Articles

Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance

Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a co...

Authors: Soheil Yousefi, Ruizhi Deng, Kristina Lanko, Eva Medico Salsench, Anita Nikoncuk, Herma C. van der Linde, Elena Perenthaler, Tjakko J. van Ham, Eskeatnaf Mulugeta and Tahsin Stefan Barakat

A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy

Advances in cancer biology are increasingly dependent on integration of heterogeneous datasets. Large-scale efforts have systematically mapped many aspects of cancer cell biology; however, it remains challengi...

Authors: Christopher Yogodzinski, Abolfazl Arab, Justin R. Pritchard, Hani Goodarzi and Luke A. Gilbert

Targeting CDC7 potentiates ATR-CHK1 signaling inhibition through induction of DNA replication stress in liver cancer

Liver cancer is one of the most commonly diagnosed cancers and the fourth leading cause of cancer-related death worldwide. Broad-spectrum kinase inhibitors like sorafenib and lenvatinib provide only modest sur...

Authors: Yuchen Guo, Jun Wang, Bente Benedict, Chen Yang, Frank van Gemert, Xuhui Ma, Dongmei Gao, Hui Wang, Shu Zhang, Cor Lieftink, Roderick L. Beijersbergen, Hein te Riele, Xiaohang Qiao, Qiang Gao, Chong Sun, Wenxin Qin…

Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion

Recent studies have suggested that individual variants do not sufficiently explain the variable expressivity of phenotypes observed in complex disorders. For example, the 16p12.1 deletion is associated with de...

Authors: Matthew Jensen, Anastasia Tyryshkina, Lucilla Pizzo, Corrine Smolen, Maitreya Das, Emily Huber, Arjun Krishnan and Santhosh Girirajan

Integrating thousands of PTEN variant activity and abundance measurements reveals variant subgroups and new dominant negatives in cancers

PTEN is a multi-functional tumor suppressor protein regulating cell growth, immune signaling, neuronal function, and genome stability. Experimental characterization can help guide the clinical interpretation o...

Authors: Kenneth A. Matreyek, Jason J. Stephany, Ethan Ahler and Douglas M. Fowler

Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants

The receptor-binding domain (RBD) variants of SARS-CoV-2 could impair antibody-mediated neutralization of the virus by host immunity; thus, prospective surveillance of antibody escape mutants and understanding...

Authors: Chunyan Yi, Xiaoyu Sun, Yixiao Lin, Chenjian Gu, Longfei Ding, Xiao Lu, Zhuo Yang, Yaguang Zhang, Liyan Ma, Wangpeng Gu, Aidong Qu, Xu Zhou, Xiuling Li, Jianqing Xu, Zhiyang Ling, Youhua Xie…

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

Clinical interpretation of genetic variants in the context of the patient’s phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artific...

Authors: Francisco M. De La Vega, Shimul Chowdhury, Barry Moore, Erwin Frise, Jeanette McCarthy, Edgar Javier Hernandez, Terence Wong, Kiely James, Lucia Guidugli, Pankaj B. Agrawal, Casie A. Genetti, Catherine A. Brownstein, Alan H. Beggs, Britt-Sabina Löscher, Andre Franke, Braden Boone…

Lethal variants in humans: lessons learned from a large molecular autopsy cohort

Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In thi...

Authors: Hanan E. Shamseldin, Lama AlAbdi, Sateesh Maddirevula, Hessa S. Alsaif, Fatema Alzahrani, Nour Ewida, Mais Hashem, Firdous Abdulwahab, Omar Abuyousef, Hiroyuki Kuwahara, Xin Gao and Fowzan S. Alkuraya

Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma

Immune checkpoint blockade (ICB) shows lasting benefits in advanced melanoma; however, not all patients respond to this treatment and many develop potentially life-threatening immune-related adverse events (ir...

Authors: Mykhaylo Usyk, Abhishek Pandey, Richard B. Hayes, Una Moran, Anna Pavlick, Iman Osman, Jeffrey S. Weber and Jiyoung Ahn

Intra-patient stability of tumor mutational burden from tissue biopsies at different time points in advanced cancers

Tumor mutational burden (TMB) may be a predictive biomarker of immune checkpoint inhibitor (ICI) responsiveness. Genomic landscape heterogeneity is a well-established cancer feature. Molecular characteristics ...

Authors: Timothy V. Pham, Aaron M. Goodman, Smruthy Sivakumar, Garrett Frampton and Razelle Kurzrock

Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer

Enhancers are distal cis-regulatory elements required for cell-specific gene expression and cell fate determination. In cancer, enhancer variation has been proposed as a major cause of inter-patient heterogeneity...

Authors: Taotao Sheng, Shamaine Wei Ting Ho, Wen Fong Ooi, Chang Xu, Manjie Xing, Nisha Padmanabhan, Kie Kyon Huang, Lijia Ma, Mohana Ray, Yu Amanda Guo, Ngak Leng Sim, Chukwuemeka George Anene-Nzelu, Mei Mei Chang, Milad Razavi-Mohseni, Michael A. Beer, Roger Sik Yin Foo…

Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus

Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover,...

Authors: Marcus M. Soliai, Atsushi Kato, Britney A. Helling, Catherine T. Stanhope, James E. Norton, Katherine A. Naughton, Aiko I. Klinger, Emma E. Thompson, Selene M. Clay, Soyeon Kim, Juan C. Celedón, James E. Gern, Daniel J. Jackson, Matthew C. Altman, Robert C. Kern, Bruce K. Tan…

Genome-wide analyses of multiple obesity-related cytokines and hormones informs biology of cardiometabolic traits

A complex set of perturbations occur in cytokines and hormones in the etiopathogenesis of obesity and related cardiometabolic conditions such as type 2 diabetes (T2D). Evidence for the genetic regulation of th...

Authors: Karlijn A. C. Meeks, Amy R. Bentley, Mateus H. Gouveia, Guanjie Chen, Jie Zhou, Lin Lei, Adebowale A. Adeyemo, Ayo P. Doumatey and Charles N. Rotimi

Molecular profiling of advanced malignancies guides first-line N-of-1 treatments in the I-PREDICT treatment-naïve study

Malignancies are molecularly complex and become more resistant with each line of therapy. We hypothesized that offering matched, individualized combination therapies to patients with treatment-naïve, advanced ...

Authors: Jason K. Sicklick, Shumei Kato, Ryosuke Okamura, Hitendra Patel, Mina Nikanjam, Paul T. Fanta, Michael E. Hahn, Pradip De, Casey Williams, Jessica Guido, Benjamin M. Solomon, Rana R. McKay, Amy Krie, Sarah G. Boles, Jeffrey S. Ross, J. Jack Lee…

Correction to: PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling

Authors: Bing Yao, Tao Gui, Xiangwei Zeng, Yexuan Deng, Zhi Wang, Ying Wang, Dongjun Yang, Qixiang Li, Peipei Xu, Ruifeng Hu, Xinyu Li, Bing Chen, Jin Wang, Ke Zen, Haitao Li, Melissa J. Davis…

Deep learning in cancer diagnosis, prognosis and treatment selection

Deep learning is a subdiscipline of artificial intelligence that uses a machine learning technique called artificial neural networks to extract patterns and make predictions from large data sets. The increasin...

Authors: Khoa A. Tran, Olga Kondrashova, Andrew Bradley, Elizabeth D. Williams, John V. Pearson and Nicola Waddell

Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis

Rapid advances in the past decade have shown that dysbiosis of the gut microbiome is a key hallmark of rheumatoid arthritis (RA). Yet, the relationship between the gut microbiome and clinical improvement in RA...

Authors: Vinod K. Gupta, Kevin Y. Cunningham, Benjamin Hur, Utpal Bakshi, Harvey Huang, Kenneth J. Warrington, Veena Taneja, Elena Myasoedova, John M. Davis III and Jaeyun Sung

Correction to: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Authors: Indhu-Shree Rajan-Babu, Junran J. Peng, Readman Chiu, Chenkai Li, Arezoo Mohajeri, Egor Dolzhenko, Michael A. Eberle, Inanc Birol and Jan M. Friedman

Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study

Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently ...

Authors: Aline Cuénod, Daniel Wüthrich, Helena M. B. Seth-Smith, Chantal Ott, Christian Gehringer, Frédéric Foucault, Roxanne Mouchet, Ali Kassim, Gunturu Revathi, Deborah R. Vogt, Stefanie von Felten, Stefano Bassetti, Sarah Tschudin-Sutter, Timm Hettich, Götz Schlotterbeck, Christina Homberger…

Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma

Colorectal cancer (CRC) is a major cancer type whose mechanism of metastasis remains elusive.

Authors: Jie Tang, Kailing Tu, Keying Lu, Jiaxun Zhang, Kai Luo, Haoxuan Jin, Lei Wang, Lie Yang, Weiran Xiao, Qilin Zhang, Xiaoling Liu, Xin yi Ge, Guibo Li, Zongguang Zhou and Dan Xie

Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes

DNA sequencing is increasingly incorporated into the routine care of cancer patients, many of whom also carry inherited, moderate/high-penetrance variants associated with other diseases. Yet, the prevalence an...

Authors: Zishan Wang, Xiao Fan, Yufeng Shen, Meghana S Pagadala, Rebecca Signer, Kamil J. Cygan, William G. Fairbrother, Hannah Carter, Wendy K. Chung and Kuan-lin Huang

The genomic architecture of EBV and infected gastric tissue from precursor lesions to carcinoma

Epstein-Barr virus (EBV)-associated gastric carcinomas (EBVaGCs) present unique molecular signatures, but the tumorigenesis of EBVaGCs and the role EBV plays during this process remain poorly understood.

Authors: Zhang-Hua Chen, Shu-Mei Yan, Xi-Xi Chen, Qi Zhang, Shang-Xin Liu, Yang Liu, Yi-Ling Luo, Chao Zhang, Miao Xu, Yi-Fan Zhao, Li-Yun Huang, Bin-Liu Liu, Tian-Liang Xia, Da-Zhi Xu, Yao Liang, Yong-Ming Chen…

Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8

We developed a sensitive sequencing approach that simultaneously profiles microsatellite instability, chromosomal instability, and subclonal structure in cancer. We assessed diverse repeat motifs across 225 mi...

Authors: GiWon Shin, Stephanie U. Greer, Erik Hopmans, Susan M. Grimes, HoJoon Lee, Lan Zhao, Laura Miotke, Carlos Suarez, Alison F. Almeda, Sigurdis Haraldsdottir and Hanlee P. Ji

Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK

The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interven...

Authors: Samuel Lipworth, Karina-Doris Vihta, Kevin Chau, Leanne Barker, Sophie George, James Kavanagh, Timothy Davies, Alison Vaughan, Monique Andersson, Katie Jeffery, Sarah Oakley, Marcus Morgan, Susan Hopkins, Timothy E. A. Peto, Derrick W. Crook, Ann Sarah Walker…

De novo transcriptomic subtyping of colorectal cancer liver metastases in the context of tumor heterogeneity

Gene expression-based subtyping has the potential to form a new paradigm for stratified treatment of colorectal cancer. However, current frameworks are based on the transcriptomic profiles of primary tumors, a...

Authors: Seyed H. Moosavi, Peter W. Eide, Ina A. Eilertsen, Tuva H. Brunsell, Kaja C. G. Berg, Bård I. Røsok, Kristoffer W. Brudvik, Bjørn A. Bjørnbeth, Marianne G. Guren, Arild Nesbakken, Ragnhild A. Lothe and Anita Sveen

The expressed mutational landscape of microsatellite stable colorectal cancers

Colorectal cancer is the 2nd leading cause of cancer-related deaths with few patients benefiting from biomarker-guided therapy. Mutation expression is essential for accurate interpretation of mutations as biom...

Authors: Anita Sveen, Bjarne Johannessen, Ina A. Eilertsen, Bård I. Røsok, Marie Gulla, Peter W. Eide, Jarle Bruun, Kushtrim Kryeziu, Leonardo A. Meza-Zepeda, Ola Myklebost, Bjørn A. Bjørnbeth, Rolf I. Skotheim, Arild Nesbakken and Ragnhild A. Lothe

A transcriptome-wide association study of Alzheimer’s disease using prediction models of relevant tissues identifies novel candidate susceptibility genes

Genome-wide association studies (GWAS) have identified over 56 susceptibility loci associated with Alzheimer’s disease (AD), but the genes responsible for these associations remain largely unknown.

Authors: Yanfa Sun, Jingjing Zhu, Dan Zhou, Saranya Canchi, Chong Wu, Nancy J. Cox, Robert A. Rissman, Eric R. Gamazon and Lang Wu

Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes

Epithelial ovarian cancer (OC) is a heterogenous disease consisting of five major histologically distinct subtypes: high-grade serous (HGSOC), low-grade serous (LGSOC), endometrioid (ENOC), clear cell (CCOC) a...

Authors: Bethany M. Barnes, Louisa Nelson, Anthony Tighe, George J. Burghel, I-Hsuan Lin, Sudha Desai, Joanne C. McGrail, Robert D. Morgan and Stephen S. Taylor

Correction to: Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes

Authors: David Z. Pan, Zong Miao, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk T. Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñoz-Hernandez, Miguel Herrera-Hernandez, Maria Teresa Tusié-Luna, Carlos Aguilar-Salinas…

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

Multidrug-resistant Mycobacterium tuberculosis (Mtb) is a significant global public health threat. Genotypic resistance prediction from Mtb DNA sequences offers an alternative to laboratory-based drug-susceptibil...

Authors: Matthias I. Gröschel, Martin Owens, Luca Freschi, Roger Vargas Jr, Maximilian G. Marin, Jody Phelan, Zamin Iqbal, Avika Dixit and Maha R. Farhat

Functional significance of gain-of-function H19 lncRNA in skeletal muscle differentiation and anti-obesity effects

Exercise training is well established as the most effective way to enhance muscle performance and muscle building. The composition of skeletal muscle fiber type affects systemic energy expenditures, and pertur...

Authors: Yajuan Li, Yaohua Zhang, Qingsong Hu, Sergey D. Egranov, Zhen Xing, Zhao Zhang, Ke Liang, Youqiong Ye, Yinghong Pan, Sujash S. Chatterjee, Brandon Mistretta, Tina K. Nguyen, David H. Hawke, Preethi H. Gunaratne, Mien-Chie Hung, Leng Han…

Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes

Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently under-re...

Authors: Chan Yeong Kim, Muyoung Lee, Sunmo Yang, Kyungnam Kim, Dongeun Yong, Hye Ryun Kim and Insuk Lee

Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program

Sleep-disordered breathing is a common disorder associated with significant morbidity. The genetic architecture of sleep-disordered breathing remains poorly understood. Through the NHLBI Trans-Omics for Precis...

Authors: Brian E. Cade, Jiwon Lee, Tamar Sofer, Heming Wang, Man Zhang, Han Chen, Sina A. Gharib, Daniel J. Gottlieb, Xiuqing Guo, Jacqueline M. Lane, Jingjing Liang, Xihong Lin, Hao Mei, Sanjay R. Patel, Shaun M. Purcell, Richa Saxena…

Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain

Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes...

Authors: Lindsay Liang, Siavash Fazel Darbandi, Sirisha Pochareddy, Forrest O. Gulden, Michael C. Gilson, Brooke K. Sheppard, Atehsa Sahagun, Joon-Yong An, Donna M. Werling, John L. R. Rubenstein, Nenad Sestan, Kevin J. Bender and Stephan J. Sanders

Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus

The enrichment of Gram-negative bacteria of oral origin in the esophageal microbiome has been associated with the development of metaplasia. However, to date, no study has comprehensively assessed the relation...

Authors: Nandan P. Deshpande, Stephen M. Riordan, Claire J. Gorman, Shaun Nielsen, Tonia L. Russell, Carolina Correa-Ospina, Bentotage S. M. Fernando, Shafagh A. Waters, Natalia Castaño-Rodríguez, Si Ming Man, Nicodemus Tedla, Marc R. Wilkins and Nadeem O. Kaakoush

X-CNV: genome-wide prediction of the pathogenicity of copy number variations

Gene copy number variations (CNVs) contribute to genetic diversity and disease prevalence across populations. Substantial efforts have been made to decipher the relationship between CNVs and pathogenesis but w...

Authors: Li Zhang, Jingru Shi, Jian Ouyang, Riquan Zhang, Yiran Tao, Dongsheng Yuan, Chengkai Lv, Ruiyuan Wang, Baitang Ning, Ruth Roberts, Weida Tong, Zhichao Liu and Tieliu Shi

An epigenetic and transcriptomic signature of immune tolerance in human monocytes through multi-omics integration

The plasticity of monocytes enables them to exert multiple roles during an immune response, including promoting immune tolerance. How monocytes alter their functions to convey immune tolerance in the context o...

Authors: Xanthe Brands, Bastiaan W. Haak, Augustijn M. Klarenbeek, Joe Butler, Fabrice Uhel, Wanhai Qin, Natasja A. Otto, Marja E. Jakobs, Daniël R. Faber, René Lutter, W. Joost Wiersinga, Tom van der Poll and Brendon P. Scicluna

Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma

Merkel cell carcinoma (MCC) is a rare but aggressive skin cancer with limited treatment possibilities. Merkel cell tumors display with neuroendocrine features and Merkel cell polyomavirus (MCPyV) infection in ...

Authors: Hemant Gujar, Arjun Mehta, Hong-Tao Li, Yvonne C. Tsai, Xiangning Qiu, Daniel J. Weisenberger, Miriam Galvonas Jasiulionis, Gino K. In and Gangning Liang

Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors

Tumor response to therapy is affected by both the cell types and the cell states present in the tumor microenvironment. This is true for many cancer treatments, including immune checkpoint inhibitors (ICIs). W...

Authors: Emily F. Davis-Marcisak, Allison A. Fitzgerald, Michael D. Kessler, Ludmila Danilova, Elizabeth M. Jaffee, Neeha Zaidi, Louis M. Weiner and Elana J. Fertig

Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets

Human pancreatic islets are a central focus of research in metabolic studies. Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing (scRNA...

Authors: Giorgio Basile, Sevim Kahraman, Ercument Dirice, Hui Pan, Jonathan M. Dreyfuss and Rohit N. Kulkarni

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability

Cancer evolution depends on epigenetic and genetic diversity. Historically, in multiple myeloma (MM), subclonal diversity and tumor evolution have been investigated mostly from a genetic perspective.

Authors: Jennifer Derrien, Catherine Guérin-Charbonnel, Victor Gaborit, Loïc Campion, Magali Devic, Elise Douillard, Nathalie Roi, Hervé Avet-Loiseau, Olivier Decaux, Thierry Facon, Jan-Philipp Mallm, Roland Eils, Nikhil C. Munshi, Philippe Moreau, Carl Herrmann, Florence Magrangeas…

Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Screening for short tandem repeat (STR) expansions in next-generation sequencing data can enable diagnosis, optimal clinical management/treatment, and accurate genetic counseling of patients with repeat expans...

Authors: Indhu-Shree Rajan-Babu, Junran J. Peng, Readman Chiu, Chenkai Li, Arezoo Mohajeri, Egor Dolzhenko, Michael A. Eberle, Inanc Birol and Jan M. Friedman

Effectiveness and safety of Bifidobacterium and berberine in human hyperglycemia and their regulatory effect on the gut microbiota: a multi-center, double-blind, randomized, parallel-controlled study

Berberine and Bifidobacterium have been reported to improve glucose tolerance in people with hyperglycemia or other metabolic disorders. This study aimed to assess the hypoglycemic effect and the regulation of th...

Authors: Jie Ming, Xinwen Yu, Xiaoqiang Xu, Li Wang, Chao Ding, Zhifeng Wang, Xuan Xie, Sheli Li, Wenjuan Yang, Shu Luo, Qingzhen He, Yafang Du, Zhufang Tian, Xiling Gao, Kaiyan Ma, Yujie Fang…

Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2

The emergence of SARS-CoV-2 underscores the need to better understand the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. In the betacoronavirus genus, which also ...

Authors: Juan Ángel Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas D. Maranas, Peter K. Sorger, Mohammed AlQuraishi and Raul Rabadan

Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes

Obesity predisposes individuals to multiple cardiometabolic disorders, including type 2 diabetes (T2D). As body mass index (BMI) cannot reliably differentiate fat from lean mass, the metabolically detrimental ...

Authors: David Z. Pan, Zong Miao, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk T. Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñoz-Hernandez, Miguel Herrera-Hernandez, Maria Teresa Tusié-Luna, Carlos Aguilar-Salinas…

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage

Gene expression is highly variable across tissues of multi-cellular organisms, influencing the codon usage of the tissue-specific transcriptome. Cancer disrupts the gene expression pattern of healthy tissue re...

Authors: Douglas Meyer, Jacob Kames, Haim Bar, Anton A. Komar, Aikaterini Alexaki, Juan Ibla, Ryan C. Hunt, Luis V. Santana-Quintero, Anton Golikov, Michael DiCuccio and Chava Kimchi-Sarfaty

An implementation science approach to evaluating pathogen whole genome sequencing in public health

Pathogen whole genome sequencing (WGS) is being incorporated into public health surveillance and disease control systems worldwide and has the potential to make significant contributions to infectious disease ...

Authors: Angeline S. Ferdinand, Margaret Kelaher, Courtney R. Lane, Anders Gonçalves da Silva, Norelle L. Sherry, Susan A. Ballard, Patiyan Andersson, Tuyet Hoang, Justin T. Denholm, Marion Easton, Benjamin P. Howden and Deborah A. Williamson

We need to bring R0 < 1 to treat cancer too

If each cancer cell produces on average more than one cancer cell, we see a net growth of the tumors and metastases and vice versa. We review recent clinical results for microsatellite stable metastatic colore...

Authors: Devabhaktuni Srikrishna and Kris Sachsenmeier

Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

Klebsiella pneumoniae, as a global priority pathogen, is well known for its capability of acquiring mobile genetic elements that carry resistance and/or virulence genes. Its virulence plasmid, previously deemed n...

Authors: Yanping Xu, Jianfeng Zhang, Meng Wang, Meng Liu, Guitian Liu, Hongping Qu, Jialin Liu, Zixin Deng, Jingyong Sun, Hong-Yu Ou and Jieming Qu

Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We...

Authors: John F. Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P. Purohit, Sadhna Ahuja, Nadejda M. Tsankova, Nathalie Jette…