not yet assessed
• Transcription levels of a long noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Widespread use of the “ascidian” mitochondrial genetic code in tunicates ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Single-individual genome sequencing of the chordate Oikopleura dioica shows massive structural variations between animals of similar morphology

  The Molecular Biology Society of Japan · 2019
  not yet assessed
• Target-Specific Precision of CRISPR-Mediated Genome Editing ↗

  Molecular Cell · 2018 · PMID 30554945
  not yet assessed
• Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease ↗

  PLoS ONE · 2018 · PMID 30169498
  not yet assessed
• Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing ↗

  Cell · 2018 · PMID 30078707
  not yet assessed
• Nervous System Regionalization Entails Axial Allocation before Neural Differentiation ↗

  Cell · 2018 · PMID 30343898
  not yet assessed
• Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS ↗

  Nature Communications · 2018 · PMID 29789581
  not yet assessed
• c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells ↗

  Nature Immunology · 2018 · PMID 29662170
  not yet assessed
• Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis ↗

  Genome biology · 2018 · PMID 30526646
  not yet assessed
• Data Science Issues in Studying Protein–RNA Interactions with CLIP Technologies ↗

  Annual Review of Biomedical Data Science · 2018 · PMID 37123514
  not yet assessed
• Somatic TP53 Mutations Are Detectable in Circulating Tumor DNA from Children with Anaplastic Wilms Tumors ↗

  Translational Oncology · 2018 · PMID 30172241
  not yet assessed
• Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells ↗

  Genome biology · 2018 · PMID 29334988
  not yet assessed
• Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome ↗

  Genome Research · 2018 · PMID 29618487
  not yet assessed
• Target-specific precision of CRISPR-mediated genome editing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Nucleosome positioning stability is a significant modulator of germline mutation rate variation across the human genome ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• A systems view of spliceosomal assembly and branchpoints with iCLIP ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Genome-Wide Reconstitution of Chromatin Transactions: RSC Preferentially disrupts H2A.Z-Containing Nucleosomes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Additional file 2: Table S1. of Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells ↗

  Figshare · 2018
  not yet assessed
• Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS ↗

  Cell Reports · 2017 · PMID 28564594
  not yet assessed
• GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data ↗

  PLoS ONE · 2017 · PMID 28379994
  not yet assessed
• Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein ↗

  Nature Protocols · 2017 · PMID 28230851
  not yet assessed
• Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Data Science Issues in Understanding Protein-RNA Interactions ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Regionalization of the nervous system requires axial allocation prior to neural lineage commitment ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2017
  not yet assessed
• Intra-Tumor Genetic Heterogeneity in Wilms Tumor: Clonal Evolution and Clinical Implications ↗

  EBioMedicine · 2016 · PMID 27333041
  not yet assessed
• Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation ↗

  Nature Structural & Molecular Biology · 2016 · PMID 27183194
  not yet assessed
• Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation ↗

  eLife · 2016 · PMID 26984279
  not yet assessed
• Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation ↗

  Nucleic Acids Research · 2016 · PMID 27492286
  not yet assessed
• Author response: Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation ↗

  2016
  not yet assessed
• Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C ↗

  Nature Genetics · 2015 · PMID 25938943
  not yet assessed
• Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome ↗

  Nature Genetics · 2015 · PMID 26323060
  not yet assessed
• hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1 ↗

  Nature · 2015 · PMID 25799984
  not yet assessed
• IntergenicAluexonisation facilitates the evolution of tissue-specific transcript ends ↗

  Nucleic Acids Research · 2015 · PMID 26400176
  not yet assessed
• Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop ↗

  Nucleic Acids Research · 2015 · PMID 26464442
  not yet assessed
• The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements ↗

  Genome Research · 2015 · PMID 25752748
  not yet assessed
• Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt ↗

  Genes & Development · 2015 · PMID 25737280
  not yet assessed
• GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2015
  not yet assessed
• Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast ↗

  Nucleic Acids Research · 2014 · PMID 24497191
  not yet assessed
• DNA-Binding Specificities of Human Transcription Factors ↗

  Cell · 2013 · PMID 23332764
  not yet assessed
• Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements ↗

  Cell · 2013 · PMID 23374342
  not yet assessed
• Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila ↗

  Molecular Cell · 2013 · PMID 23870142
  not yet assessed
• Cellular resolution models for even skipped regulation in the entire Drosophila embryo ↗

  eLife · 2013 · PMID 23930223
  not yet assessed
• Response to Comments on “ Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters” ↗

  Science · 2013 · PMID 23599465
  not yet assessed
• Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements ↗

  Genome Research · 2013 · PMID 24065776
  not yet assessed
• Response to No gene-specific optimization of mutation rate in Escherichia coli ↗

  arXiv (Cornell University) · 2013
  not yet assessed
• Cellular resolution models of cis-regulatory input function in the entire Drosophila embryo

  eLife · 2013
  not yet assessed
• Author response: Cellular resolution models for even skipped regulation in the entire Drosophila embryo ↗

  2013
  not yet assessed
• Response to No gene-specific optimization of mutation rate in\n Escherichia coli ↗

  arXiv (Cornell University) · 2013
  not yet assessed
• An integrated encyclopedia of DNA elements in the human genome ↗

  Nature · 2012 · PMID 22955616
  not yet assessed
• An integrated encyclopedia of DNA elements in the human genome

  The Journal of the American Medical Association (JAMA) Network (American Medical Association) · 2012
  not yet assessed
• Protein–RNA interactions: new genomic technologies and perspectives ↗

  Nature Reviews Genetics · 2012 · PMID 22251872
  not yet assessed
• Gene Loops Enhance Transcriptional Directionality ↗

  Science · 2012 · PMID 23019609
  not yet assessed
• Evidence of non-random mutation rates suggests an evolutionary risk management strategy ↗

  Nature · 2012 · PMID 22522932
  not yet assessed
• Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription ↗

  Nature Communications · 2012 · PMID 22673913
  not yet assessed
• DrosophilaDosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters ↗

  Science · 2012 · PMID 22821985
  not yet assessed
• The NSL Complex Regulates Housekeeping Genes in Drosophila ↗

  PLoS Genetics · 2012 · PMID 22723752
  not yet assessed
• Non‐random mutation: The evolution of targeted hypermutation and hypomutation ↗

  BioEssays · 2012 · PMID 23281172
  not yet assessed
• The MOF Chromobarrel Domain Controls Genome-wide H4K16 Acetylation and Spreading of the MSL Complex ↗

  Developmental Cell · 2012 · PMID 22421046
  not yet assessed
• m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence ↗

  Genome biology · 2012 · PMID 22720667
  not yet assessed
• Protein-RNA interactions: new genomic technologies and perspectives (vol 13, pg 77, 2012)

  UCL Discovery (University College London) · 2012
  not yet assessed
• Response to Horizontal gene transfer may explain variation in theta_s ↗

  arXiv (Cornell University) · 2012
  not yet assessed
• Erratum: Protein–RNA interactions: new genomic technologies and perspectives ↗

  Nature Reviews Genetics · 2012
  not yet assessed
• A pipeline for ChIP-seq data analysis (Prot 56)

  2012
  not yet assessed
• Advances in Intelligent and Soft Computing: Preface

  UCL Discovery (University College London) · 2012
  not yet assessed
• iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution ↗

  Journal of Visualized Experiments · 2011 · PMID 21559008
  not yet assessed
• Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12 ↗

  Nucleic Acids Research · 2011 · PMID 22180530
  not yet assessed
• An Overview of Prokaryotic Transcription Factors ↗

  Sub-cellular biochemistry/Subcellular biochemistry · 2011 · PMID 21557077
  not yet assessed
• The RNA-Binding Protein Rrm4 is Essential for Efficient Secretion of Endochitinase Cts1 ↗

  Molecular & Cellular Proteomics · 2011 · PMID 21808052
  not yet assessed
• iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution ↗

  Journal of Visualized Experiments · 2011
  not yet assessed
• SpeCond: a method to detect condition-specific gene expression ↗

  Genome biology · 2011 · PMID 22008066
  not yet assessed
• Comparative genomics suggests differential deployment of linear and branched signaling across bacteria ↗

  Molecular BioSystems · 2011 · PMID 21879110
  not yet assessed
• How Do You Find Transcription Factors? Computational Approaches to Compile and Annotate Repertoires of Regulators for Any Genome ↗

  Methods in molecular biology · 2011 · PMID 21938617
  not yet assessed
• Large-Scale Nuclear Architecture and Transcriptional Control ↗

  Sub-cellular biochemistry/Subcellular biochemistry · 2011 · PMID 21557088
  not yet assessed
• A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast ↗

  Genome Research · 2011 · PMID 21930892
  not yet assessed
• Correction: SpeCond: a method to detect condition-specic gene expression

  2011
  not yet assessed
• SpeCond: a method to detect condition-specific gene expression ↗

  Genome biology · 2011
  not yet assessed
• iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution ↗

  Nature Structural & Molecular Biology · 2010 · PMID 20601959
  not yet assessed
• Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli ↗

  Nucleic Acids Research · 2010 · PMID 21097887
  not yet assessed
• iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions ↗

  PLoS Biology · 2010 · PMID 21048981
  not yet assessed
• Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome ↗

  PLoS Genetics · 2010 · PMID 20174442
  not yet assessed
• The Nonspecific Lethal Complex Is a Transcriptional Regulator in Drosophila ↗

  Molecular Cell · 2010 · PMID 20620954
  not yet assessed
• Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity ↗

  Nucleic Acids Research · 2010 · PMID 20483912
  not yet assessed
• Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets ↗

  Nucleic Acids Research · 2010 · PMID 20385592
  not yet assessed
• Sensitized phenotypic screening identifies gene dosage sensitive region on chromosome 11 that predisposes to disease in mice ↗

  EMBO Molecular Medicine · 2010 · PMID 21204268
  not yet assessed
• Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities ↗

  Genome Research · 2010 · PMID 20378718
  not yet assessed
• A census of human transcription factors: function, expression and evolution ↗

  Nature Reviews Genetics · 2009 · PMID 19274049
  not yet assessed
• Know your limits: Assumptions, constraints and interpretation in systems biology ↗

  Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · 2009 · PMID 19439202
  not yet assessed
• Complete Genome Sequence of Uropathogenic Proteus mirabilis , a Master of both Adherence and Motility ↗

  Journal of Bacteriology · 2008 · PMID 18375554
  not yet assessed
• Genome-wide Analysis Reveals MOF as a Key Regulator of Dosage Compensation and Gene Expression in Drosophila ↗

  Cell · 2008 · PMID 18510926
  not yet assessed
• Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972 ↗

  Molecular Genetics and Genomics · 2008 · PMID 18317809
  not yet assessed
• Principles of transcriptional regulation and evolution of the metabolic system inE. coli ↗

  Genome Research · 2008 · PMID 18836036
  not yet assessed
• Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of Yeast ↗

  Journal of Molecular Biology · 2006 · PMID 16762362
  not yet assessed
• Transcriptional regulatory networks in bacteria: from input signals to output responses ↗

  Current Opinion in Microbiology · 2006 · PMID 16942903
  not yet assessed
• [15] Extrapolating Traditional DNA Microarray Statistics to Tiling and Protein Microarray Technologies ↗

  Methods in enzymology on CD-ROM/Methods in enzymology · 2006 · PMID 16939796
  not yet assessed
• Analytical Evolutionary Model for Protein Fold Occurrence in Genomes, Accounting for the Effects of Gene Duplication, Deletion, Acquisition and Selective Pressure ↗

  2006
  not yet assessed
• Transcription regulation: a genomic network ↗

  BMC Bioinformatics · 2005
  not yet assessed
• Transcriptional networking. ↗

  Genome biology · 2005 · PMID 16168097
  not yet assessed
• Genomic analysis of regulatory network dynamics reveals large topological changes ↗

  Nature · 2004 · PMID 15372033
  not yet assessed
• Structure and evolution of transcriptional regulatory networks ↗

  Current Opinion in Structural Biology · 2004 · PMID 15193307
  not yet assessed
• CREB Binds to Multiple Loci on Human Chromosome 22 ↗

  Molecular and Cellular Biology · 2004 · PMID 15082775
  not yet assessed
• Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs ↗

  Genome Research · 2004 · PMID 15173116
  not yet assessed
• GenCompass: a universal system for analysing gene expression for any genome ↗

  Trends in biotechnology · 2004 · PMID 15491796
  not yet assessed
• Genomic analysis of gene expression relationships in transcriptional regulatory networks ↗

  Trends in Genetics · 2003 · PMID 12902159
  not yet assessed
• Distribution of NF-κB-binding sites across human chromosome 22 ↗

  Proceedings of the National Academy of Sciences · 2003 · PMID 14527995
  not yet assessed
• Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data ↗

  Bioinformatics · 2003 · PMID 14555624
  not yet assessed
• ExpressYourself: a modular platform for processing and visualizing microarray data ↗

  Nucleic Acids Research · 2003 · PMID 12824348
  not yet assessed
• The transcriptional activity of human Chromosome 22 ↗

  Genes & Development · 2003 · PMID 12600945
  not yet assessed
• Identification of Novel Functional Elements in the Human Genome ↗

  Cold Spring Harbor Symposia on Quantitative Biology · 2003 · PMID 15338632
  not yet assessed
• Protein–DNA Interactions: Amino Acid Conservation and the Effects of Mutations on Binding Specificity ↗

  Journal of Molecular Biology · 2002 · PMID 12126620
  not yet assessed
• The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties ↗

  Genome biology · 2002 · PMID 12186647
  not yet assessed
• GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis ↗

  Proceedings of the National Academy of Sciences · 2002 · PMID 11867748
  not yet assessed
• SNPs on human chromosomes 21 and 22 – analysis in terms of protein features and pseudogenes ↗

  Pharmacogenomics · 2002 · PMID 12052146
  not yet assessed
• Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae ↗

  Genes & Development · 2002 · PMID 12464632
  not yet assessed
• Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22 ↗

  Genome Research · 2002 · PMID 11827946
  not yet assessed
• Structural genomics: a new era for pharmaceutical research. ↗

  Genome biology · 2002 · PMID 11864367
  not yet assessed
• Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level ↗

  Nucleic Acids Research · 2001 · PMID 11433033
  not yet assessed
• What is Bioinformatics? A Proposed Definition and Overview of the Field ↗

  Methods of Information in Medicine · 2001 · PMID 11552348
  not yet assessed
• Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model ↗

  Journal of Molecular Biology · 2001 · PMID 11697896
  not yet assessed
• What is bioinformatics? An introduction and overview ↗

  Yearbook of Medical Informatics · 2001 · PMID 27701604
  not yet assessed
• Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function ↗

  Genome Research · 2001 · PMID 11544189
  not yet assessed
• An overview of the structures of protein-DNA complexes. ↗

  Genome biology · 2000 · PMID 11104519
  not yet assessed
• A computational analysis of protein-DNA complex structures

  UCL Discovery (University College London) · 2000
  not yet assessed
• New Tools and Resources for Analysing Protein Structures and Their Interactions ↗

  Acta Crystallographica Section D Biological Crystallography · 1998 · PMID 10089489
  not yet assessed
• NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions ↗

  Nucleic Acids Research · 1997 · PMID 9396800
  not yet assessed
• Protein clefts in molecular recognition and function. ↗

  PubMed · 1996 · PMID 8976552
  not yet assessed