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Articles by Manolis Kellis
Single-cell profiling and genetic regulation of alternative polyadenylation in the human brain
Abstract Alternative polyadenylation (APA) has a central role in regulation of the fate of mRNA and exhibits high variability in the brain and in neurons. However, brain APA regulation has not been mapped at cell type resolution, and the genetic control of APA in brain cell types and its contribution to genetic disease have remained unclear.
Computer Science > Computation and Language
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Cross-species single-cell atlas of the striatum defines cell-type and subregion disease vulnerabilities
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Keywords striatum medium spiny neurons single-cell RNA sequencing spatial transcriptomics cross-species comparison opioid receptors antipsychotics Huntington’s disease repeat instability Get full text access Log in, subscribe or purchase for full access. References 1. Gerfen, C.R. The neostriatal mosaic: compartmentalization of corticostriatal input and striatonigral output systems Nature. 1984; 311:461-464 2. Donoghue, J.P. ∙ Herkenham, M.
By Raleigh M. Linville, Benjamin James, Kyriaki Galani, Li-Lun Ho, Stuart B. Fass, James Cameron, Brent E. Fitzwalter, Roland Bock, Erin Murray, Mathilde Louçã, Oluwamayowa Oke, Charlotte Wang, Erica Engelberg-Cook, Michael DeTure, Sergio Pineda, Suphinya Sathitloetsakun, Xinyue Liang, Bertha Madras, Dennis W. Dickson, Deborah C Mash, Gustavo Turecki, Vanessa Wheeler, Veronica A. Alvarez, Verónica Álvarez, Dana Gabuzda, Manolis Kellis, Myriam Heiman, Esaria Oliver, Vanessa Farrell
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Cell Press
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Author Correction: Specific oncogene activation of the cell of origin in mucosal melanoma
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Correction to: Nature Communications https://doi.org/10.1038/s41467-025-61937-1, published online 22 July 2025 In the version of this article initially published, there was an error in the plasmid number reported in the first paragraph of the Methods “Zebrafish” section (176360), which is now amended to read “Human PAX3 (hPAX3) coding sequence was amplified from Addgene plasmid 78335” in the HTML and PDF versions of the article.
By JiaJia Chen, Chloé S. Baron, Kaiwen Sun, Emily J. Robitschek, Alicia M. McConnell, Constance Wu, Aikaterini Dedeilia, Moshe Sade-Feldman, Michael Manos, Kevin Chen, Anna Cox, Calvin G. Ludwig, Manolis Kellis, Elizabeth I. Buchbinder, Nir Hacohen, Jiekun Yang, Genevieve M. Boland, Brian J. Abraham, David R. Liu, Leonard I. Zon, Megan L Insco, Rodsy Modhurima
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Nature
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An encyclopedia of human enhancer–gene regulatory interactions
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Abstract Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the effect of human genetic variation on disease1,2,3,4,5,6. Here we create and evaluate a resource of more than 92 million enhancer–gene regulatory interactions across 1,458 biosamples covering 369 cell types and tissues, by integrating predictive models, chromatin states, three-dimensional contacts and large-scale genetic perturbations generated by the ENCODE Consortium7.
By Andreas R. Gschwind, Kristy S. Mualim, Alireza Karbalayghareh, Maya U. Sheth, Kushal Dey, Evelyn Jagoda, Ramil Nurtdinov, Wang Xi, Anthony Tan, Hank Jones, X. Rosa Ma, David Yao, Dulguun Amgalan, Judhajeet Ray, Chad Munger, Joseph Nasser, Ziga Avsec, Benjamin James, Muhammad S. Shamim, Neva C. Durand, Suhas S. P. Rao, Benjamin Doughty, Kalina Andreeva, Jacob C. Ulirsch, Kaili Fan, Elizabeth Perez, Elizabeth Pérez, Tri C. Nguyen, Trí Nguyễn, David Kelley, Hilary Finucane, Jill Moore, Zhiping Weng, Manolis Kellis, Michael Bassik, Berk Ustun, Alkes L Price, Michael Beer, Roderic Guigó, John A. Stamatoyannopoulos, Erez Lieberman Aiden, William J. Greenleaf, Christina Leslie, Lars M. Steinmetz, Anshul Kundaje, Jesse M. Engreitz, James Galante, Ragini Mahajan
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Nature
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Genotype epigenome phenotype integration reveals peripheral immune contributions to type I bipolar disorder
Abstract Immune dysfunction has been increasingly implicated in bipolar disorder, but the underlying mechanisms remain unclear. To address this, we profile 833 genome-wide chromatin immunoprecipitation sequencing datasets spanning five histone marks in peripheral blood immune cells from 88 Type I bipolar disorder patients and 92 controls, integrating them with whole-genome sequencing and clinical data.
Expanding the human proteome with microproteins and peptideins
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Abstract A major scientific drive is to characterize the protein-coding genome, which is a primary basis for studying human health. But the fundamental question remains of what has been missed in previous analyses. Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states1,2,3, with major implications for biomedical science.
By Eric Deutsch, Leron W. Kok, Jonathan Mudge, Cristian Valls, Irwin Jungreis, Jorge Ruiz-Orera, Zhi Sun, Ulrike Kusebauch, Ivo Fierro-Monti, Jennifer G. Abelin, M. Mar Albà, Julie L Aspden, Sreejan Bandyopadhyay, Kaushik Banerjee, Pavel V. Baranov, Ariel A. Bazzini, Francis Bourassa, Elspeth A. Bruford, Lorenzo Calviello, Steven Carr, Anne-Ruxandra Carvunis, Sonia Chothani, Jim Clauwaert, Kellie Dean, Pouya Faridi, Adam Frankish, Amy Goodale, Thomas Green, Norbert Hubner, Nicholas T. Ingolia, Manolis Kellis, Michele Magrane, Maria Martin Verified, María Martín Verified, Thomas Martinez, Gerben Menschaert, Uwe Ohler, Sandra Orchard, Alisa Potter, Owen Rackham, Matthew Rees, David Root, Jennifer Roth, Xavier Roucou, Fernando J. Sialana, Sarah A. Slavoff, Michał Świrski, Jack Tierney, Félix-Antoine Trifiro, Eivind Valen, Valeriia Vasylieva, Aaron Wacholder, Shengbo Wang, Li Wang, Jonathan S. Weissman, Wei Wu, Zhi Xie, Jyoti Choudhary, Michal Bassani-Sternberg, Juan Antonio Vizcaino, Nicola Ternette, Marie A. Brunet, Robert L. Moritz, John R. Prensner, Sebastiaan van Heesch
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Nature
Verified
Multi-omics analysis of a pig-to-human decedent kidney xenotransplant - Nature
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Abstract Organ shortage remains a major challenge in transplantation, and gene-edited pig organs offer a promising solution1–3. Despite gene-editing, the immune reactions following xenotransplantation can still cause transplant failure4. To understand the immunological response of a pig-to-human kidney xenotransplantation, we conducted large-scale multi-omics profiling of the xenograft and the host’s blood over a 61-day procedure in a brain-dead human (decedent) recipient.
By Eloi Schmauch, Brian D. Piening, Alexa K. Dowdell, Maedeh Mohebnasab, Alexey Stukalov, Ian Jaffe, Jacqueline I. Kim, Tal Eitan, Darragh O’Brien, Alexandra Bartlett, Francesca Zanoni, David Andrijevic, Berk Maden, Weimin Zhang, Loren Gragert, Lauren Hamilton, Larisa Kagermazova, Brendan Camellato, Sarah J. Gao, Alawi Habara, Scott Thomas, Deepak Saxena, Adriana Heguy, Michael Snyder, Asim Rais Siddiqui, Anita S. Chong, Minna Kaikkonen, Suvi Linna-Kuosmanen, Massimo Mangiola, Ramin S Herati, Jeffrey S. Stern, Adam D. Griesemer, Manolis Kellis, Jef Boeke, Robert Montgomery
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Nature
Verified
Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active proteoform that supports myocardial function
Abstract Programmed ribosomal frameshifting is a process where a proportion of ribosomes change their reading frame on an mRNA. While frameshifting is commonly used by viruses, very few phylogenetically conserved examples are known in nuclear encoded genes. Here, we report a +1 frameshifting event during decoding of the human gene PLEKHM2 that provides access to a second internally overlapping ORF.
ABCA7 variants impact phosphatidylcholine and mitochondria in neurons - Nature
Abstract Loss-of-function variants in the lipid transporter ABCA7 substantially increase the risk of Alzheimer’s disease1,2, yet how they impact cellular states to drive disease remains unclear. Here, using single-nucleus RNA-sequencing analysis of human brain samples, we identified widespread gene expression changes across multiple neural cell types associated with rare ABCA7 loss-of-function variants.
Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience
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Keywords Alzheimer's disease cognitive resilience single-cell multiomics epigenomics epigenomic stability epigenomic erosion epigenomic information microglial activation exhaustion regulatory network Introduction Alzheimer’s disease (AD) is the most common cause of dementia, characterized by progressive cognitive decline and neurodegeneration.1,2,3 A hallmark of AD is the accumulation of amyloid plaques and tau neurofibrillary tangles (NFTs), which disrupt synaptic integrity and drive...
By Zunpeng Liu, Shanshan Zhang, Benjamin James, Kyriaki Galani, Riley J. Mangan, Stuart Benjamin Fass, Chuqian Liang, Manoj M. Wagle, Carles Boix, Yosuke Tanigawa, Sukwon Yun, Yena Sung, Xushen Xiong, Na Sun, Lei Hou, Martin Wohlwend, Mufan Qiu, Xikun Han, Lei Xiong, Efthalia Preka, Lei Huang, William Li Verified, Li-Lun Ho, Amy Grayson, Julio C. Mantero, Alexey Kozlenkov, Hansruedi Mathys, Tianlong Chen, Stella Dracheva, David Bennett, Li-Huei Tsai, Manolis Kellis
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Cell Press
Verified
Specific oncogene activation of the cell of origin in mucosal melanoma - Nature Communications
Abstract Mucosal melanoma (MM) is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics, we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly, melanoma only develops from melanocytes lining internal organs, analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanomas.
Complete sequencing of ape genomes - Nature
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Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies1,2,3. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang.
By DongAhn Yoo, Arang Rhie, Prajna hebbar, Francesca Antonacci, Glennis A. Logsdon, Brandon Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Abigail N. Sequeira, Glenn Hickey, Graciela Monfort Anez, Christine R. Beck, Arjun Biddanda, Gerard G. Bouffard, Lucia Carbone, Laura Carrel, Agnes Chan, Juyun Crawford, Mark Diekhans, Gage H. Garcia, David Gilbert, Richard Green, Andrea Guarracino, Gabrielle Hartley, Michael Hiller, Manolis Kellis, William Lees, Mark Loftus, Jian Ma, Yafei Mao, Rajiv C. McCoy, Sean McKinney, Britta Meyer, Karen H Miga, Katherine Munson, Matt Pennell, Pavel A. Pevzner, David Porubsky, Tamara A. Potapova, Joana Rocha, Oliver A. Ryder, Swati Saha, Takayo Sasaki, Michael C Schatz, Nicholas J. Schork, Linnéa Smeds, Dongmin Son, Alexander P. Sweeten, Michael Tassia, Francoise Thibaud-Nissen, Julie Wertz, Shilong Zhang, Sarah Zhao, Erich D. Jarvis, Jennifer L. Gerton, Benedict Paten, Christian D. Huber, Tobias Lenz, Miriam K. Konkel, Soojin V. Yi, Stefan Canzar, Corey T. Watson, Peter H. Sudmant, Erin K Molloy, Erik Garrison, Craig B. Lowe, Mario Ventura, Rachel O’Neill, Sergey Koren, Kateryna D. Makova, Adam M. Phillippy
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Nature
Verified
Author Correction: APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes - Nature
Correction to: Nature https://doi.org/10.1038/s41586-022-05439-w Published online 16 November 2022 In the version of the article initially published, the “Isolation of nuclei from frozen post-mortem brain tissue” and “Droplet-based snRNA-seq” sections of the Methods did not reference a partial overlap of human snRNA-sequencing samples with samples reported in a previous study1 (ref. 12 in the original article).
Deep learning prediction of ribosome profiling with Translatomer reveals translational regulation and interprets disease variants - Nature Machine Intelligence
Abstract Gene expression involves transcription and translation. Despite large datasets and increasingly powerful methods devoted to calculating genetic variants’ effects on transcription, discrepancy between messenger RNA and protein levels hinders the systematic interpretation of the regulatory effects of disease-associated variants. Accurate models of the sequence determinants of translation are needed to close this gap and to interpret disease-associated variants that act on translation.
A polygenic score method boosted by non-additive models - Nature Communications
Abstract Dominance heritability in complex traits has received increasing recognition. However, most polygenic score (PGS) approaches do not incorporate non-additive effects. Here, we present GenoBoost, a flexible PGS modeling framework capable of considering both additive and non-additive effects, specifically focusing on genetic dominance.
Integrative multi-omics profiling in human decedents receiving pig heart xenografts - Nature Medicine
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Abstract In a previous study, heart xenografts from 10-gene-edited pigs transplanted into two human decedents did not show evidence of acute-onset cellular- or antibody-mediated rejection.
By Brian D. Piening, Maedeh Mohebnasab, Bo Xia, Jeffrey S. Stern, Weimin Zhang, Jacqueline I. Kim, David Andrijevic, Karen Abou Khalil, Ian Jaffe, Darragh O’Brien, Han Chen, Andrew Chang, Xiangping Lin, Alawi Habara, Feng-Xia Liang, Adriana Heguy, Basil Michael, Minna Kaikkonen, Nader Moazami, Ramin S Herati, Adam D. Griesemer, Manolis Kellis, Michael Snyder, Jef Boeke, Alexa K. Dowdell, Suvi Linna-Kuosmanen
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Nature
Verified
TDP-43 proteinopathy in ALS is triggered by loss of ASRGL1 and associated with HML-2 expression - Nature Communications
Abstract TAR DNA-binding protein 43 (TDP-43) proteinopathy in brain cells is the hallmark of amyotrophic lateral sclerosis (ALS) but its cause remains elusive. Asparaginase-like-1 protein (ASRGL1) cleaves isoaspartates, which alter protein folding and susceptibility to proteolysis. ASRGL1 gene harbors a copy of the human endogenous retrovirus HML-2, whose overexpression contributes to ALS pathogenesis.
Multisensory gamma stimulation promotes glymphatic clearance of amyloid - Nature
Abstract The glymphatic movement of fluid through the brain removes metabolic waste1,2,3,4. Noninvasive 40 Hz stimulation promotes 40 Hz neural activity in multiple brain regions and attenuates pathology in mouse models of Alzheimer’s disease5,6,7,8. Here we show that multisensory gamma stimulation promotes the influx of cerebrospinal fluid and the efflux of interstitial fluid in the cortex of the 5XFAD mouse model of Alzheimer’s disease.
Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types - Nature Communications
Abstract Prioritizing disease-critical cell types by integrating genome-wide association studies (GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) have characterized cell types at high resolution, and studies integrating GWAS with scRNA-seq have shown promise, but studies integrating GWAS with scATAC-seq have been limited.
Power of inclusion: Enhancing polygenic prediction with admixed individuals
Keywords polygenic score polygenic risk score genetic risk score diversity transferability population stratification population biobanks UK Biobank Lasso Elastic Net Introduction Polygenic scores (PGSs), used for aggregating genetic effects into the individual-level genetic liability of diseases or non-disease traits,1,2 have attracted significant research interest as a result of the recent expansion of genotyped cohort sample sizes, increased recognition of the polygenicity of complex...
Power of inclusion: Enhancing polygenic prediction with admixed individuals
Summary Admixed individuals offer unique opportunities for addressing limited transferability in polygenic scores (PGSs), given the substantial trans-ancestry genetic correlation in many complex traits. However, they are rarely considered in PGS training, given the challenges in representing ancestry-matched linkage-disequilibrium reference panels for admixed individuals.
Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington’s disease - Nature Communications
Author notes These authors contributed equally: Ayano Matsushima, Sergio Sebastian Pineda. These authors jointly supervised this work: Manolis Kellis, Myriam Heiman, Ann M. Graybiel. Authors and Affiliations McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA Ayano Matsushima, Jill R. Crittenden & Ann M. Graybiel Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA Ayano Matsushima, Jill R.
APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes - Nature
Abstract APOE4 is the strongest genetic risk factor for Alzheimer’s disease1,2,3. However, the effects of APOE4 on the human brain are not fully understood, limiting opportunities to develop targeted therapeutics for individuals carrying APOE4 and other risk factors for Alzheimer’s disease4,5,6,7,8.
A synthetic transcription platform for programmable gene expression in mammalian cells - Nature Communications
Abstract Precise, scalable, and sustainable control of genetic and cellular activities in mammalian cells is key to developing precision therapeutics and smart biomanufacturing. Here we create a highly tunable, modular, versatile CRISPR-based synthetic transcription system for the programmable control of gene expression and cellular phenotypes in mammalian cells.
Standardized annotation of translated open reading frames - Nature Biotechnology
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To the Editor — Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs because of uncertainties about their experimental reproducibility and physiological roles.
By Jonathan Mudge, Jorge Ruiz-Orera, John R. Prensner, Marie A. Brunet, Irwin Jungreis, Jose Gonzalez, José González Verified, Thomas Martinez, Yucheng Yang, Pavel V. Baranov, Ariel A. Bazzini, Elspeth A. Bruford, Anne-Ruxandra Carvunis, Jin Chen, Eric Deutsch, Paul Flicek, Norbert Hubner, Nicholas T. Ingolia, Manolis Kellis, Uwe Ohler, Xavier Roucou, Alan Saghatelian, Sebastiaan van Heesch, Ferriol Calvet, Michele Magrane, Jana Felicitas Schulz, Juan Pablo Couso, Robert L. Moritz
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Nature
Verified
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes - Nature
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Correction to: Nature https://doi.org/10.1038/s41586-020-2493-4 Published online 29 July 2020 In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list.
By Jill Moore, Michael J. Purcaro, Charles Epstein, Rajinder Kaul, David U. Gorkin, Yin Shen, Mark Mackiewicz, Ali Mortazavi, Cheryl A. Keller, Diane E. Dickel, Juan Carlos Rivera-Mulia, Joel Rozowsky, Axel Visel, Gene W. Yeo, Christopher Burge, David Gilbert, Job Dekker, John L. Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert Klein, Anshul Kundaje, Peggy J. Farnham, J. Michael Cherry, Bing Ren, Len A. Pennacchio, Michael Snyder, Bradley E. Bernstein, Ross C. Hardison, Zhiping Weng
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Nature
Verified
Immune genes outside immune cells for multiple sclerosis
In this issue of Neuron, Meijer et al., 2022 Meijer M. Agirre E. Kabbe M. van Tuijn C.A. Heskol A. Zheng C. Mendanha Falcão A. Bartosovic M. Kirby L. Calini D. et al. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes - Nature Communications
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
A wealth of discovery built on the Human Genome Project - by the numbers
The 20th anniversary of the publication of the first draft of the human genome1,2 offers an opportunity to track how the project has empowered research into the genetic roots of human disease, changed drug discovery and helped to revise the idea of the gene itself. Here we distil these impacts and trends.
Regulatory genomic circuitry of human disease loci by integrative epigenomics
Abstract Annotating the molecular basis of human disease remains an unsolved challenge, as 93% of disease loci are non-coding and gene-regulatory annotations are highly incomplete1,2,3. Here we present EpiMap, a compendium comprising 10,000 epigenomic maps across 800 samples, which we used to define chromatin states, high-resolution enhancers, enhancer modules, upstream regulators and downstream target genes.
Author Correction: Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes
Correction to: Nature Medicine https://doi.org/10.1038/s41591-020-0886-4, published online 8 June 2020. In the version of this article initially published, the units used for TEER results (ohm cm–2) were incorrect in the third, fourth, fifth and final sentences of the fourth paragraph in the first subsection of Results; along the vertical axis of Fig. 1k; and in the fourth sentence of the second subsection of Methods (‘iBBB permeability studies’). The correct units are ‘ohm cm2’.
Mathematical analysis of Córdoba calcifediol trial suggests strong role for Vitamin D in reducing ICU admissions of hospitalized COVID-19 patients
Abstract A randomized controlled trial of calcifediol (25-hydroxyvitamin D3) as a treatment for hospitalized COVID-19 patients in Córdoba, Spain, found that the treatment was associated with reduced ICU admissions with very large effect size and high statistical significance, but the study has had limited impact because it had only 76 patients and imperfect blinding, and did not measure vitamin D levels pre- and post-treatment or adjust for several comorbidities.
Mathematical analysis of Córdoba calcifediol trial suggests strong role for Vitamin D in reducing ICU admissions of hospitalized COVID-19 patients
Abstract A randomized controlled trial of calcifediol (25-hydroxyvitamin D3) as a treatment for hospitalized COVID-19 patients in Córdoba, Spain, found that the treatment was associated with reduced ICU admissions with very large effect size and high statistical significance, but the study has had limited impact because it had only 76 patients and imperfect blinding, and did not measure vitamin D levels pre- and post-treatment or adjust for several comorbidities.
A multiresolution framework to characterize single-cell state landscapes
Abstract Dissecting the cellular heterogeneity embedded in single-cell transcriptomic data is challenging. Although many methods and approaches exist, identifying cell states and their underlying topology is still a major challenge. Here, we introduce the concept of multiresolution cell-state decomposition as a practical approach to simultaneously capture both fine- and coarse-grain patterns of variability.
Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble
Abstract The epigenome and three-dimensional (3D) genomic architecture are emerging as key factors in the dynamic regulation of different transcriptional programs required for neuronal functions. In this study, we used an activity-dependent tagging system in mice to determine the epigenetic state, 3D genome architecture and transcriptional landscape of engram cells over the lifespan of memory formation and recall.
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
Abstract Haplotype reconstruction of distant genetic variants remains an unsolved problem due to the short-read length of common sequencing data. Here, we introduce HapTree-X, a probabilistic framework that utilizes latent long-range information to reconstruct unspecified haplotypes in diploid and polyploid organisms.
Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes
Abstract In Alzheimer’s disease, amyloid deposits along the brain vasculature lead to a condition known as cerebral amyloid angiopathy (CAA), which impairs blood–brain barrier (BBB) function and accelerates cognitive degeneration. Apolipoprotein (APOE4) is the strongest risk factor for CAA, yet the mechanisms underlying this genetic susceptibility are unknown.
Joint profiling of DNA methylation and chromatin architecture in single cells - Nature Methods
Abstract We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues.
Defining functional DNA elements in the human genome
Abstract With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types.
A causal inference framework for estimating genetic variance and pleiotropy from GWAS summary data
A causal inference framework for estimating genetic variance and pleiotropy from GWAS summary data Yongjin Park, Liang He, Manolis Kellis bioRxiv 531673; doi: https://doi.org/10.1101/531673
Manolis Kellis, "Mediation analysis, multi-tissue factor QTLs, EHRs, transfer learning in deep CNNs for genetics"
Manolis Kellis, Mediation analysis, multi-tissue factor QTLs, EHRs, transfer learning in deep CNNs for genetics, Statistical and Computational Challenges in Large Scale Molecular Biology, BIRS, BIRS talk, 17w5131, math, mathematics, video
A metabolic master switch underlying human obesity
Obesity is one of the biggest public health challenges of the 21st century. Affecting more than 500 million people worldwide, obesity costs at least $200 billion each year in the United States alone, and contributes to potentially fatal disorders such as cardiovascular disease, type 2 diabetes, and cancer.
Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type
To capture epigenomic differences between groups of epigenomes, we focus on the set of chromatin states associated with each protein-coding gene (Fig. 1), while generating an information-theoretic encoding of these chromatin states and correcting for external factors to isolate differences due to the comparison.
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