Add abstracts for all 12 missing papers

Author: suhas-r

publication-data.json

@@ -2403,7 +2403,7 @@
       ],
       "title": "Chromoscope: interactive multiscale visualization for structural variation in human genomes",
       "title_link": "https://www.nature.com/articles/s41592-023-02056-x?utm_source=twitter&utm_medium=social&utm_campaign=nmeth",
-      "abstract": "",
+      "abstract": "With the wider adoption of whole-genome sequencing (WGS) for genome analysis, researchers can profile structural variants (SVs) in addition to smaller insertions, deletions and point mutations. Somatic SVs—such as copy number variants, translocations, transposable element insertions, and complex rearrangements—have been shown to play a critical role in cancer development and therapy selection. Germline SVs can also perturb disease-associated genes, with WGS leading to increased diagnostic yields in rare disease cohorts. However, the size and complexity of the data, combined with the difficulty of obtaining accurate SV calls, pose challenges in the interpretation of SVs, often requiring laborious visual inspection of potentially pathogenic variants using multiple visualization tools. To facilitate the identification of functionally relevant SVs and the characterization of genome-wide SV patterns, efficient browsing of candidate variants and visual assessment at multiple resolutions—from the whole genome to base-pair resolution at the sequencing read level—are vital.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/s41592-023-02056-x.pdf",
       "year": "2023",
@@ -4742,7 +4742,7 @@
       ],
       "title": "Somatic mutation accumulation seen through a single-molecule lens",
       "title_link": "https://www.nature.com/articles/s41422-021-00537-2",
-      "abstract": "",
+      "abstract": "Somatic mutations (SMs) accumulate over the lifetime of cells and can lead to cancer and other diseases; however, SMs can be difficult to detect, especially when they are present in very few cells. In a recent Nature paper, Abascal et al. develop a protocol capable of detecting SMs present on only a single molecule of DNA and apply it to both mitotic and post-mitotic human tissues.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/s41422-021-00537-2_01.pdf",
       "year": "2021",
@@ -5597,7 +5597,7 @@
       ],
       "title": "Genomic Determinants of De Novo Resistance to Immune Checkpoint Blockade in Mismatch Repair-Deficient Endometrial Cancer",
       "title_link": "https://ascopubs.org/doi/10.1200/PO.20.00009",
-      "abstract": "",
+      "abstract": "Despite the success of programmed death 1 (PD-1)/PD ligand 1 (PD-L1) inhibitors in mismatch repair-deficient (MMRD) endometrial cancer (EC), many patients exhibit de novo resistance. To identify determinants of resistance to immune checkpoint blockade (ICB) in MMRD EC, we evaluated genomic data from patients who were enrolled in an investigator-initiated clinical trial of avelumab. Here, we report Janus kinase 1 (JAK1) and β2-microglobulin (B2M) mutations and a higher number of insertions and deletions (indels) and exposure to an MMRD-associated mutational signature—Signature 20 in the Catalogue Of Somatic Mutations In Cancer—as candidate genomic determinants of de novo resistance to ICB in MMRD EC.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/po.20.00009.pdf",
       "year": "2020",
@@ -10155,7 +10155,7 @@
       ],
       "title": "The impact of environmental and endogenous damage on somatic mutation load in human skin fibroblasts.",
       "title_link": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006385",
-      "abstract": "",
+      "abstract": "Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding the etiology, and improving the prognosis and prevention of cancers and other genetic diseases. Previous methods relying on either the generation of induced pluripotent stem cells, or sequencing of single-cell genomes were inherently error-prone and did not allow independent validation of the mutations. In the current study we eliminated these potential sources of error by high coverage genome sequencing of single-cell derived clonal fibroblast lineages, obtained after minimal propagation in culture, prepared from skin biopsies of two healthy adult humans. We report here accurate measurement of genome-wide magnitude and spectra of mutations accrued in skin fibroblasts of healthy adult humans. We found that every cell contains at least one chromosomal rearrangement and 600–13,000 base substitutions. The spectra and correlation of base substitutions with epigenomic features resemble many cancers. Moreover, because biopsies were taken from body parts differing by sun exposure, we can delineate the precise contributions of environmental and endogenous factors to the accrual of genetic changes within the same individual. We show here that UV-induced and endogenous DNA damage can have a comparable impact on the somatic mutation loads in skin fibroblasts.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/file.pdf",
       "year": "2016",
@@ -10707,7 +10707,7 @@
       ],
       "title": "Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma",
       "title_link": "https://www.sciencedirect.com/science/article/pii/S153561081630160X?via%3Dihub=",
-      "abstract": "",
+      "abstract": "We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/1-s2.0-s153561081630160x-mainext.pdf",
       "year": "2016",
@@ -12296,7 +12296,7 @@
       ],
       "title": "Failure to replicate the STAP cell phenomenon",
       "title_link": "https://www.nature.com/articles/nature15513",
-      "abstract": "",
+      "abstract": "During extensive revisions of this Brief Communications Arising, we inadvertently omitted a citation by Takaho A. Endo that used variant calls from RNA-seq data to conclude that the purported Fgf4-induced stem cells (FI-SCs) described in Obokata et al. constituted a mixture of trophoblastic and embryonic stem cells. Our analysis, performed independently, reached similar conclusions. We regret this oversight.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/nature16479.pdf",
       "year": "2015",
@@ -13370,7 +13370,7 @@
       ],
       "title": "Guided visual exploration of genomic stratifications in cancer.",
       "title_link": "https://www.nature.com/articles/nmeth.3088",
-      "abstract": "",
+      "abstract": "Cancer is a heterogeneous disease, and molecular profiling of tumors from large cohorts has enabled characterization of new tumor subtypes. This is a prerequisite for improving personalized treatment and ultimately better patient outcomes. Potential tumor subtypes can be identified with methods such as unsupervised clustering or network-based stratification, which assign patients to sets based on high-dimensional molecular profiles. Detailed characterization of identified sets and their interpretation, however, remain a time-consuming exploratory process. To address these challenges, we combine StratomeX, an interactive visualization tool, with exploration tools to efficiently compare multiple patient stratifications, to correlate patient sets with clinical information or genomic alterations, and to view the differences between molecular profiles across patient sets.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/emss-60637.pdf",
       "year": "2014",
@@ -13882,7 +13882,7 @@
       ],
       "title": "Rearranging the chromatin for pluripotency.",
       "title_link": "https://compbio.hms.harvard.edu/publications/rearranging-chromatin-pluripotency",
-      "abstract": "",
+      "abstract": "Pluripotent cells are characterized by infinite self-renewal and unrestricted differentiation potential with far-reaching implications in developmental biology and regenerative medicine. Somatic cells can be reprogrammed to a pluripotent state by ectopic expression of defined transcription factors (TFs) such as Oct4, Klf4, Sox2, and c-Myc, generating induced pluripotent stem cells (iPSCs). This process shows the power of TFs to overcome the epigenetic barriers that normally guard somatic cell identity and their ability to reestablish molecular and functional characteristics of pluripotency.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/rearranging_the_chromatin_for_pluripotency.pdf",
       "year": "2014",
@@ -15164,7 +15164,7 @@
       ],
       "title": "Genome-wide mapping of protein-DNA interactions by ChIP-seq",
       "title_link": "https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527644582.ch9",
-      "abstract": "",
+      "abstract": "Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/ho_2012_chipseq_book_chapter.pdf",
       "year": "2012",
@@ -15204,7 +15204,7 @@
       ],
       "title": "StratomeX: Visual analysis of large-scale heterogeneous genomics data for cancer subtype characterization",
       "title_link": "https://onlinelibrary.wiley.com/doi/10.1111/j.1467-8659.2012.03110.x",
-      "abstract": "",
+      "abstract": "Identification and characterization of cancer subtypes are important areas of research that are based on the integrated analysis of multiple heterogeneous genomics datasets. Since there are no tools supporting this process, much of this work is done using ad-hoc scripts and static plots, which is inefficient and limits visual exploration of the data. To address this, we have developed StratomeX, an integrative visualization tool that allows investigators to explore the relationships of candidate subtypes across multiple genomic data types such as gene expression, DNA methylation, or copy number data. StratomeX represents datasets as columns and subtypes as bricks in these columns. Ribbons between the columns connect bricks to show subtype relationships across datasets. Drill-down features enable detailed exploration. StratomeX provides insights into the functional and clinical implications of candidate subtypes by employing small multiples, which allow investigators to assess the effect of subtypes on molecular pathways or outcomes such as patient survival. As the configuration of viewing parameters in such a multi-dataset, multi-view scenario is complex, we propose a meta visualization and configuration interface for dataset dependencies and data-view relationships. StratomeX is developed in close collaboration with domain experts. We describe case studies that illustrate how investigators used the tool to explore subtypes in large datasets and demonstrate how they efficiently replicated findings from the literature and gained new insights into the data.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/nihms-829777.pdf",
       "year": "2012",
@@ -16673,7 +16673,7 @@
       ],
       "title": "Evidence for dosage compensation between the X chromosome and autosomes in mammals.",
       "title_link": "https://www.nature.com/articles/ng.991",
-      "abstract": "",
+      "abstract": "It has been hypothesized that, in addition to the inactivation of one of the female X chromosomes, X-linked expression in mammals is regulated through dosage compensation that involves a twofold upregulation of expression from the active X chromosome. This idea was initially based on evolutionary arguments and has subsequently been supported by the analysis of microarray expression data, which suggested that the median transcriptional magnitude of genes on the single active X chromosome is similar to that of genes on the two-copy autosomes (X:AA ratio of ~1). However, in a recent Nature Genetics article, Xiong et al. state, on the basis of their examination of multiple human and mouse RNA sequencing (RNA-seq) data sets, that global X-chromosome upregulation is absent, thus necessitating a major revision of the current model. The authors argue that the increased accuracy of the RNA-seq data reveals the true X:AA ratio to be close to 0.5, about half of the value obtained by examining microarray data. Here we contend that the low estimate of the X:AA ratio by Xiong et al. stems from the disproportionate contribution of transcriptionally inactive genes, which are not relevant for the evaluation of dosage compensation mechanisms, to the X chromosome average. We show that when only active genes are considered, the RNA-seq data give X:AA ratios closer to 1, and the observed minor deviation of the X:AA ratio from 1 is within the range expected when taking into account chromosome-to-chromosome variability.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/ng.991.pdf",
       "year": "2011",
@@ -20064,7 +20064,7 @@
       ],
       "title": "Gene Expression Data and Survival Analysis",
       "title_link": "https://compbio.hms.harvard.edu/publications/gene-expression-data-and-survival-analysis",
-      "abstract": "",
+      "abstract": "Finding associations between expression profiles and simple phenotypic data such as class labels has been studied extensively, including prediction algorithms for new samples based on these relationships. However, much work is needed to link expression profiles to more complex response variables, most notably survival data with censoring. Reducing the survival data to a short-term versus long-term survival indicator or using survival curves merely to demonstrate the difference between clusters of samples is not an efficient use of the data. We review some of the progress and challenges in this area. We discuss the need for more consistent results among studies done on different microarray platforms, for development of sample-specific predictive scoring schemes, and for a more comprehensive analysis that incorporates other prognostic factors and clearly demonstrates the added value of expression profiling over current protocols.",
       "abstract_link": "",
       "pdf_link": "/publications/pdf/park_2005_gene_expression_survival_analysis.pdf",
       "year": "2005",