It furthers the universitys objective of excellence in research, scholarship, and education by publishing worldwide. All content in this area was uploaded by yongjin li on may 14, 2014. The resid database of protein modifications as a resource and annotation tool. Software for dynamic analysis of tracerbased metabolomic data. Identification and characterization of n 9methyltransferase. A hubattachment based method to detect functional modules from confidencescored protein interactions and expression profiles. New fusion transcripts identified in normal karyotype. Bioinformatics, volume 22, issue 22, 15 november 2006. Clients from the biotech pharmaceutical therapeutic molecular diagnosis industries, please visit this web site instead. This book constitutes the refereed proceedings of the fourth international symposium on bioinformatics research and applications, isbra 2008, held in atlanta, ga, usa in may 2008. Tc and rac developed the bioinformatics pipeline and analyzed the data under the supervision of jz, yl, me, xc, and gw. Mar 19, 2020 caffeine is a major component of xanthine alkaloids and commonly consumed in many popular beverages. The international journal of knowledge discovery in bioinformatics ijkdb collects the most significant research and latest practices in computational knowledge discovery approaches to bioinformatics.
Jude researchers develop powerful interactive tool to mine data from cancer genome. S1ac, somatically acquired genetic alterations in the tumor were detected via highthroughput genomic sequencing of diagnostic biopsies and matched germline tissue obtained from a cohort of pediatric patients with all. This database is freely accessible on the internet. Tianhan zhang computational designer, innovation kitchen at nike. Mar 14, 2019 sequencing errors are key confounding factors for detecting lowfrequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep nextgeneration sequencing ngs. His paper, coauthored with yongjin li was entitled. Genetic aberrations contribute to acute myeloid leukemia aml.
Caffeine is a major component of xanthine alkaloids and commonly consumed in many popular beverages. We sought to define the prevalence and genomic landscape of phlike all in adults and assess response to conventional chemotherapy. Effects of replacing the unreliable cdna microarray measurements on the disease classification based on gene expression profiles and functional modules. Jude childrens research hospital, memphis, tennessee. Jude childrens research hospital has redefined the gold standard for diagnostic testing of childhood cancer patients in the precisionmedicine era and has implemented the testing for new cancer patients. We describe four different rearrangements of the erythropoietin receptor gene epor in philadelphia chromosomelike phlike all.
Atcc 8456 has been wellknown to catalyze the unusual onestep decarboxylation of free fatty acids towards the formation of terminal alkenes. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Purpose philadelphia chromosome ph like acute lymphoblastic leukemia all is a highrisk subtype of childhood all characterized by kinaseactivating alterations that are amenable to treatment with tyrosine kinase inhibitors. Yong li senior bioinformatics scientist illumina linkedin.
The best paper title was awarded to yongjin li and jinyan li for their advancement of disease gene identification using a new random walk model that allows crosswalking between phenotype. We have successfully developed a computational tool named powercore that aims to support the development of core sets by reducing the redundancy of useful alleles and thus enhancing their richness. Computational approaches for disease gene identification. Yu liu, yongjin li, zhaojie zhang, michael rusch, jared becksfort and. Li received his phd from the institute of theoretical physics at the chinese academy of sciences in 2006. He won the best paper award at the 11th international conference on bioinformatics that was held in bangkok, thailand from 3 5 october 2012. Zhou added that the proteinpaint software has the potential to help. Nov 21, 2016 purpose philadelphia chromosome ph like acute lymphoblastic leukemia all is a highrisk subtype of childhood all characterized by kinaseactivating alterations that are amenable to treatment with tyrosine kinase inhibitors. Sequencing errors are key confounding factors for detecting lowfrequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep nextgeneration sequencing ngs. Discovering diseasegenes by topological features in human proteinprotein interaction network.
A curated list of awesome deep learning applications in the field of computational biology doudouzawesomedeepbio. Chromosomal rearrangements are a hallmark of acute lymphoblastic leukemia all and are important all initiating events. Working in a highly collaborative team including scientists, clinicians and software engineers. Its architecture and capabilities as well as the development as an opensource project by a team of international collaborators from academic and industrial institutions is described.
Jude researchers develop powerful interactive tool to. The landscape of somatic mutations in infant mll rearranged. High frequency and poor outcome of philadelphia chromosome. Jude childrens research hospital has developed a webbased application to advance pediatric cancer research, collaboration and clinical care through enhanced exploration of the pediatric cancer genome. This cited by count includes citations to the following articles in scholar. The resid database of protein modifications is a comprehensive collection of annotations and structures for protein modifications and crosslinks including pre, co, and posttranslational modifications. Ligand binding site superposition and comparison based on atomic property fields. However, half of aml cases do not contain the wellknown aberrations detectable mostly by cytogenetic analysis, and these cases are classified as normal karyotype aml. I am a senior associate scientist at the center for cancer research at the national cancer institute, part of the intramural research program at the national institutes of health. Essential bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field.
Jude senior bioinformatics research scientist, developed. Drg, and jrd contributed to the conception and design of the study. Utr of the hemereceptor gene shmr are required for hmupdependent expression of shmr in ensifer meliloti. The findings appeared online recently in the scientific journal nature communications researchers showed that incorporating wholegenome sequencing into clinical genomic testing led. In this crosssectional study, three clinical tools, the osteoporosis selfassessment tool for asians osta, fracture risk assessment tool frax without bone mineral density bmd, and body mass index bmi, for predicting primary osteoporosis op were compared and ideal thresholds for omission of screening bmd were proposed in a communitydwelling elderly han beijing male population. View yong lis profile on linkedin, the worlds largest professional community. A new variant of anaplastic lymphoma kinasealk fusion in a case of anaplastic large cell lymphoma involving eef1g, a subunit of the elongation factor1 complex. I am a senior associate scientist at the center for cancer research at the national cancer institute, part of the intramural research program at the national institutes of health i received my b. Oxford university press is a department of the university of oxford. Dong wang, yingli lv, zheng guo, xia li, yanhui li, jing zhu, da yang, jianzhen xu, chenguang wang, shaoqi rao, baofeng yang. This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment.
Strong emphasis on open access to biological information as well as free and open source software. Physiological responses of pepper seedlings to various. Genomewide inferring genephenotype relationship by walking on the heterogeneous network. Fast and accurate short read alignment with burrowswheeler transform. Mar, 2006 essential bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Containing articles on topics such as systems biology, protein structure, gene expression, and bio.
In this crosssectional study, three clinical tools, the osteoporosis selfassessment tool for asians osta, fracture risk assessment tool frax without bone mineral density bmd, and body mass index bmi, for predicting primary osteoporosis op were compared and ideal thresholds for omission of screening bmd were proposed in a communitydwelling elderly han beijing male. However, the potential for such therapies in targeting these epitopes remains uncertain due to a lack of knowledge of. Bioinformatics analysis of differentially expressed genes. Heng li is a research scientist at the broad institute, working with david reich and david altshuler. Cancers with lower mutation rates, such as pediatric acute lymphoblastic leukemia all, have not shown high immunotherapy response rates, possibly because there are fewer neoepitopes for t cells to recognize. Anna andersson, tanja gruber, james downing and colleagues report a genomic analysis of infant acute lymphoblastic leukemias with mll rearrangements.
Deregulation of dux4 and erg in acute lymphoblastic leukemia. Bibliographic content of bmc bioinformatics, volume 11 supplements. Jude researchers develop powerful interactive tool to mine data. See structural alignment software for structural alignment of proteins. Additional details of bioinformatic analysis are provided in the. Pdf discovering diseasegenes by topological features in.
His current interests include the analysis of new sequencing data, population genetics and phylogenetics. Jianguo li research scientist bioinformatics institute, a. Pediatric patients with acute lymphoblastic leukemia generate. Rice stripe, a virus disease, transmitted by a small brown planthopper sbph, has greatly reduced production of japonica rice in east asia, especially in china. Bioinformatics is the application of tools of computation and analysis to the capture and interpretation of biological data. View jianguo lis profile on linkedin, the worlds largest professional community. Delineating the venom toxin arsenal of malabar pit viper trimeresurus malabaricus from the western ghats of india and evaluating its immunological crossreactivity and in vitro cytotoxicity apr. Patra, genomewide inferring genephenotype relationship by walking on the heterogeneous network, bioinformatics, 26, 9, 1219, 2010. We thank the staff of the st jude biorepository, the hartwell centre for bioinformatics and biotechnology, the flow cytometry and. The cyp152 family member oletje from jeotgalicoccus sp.
The neoepitope landscape in pediatric cancers genome. However, the potential for such therapies in targeting these epitopes remains uncertain due to a lack of knowledge of the neoepitope landscape in childhood cancer. They predicted peptide neoepitopes that could bind patients hla for. Li d, et al 2016 1methyltryptophan attenuates regulatory t cells differentiation due to the inhibition of estrogenido1mrc2 axis in. The resid database of protein modifications as a resource. Bioinformatics, volume 22, issue 22, 15 november 2006, pages 27112714. Xiaotu ma,1 yongjin li,1 bensheng ju,1 li dong,1 scott newman,1. Li yongjin, from whom i was inspired to learn a lot of knowledge and approaches related with disease gene prediction. The 19th annual advances in genome biology and technology agbt meeting came back to marco island, florida, and was held in the renovated venue from 27 february to 2 march 2019. Studies to date have focused primarily on missense mutations without exploring gene fusions, which are a major. Yongjin li read 176 publications contact yongjin li.
Bioinformatics research centre birc annual report 2010 director. Jude senior bioinformatics research scientist, developed the infographics to display the range of genomic. Researchers develop powerful interactive tool to mine data. Yongjin li phd sun yatsen university, guangzhou sysu. Bioinformatics is essential for management of data in modern biology and medicine. My current interests include the analysis of new sequencing data, population genetics and phylogenetics. Analysis of error profiles in deep nextgeneration sequencing. Predicted splice junction sites were postprocessed with a software. Although we have made great progress in mapping resistance genes, little is known about the mechanism of resistance. With the advent of omic data era, networkbased methods have prominently boosted disease gene discovery. Bmc bioinformatics research integration of multiple data sources to prioritize candidate genes using discounted rating system yongjin li and jagdish c patra. The chemistry development kit cdk is a freely available opensource java library for structural chemo and bioinformatics.
Different outcomes of normal karyotype aml suggest that this subgroup of aml could be genetically heterogeneous. Researchers develop powerful interactive tool to mine data from cancer genome. Likely or suspected pathogenic variants were identified. Targetable kinaseactivating lesions in phlike acute. Yu liu, yongjin li, zhaojie zhang, michael rusch, jared becksfort and james downing, all of st.
Identification of putative neoepitopes in pediatric acute lymphoblastic leukemia. Mobbiotools is a logical step forward towards bringing essential bioinformatics functionality to your mobile java. Core sets are necessary to ensure that access to useful alleles or characteristics retained in genebanks is guaranteed. Comparison of three tools for predicting primary osteoporosis. See the complete profile on linkedin and discover jins connections and. Analysis of error profiles in deep nextgeneration sequencing data. Leukaemia, computational biology and bioinformatics. Members of the society receive a 15% on article processing charges when publishing open access in the journal. Xiaotu ma,1 yongjin li,1 bensheng ju,1 li dong,1 scott newman,1 xin zhou,1. Bibliographic content of bmc bioinformatics, volume 12 supplements.
The neoepitope landscape in pediatric cancers europe pmc. Comparative transcriptome analysis of two rice varieties. To better understand antitumor responses, zamora et al. Jude childrens research hospital researchers develop powerful interactive tool to mine data from cancer genome read this article along. Chiahao chin, shuhwa chen, chinwen ho, mingtat ko, chungyen lin. Bioinformatics is an official journal of the international society for computational biology, the leading professional society for computational biology and bioinformatics.
Our current lead bioinformatician lb team includes the following highly experienced bioinformatics experts. Although many resources and guidelines are available to assist with this task, few integrated endtoend tools exist. The bioinformatics toolbox includes computer software programs such as blast and ensembl, which depend on the availability of the internet. The cdk provides methods for many common tasks in molecular informatics, including 2d. Sebastiao m, jessica w, nhuan p, quan li,et al egfrmutated lung adenocarcinomas from patients who progressed on egfrinhibitors show high engraftment rates in xenograf lung cancer, 2020 accepted. Longread sequencing unveils ighdux4 translocation into. Today the pipeline provides reported results in an average of 31 days. Due to its occasional side effects, reduction of caffeine in a natural way is of great. Although several computational approaches have been proposed to prioritize candidate genes relying on proteinprotein interaction ppi networks, these methods can usually cover.
View jin chens profile on linkedin, the worlds largest professional community. All of these rearrangements result in truncation of the cytoplasmic tail of epor at residues similar to those mutated in primary familial. To identify putative patientspecific cancer neoantigens fig. Neoepitopes derived from tumorspecific somatic mutations are promising targets for immunotherapy in childhood cancers. Constructing a gene semantic similarity network for the. Bioinformatics, volume 26, issue 9, 1 may 2010, pages 12191224.
My name is heng li, a research scientist at the broad institute, working with david reich and david altshuler. Several observations indicate that the epor rearrangements are driver events. However, how to make better use of different types of data for the prediction of disease. Our vision is to dedicate to the advancement of bioinformatics through education, research, and scientific breakthroughs, leading to discoveries of novel medical drugs and therapies. Bioinformatics analysis of differentially expressed genes and their functional enrichment in acute myeloid leukemia bearing mll translocation, yongjin t. I also enjoyed the time that i spent with my other colleagues in bioinformatics research center. Disease gene identification by randomwalk on multigraphs merging heterogeneous genomic and phenotype data. Pediatric patients with acute lymphoblastic leukemia. Polygenic diseases are usually caused by the dysfunction of multiple genes. Highly conserved nucleotide motifs present in the 5.
Motivationthe inference of genes that are truly associated with inherited human diseases from a set of candidates resulting from genetic linkage studies has been one of the most challenging tasks in human genetics. Essential bioinformatics ebook by jin xiong rakuten kobo. View zhiwen simon lis profile on linkedin, the worlds largest professional community. Jun 26, 2019 identification of putative neoepitopes in pediatric acute lymphoblastic leukemia. Gene gravitylike algorithm for disease gene prediction. The resid database of protein modifications as a resource and. Aug 31, 2017 neoepitopes derived from tumorspecific somatic mutations are promising targets for immunotherapy in childhood cancers. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the stateoftheart computational tools available to solve biological research problems. Truncating erythropoietin receptor rearrangements in acute. Unravelling such disease genes is crucial to fully understand the genetic landscape of diseases on molecular level. The ones marked may be different from the article in the profile. The open software engineering journal, bentham science publishers lin feng. Efforts to tune up its decarboxylation activity for better production of biological alkenes have been extensively explored via approaches such as sitedirected mutagenesis and electron source.
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