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Mutations causing Lopes-Maciel-Rodan Syndrome are huntingtin hypomorphs.

Roy Jung, Yejin Lee, Douglas Barker, Kevin Correia, Baehyun Shin, Jacob Loupe, Ryan L Collins, Diane Lucente, Jayla Ruliera, Tammy Gillis, Jayalakshmi S Mysore, Lance Rodan, Jonathan Picker, Jong-Min Lee, David Howland, Ramee Lee, Seung Kwak, Marcy E MacDonald, James F Gusella, Ihn Sik Seong,

Huntington's disease (HD) pathogenesis involves a genetic gain-of-function toxicity mechanism triggered by the expanded HTT CAG repeat. Current therapeutic efforts aim to suppress expression of total or mutant huntingtin, though the relationship of huntingtin's normal activities to the gain-of-function mechanism and what the effects of huntingtin-lowering might be are unclear. ... Read more >>

Hum Mol Genet (Human molecular genetics)
[2021, :]

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Patterns of CAG repeat instability in the central nervous system and periphery in Huntington's disease and in spinocerebellar ataxia type 1.

Ricardo Mouro Pinto, Larissa Arning, James V Giordano, Pedram Razghandi, Marissa A Andrew, Tammy Gillis, Kevin Correia, Jayalakshmi S Mysore, Debora-M Grote Urtubey, Constanze R Parwez, Sarah M von Hein, H Brent Clark, Huu Phuc Nguyen, Eckart Förster, Allison Beller, Suman Jayadaev, C Dirk Keene, Thomas D Bird, Diane Lucente, Jean-Paul Vonsattel, Harry Orr, Carsten Saft, Elisabeth Petrasch-Parwez, Vanessa C Wheeler,

The expanded HTT CAG repeat causing Huntington's disease (HD) exhibits somatic expansion proposed to drive the rate of disease onset by eliciting a pathological process that ultimately claims vulnerable cells. To gain insight into somatic expansion in humans, we performed comprehensive quantitative analyses of CAG expansion in ~50 central nervous ... Read more >>

Hum Mol Genet (Human molecular genetics)
[2020, 29(15):2551-2567]

Cited: 3 times

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Pan-Genome-Scale Network Reconstruction: Harnessing Phylogenomics Increases the Quantity and Quality of Metabolic Models.

Kevin Correia, Radhakrishnan Mahadevan,

A genome-scale network reconstruction (GENRE) is a knowledgebase for an organism and has various applications. Available genome sequences have risen in recent years, but the number of curated GENREs has not kept pace. Existing yeast GENREs contain significant commission and omission errors. Current practices limit the quantity and quality of ... Read more >>

Biotechnol J (Biotechnology journal)
[2020, 15(10):e1900519]

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A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution.

Yilan Liu, Jinjin Chen, Anna N Khusnutdinova, Kevin Correia, Patrick Diep, Khorcheska A Batyrova, Kayla Nemr, Robert Flick, Peter Stogios, Alexander F Yakunin, Radhakrishnan Mahadevan,

Background:Aldehyde decarbonylases (ADs), which convert acyl aldehydes into alkanes, supply promising solution for producing alkanes from renewable feedstock. However the instability of ADs impedes their further application. Therefore, the current study aimed to investigate the degradation mechanism of ADs and engineer it towards high stability. Results:Here, we describe the discovery ... Read more >>

Biotechnol Biofuels (Biotechnology for biofuels)
[2020, 13:114]

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A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution

yilan liu, jinjin chen, Anna Khusnutdinova, Kevin Correia, Patrick Diep, Khorcheska Batyrovaa, Kayla Nemr, Robert Flick, Peter Stogios, Alexander Yakunin, Radhakrishnan Mahadevan,

<h4>Background: </h4> Aldehyde decarbonylases (ADs), which convert acyl aldehydes into alkanes, supply promising solution for producing alkanes from renewable feedstock. However the instability of ADs impedes their further application. Therefore, the current study aimed to investigate the degradation mechanism of ADs and engineer it towards high stability. <h4>Results: </h4>: Here, ... Read more >>

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MEMOTE for standardized genome-scale metabolic model testing.

Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang,

Nat Biotechnol (Nature biotechnology)
[2020, 38(3):272-276]

Cited: 24 times

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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.

Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Biotechnol (Nature biotechnology)
[2020, 38(4):504]

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Genetic Risk Underlying Psychiatric and Cognitive Symptoms in Huntington's Disease.

Natalie Ellis, Amelia Tee, Branduff McAllister, Thomas Massey, Duncan McLauchlan, Timothy Stone, Kevin Correia, Jacob Loupe, Kyung-Hee Kim, Douglas Barker, Eun Pyo Hong, Michael J Chao, Jeffrey D Long, Diane Lucente, Jean Paul G Vonsattel, Ricardo Mouro Pinto, Kawther Abu Elneel, Eliana Marisa Ramos, Jayalakshmi Srinidhi Mysore, Tammy Gillis, Vanessa C Wheeler, Christopher Medway, Lynsey Hall, Seung Kwak, Cristina Sampaio, Marc Ciosi, Alastair Maxwell, Afroditi Chatzi, Darren G Monckton, Michael Orth, G Bernhard Landwehrmeyer, Jane S Paulsen, Ira Shoulson, Richard H Myers, Erik van Duijn, Hugh Rickards, Marcy E MacDonald, Jong-Min Lee, James F Gusella, Lesley Jones, Peter Holmans,

<h4>Background</h4>Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the HTT gene. It is diagnosed following a standardized examination of motor control and often presents with cognitive decline and psychiatric symptoms. Recent studies have detected genetic loci modifying the age at onset of motor ... Read more >>

Biol Psychiatry (Biological psychiatry)
[2020, 87(9):857-865]

Cited: 1 time

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CAG Repeat Not Polyglutamine Length Determines Timing of Huntington's Disease Onset.

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Variable, glutamine-encoding, CAA interruptions indicate that a property of the uninterrupted HTT CAG repeat sequence, distinct from the length of huntingtin's polyglutamine segment, dictates the rate at which Huntington's disease (HD) develops. The timing of onset shows no significant association with HTT cis-eQTLs but is influenced, sometimes in a sex-specific ... Read more >>

Cell (Cell)
[2019, 178(4):887-900.e14]

Cited: 35 times

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Genetic risk underlying psychiatric and cognitive symptoms in Huntington’s Disease

Natalie Ellis, Amelia Tee, Branduff McAllister, Thomas Massey, Duncan McLauchlan, Timothy Stone, Kevin Correia, Jacob Loupe, Kyung-Hee Kim, Douglas Barker, Eun Pyo Hong, Michael Chao, Jeffrey Long, Diane Lucente, Jean Paul Vonsattel, Ricardo Mouro Pinto, Kawther Abu Elneel, Eliana Marisa Ramos, Jayalakshmi Srinidhi Mysore, Tammy Gillis, Vanessa Wheeler, Christopher Medway, Lynsey Hall, Seung Kwak, Cristina Sampaio, Marc Ciosi, Alastair Maxwell, Afroditi Chatzi, Darren Monckton, Michael Orth, Bernhard Landwehrmeyer, Jane Paulsen, Ira Shoulson, Richard Myers, Erik van Duijn, Hugh Rickards, Marcy MacDonald, Jong-min Lee, James Gusella, Lesley Jones, Peter Holmans,

Huntington’s disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the HTT gene. It is diagnosed following a standardized exam of motor control and often presents with cognitive decline and psychiatric symptoms. Recent studies have detected genetic loci modifying the age at onset of motor ... Read more >>

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Huntington’s disease onset is determined by length of uninterrupted CAG, not encoded polyglutamine, and is modified by DNA maintenance mechanisms

, Jong-Min Lee, Kevin Correia, Jacob Loupe, Kyung-Hee Kim, Douglas Barker, Eun Pyo Hong, Michael Chao, Jeffrey Long, Diane Lucente, Jean-Paul Vonsattel, Ricardo Mouro Pinto, Kawther Abu Elneel, Eliana Marisa Ramos, Jayalakshmi Srinidhi Mysore, Tammy Gillis, Vanessa Wheeler, Marcy MacDonald, James Gusella, Thomas Massey, Branduff McAllister, Christopher Medway, Timothy Stone, Lynsey Hall, Lesley Jones, Peter Holmans, Seung Kwak, Anka Ehrhardt, Cristina Sampaio, Marc Ciosi, Alastair Maxwell, Afroditi Chatzi, Darren Monckton, Michael Orth, Bernhard Landwehrmeyer, Jane Paulsen, Ray Dorsey, Ira Shoulson, Richard Myers,

<h4>SUMMARY</h4> The effects of variable, glutamine-encoding, CAA interruptions indicate that a property of the uninterrupted HTT CAG repeat sequence, distinct from huntingtin’s polyglutamine segment, dictates the rate at which HD develops. The timing of onset shows no significant association with HTT cis -eQTLs but is influenced, sometimes in a sex-specific ... Read more >>

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AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution.

Kevin Correia, Shi M Yu, Radhakrishnan Mahadevan,

Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. Insight into the evolution of orthologs, paralogs and xenologs in the yeast pan-genome can help bridge these ... Read more >>

Database (Oxford) (Database : the journal of biological databases and curation)
[2019, 2019:]

Cited: 1 time

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Flux balance analysis predicts NADP phosphatase and NADH kinase are critical to balancing redox during xylose fermentation inScheffersomyces stipitis

Kevin Correia, Anna Khusnutdinova, Peter Yan Li, Jeong Chan Joo, Greg Brown, Alexander Yakunin, Radhakrishnan Mahadevan,

<h4>ABSTRACT</h4> Xylose is the second most abundant sugar in lignocellulose and can be used as a feedstock for next-generation biofuels by industry. Saccharomyces cerevisiae , one of the main workhorses in biotechnology, is unable to metabolize xylose natively but has been engineered to ferment xylose to ethanol with the xylose ... Read more >>

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Pan-genome-scale network reconstruction: a framework to increase the quantity and quality of metabolic network reconstructions throughout the tree of life

Kevin Correia, Radhakrishnan Mahadevan,

<h4>ABSTRACT</h4> A genome-scale network reconstruction (GENRE) represents the knowledgebase of an organism and can be used in a variety of applications. The drop in genome sequencing costs has led to an increase in sequenced genomes, but the number of curated GENRE’ s has not kept pace. This gap hinders our ... Read more >>

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An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community.

Po-Hsiang Wang, Kevin Correia, Han-Chen Ho, Naveen Venayak, Kayla Nemr, Robert Flick, Radhakrishnan Mahadevan, Elizabeth A Edwards,

Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete ... Read more >>

ISME J (The ISME journal)
[2019, 13(4):1042-1055]

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Memote: A community driven effort towards a standardized genome-scale metabolic model test suite

Christian Lieven, Moritz Beber, Brett Olivier, Frank Bergmann, Meric Ataman, Parizad Babaei, Jennifer Bartell, Lars Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta Ebert, Janaka Edirisinghe, Jose Faria, Adam Feist, Georgios Fengos, Ronan Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher Henry, Henning Hermjakob, Markus Herrgård, Hyun Uk Kim, Zachary King, Jasper Koehorst, Steffen Klamt, Edda Klipp, Meiyappan Lakshmanan, Nicolas Le Novère, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan Lewis, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory Medlock, Jonathan Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Osbaldo Resendis-Antonio, Bernhard Palsson, Jason Papin, Kiran Patil, Mark Poolman, Nathan Price, Anne Richelle, Isabel Rocha, Benjamin Sanchez, Peter Schaap, Rahuman Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith Wodke, Joana Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang,

Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed. Here, we present memote ( https://github.com/opencobra/memote ) an open-source software containing ... Read more >>

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Cited: 5 times

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Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF

Kevin Correia, Hanchen Ho, Radhakrishnan Mahadevan,

<h4>ABSTRACT</h4> <h4>Background</h4> Organohalide-respiring bacteria (OHRB) play an important role in the global halogen cycle and bioremediation of industrial sites contaminated with chlorinated organics. One notable OHRB is Dehalobacter restrictus strain CF, which is capable of respiring chloroform to dichloromethane. Improved bioremediation strategies could be employed with a greater understanding of ... Read more >>

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Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

Po-Hsiang Wang, Kevin Correia, Han-Chen Ho, Naveen Venayak, Kayla Nemr, Robert Flick, Radhakrishnan Mahadevan, Elizabeth Edwards,

Most microorganisms in the biosphere live in communities and develop coordinated metabolisms via trading metabolites. In this study, we sought to deconstruct the metabolic interdependency in organohalide-respiring microbial communities enriched with Dehalobacter restrictus ( Dhb ), using a complementary approach of computational metabolic modeling and experimental validation. Dhb possesses a ... Read more >>

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Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid.

Victor E Balderas-Hernández, Kevin Correia, Radhakrishnan Mahadevan,

Toxic concentrations of monocarboxylic weak acids present in lignocellulosic hydrolyzates affect cell integrity and fermentative performance of Saccharomyces cerevisiae. In this work, we report the deletion of the general catabolite repressor Mig1p as a strategy to improve the tolerance of S. cerevisiae towards inhibitory concentrations of acetic, formic or levulinic ... Read more >>

J Ind Microbiol Biotechnol (Journal of industrial microbiology & biotechnology)
[2018, 45(8):735-751]

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Biocatalytic production of adipic acid from glucose using engineered Saccharomyces cerevisiae.

Kaushik Raj, Siavash Partow, Kevin Correia, Anna N Khusnutdinova, Alexander F Yakunin, Radhakrishnan Mahadevan,

Adipic acid is an important industrial chemical used in the synthesis of nylon-6,6. The commercial synthesis of adipic acid uses petroleum-derived benzene and releases significant quantities of greenhouse gases. Biocatalytic production of adipic acid from renewable feedstocks could potentially reduce the environmental damage and eliminate the need for fossil fuel ... Read more >>

Metab Eng Commun (Metabolic engineering communications)
[2018, 6:28-32]

Cited: 6 times

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AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution

Kevin Correia, Shi Yu, Radhakrishnan Mahadevan,

<h4>ABSTRACT</h4> Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by ... Read more >>

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The Genetic Modifiers of Motor OnsetAge (GeM MOA) Website: Genome-wide Association Analysis for Genetic Modifiers of Huntington's Disease.

Kevin Correia, Denise Harold, Kyung-Hee Kim, Peter Holmans, Lesley Jones, Michael Orth, Richard H Myers, Seung Kwak, Vanessa C Wheeler, Marcy E MacDonald, James F Gusella, Jong-Min Lee,

<h4>Background</h4>Huntington's disease (HD) is a dominantly inherited disease caused by a CAG expansion mutation in HTT. The age at onset of clinical symptoms is determined primarily by the length of this CAG expansion but is also influenced by other genetic and/or environmental factors.<h4>Objective</h4>Recently, through genome-wide association studies (GWAS) aimed at ... Read more >>

J Huntingtons Dis (Journal of Huntington's disease)
[2015, 4(3):279-284]

Cited: 11 times

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