Phenobiome

Microbiome

Data Mining

Epigenetics

Microbiome

The key papers describing PhenoBiome's technology and applications

PhenoBiome's foundational paper

Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.

Rodionov DA, Arzamasov AA, Khoroshkin MS, Iablokov SN, Leyn SA, Peterson SN, Novichkov PS, Osterman AL

Front Microbiol. 2019 Jun 12;10:1316

PhenoBiome's technology application and validation (selected papers)

Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans.

Delannoy-Bruno O, Desai C, Raman AS, Chen RY, Hibberd MC, Cheng J, Han N, Castillo JJ, Couture G, Lebrilla CB, Barve RA, Lombard V, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Kirbach K, Wilmot T, Heath AC, Klein S, Barratt MJ, Gordon JI.

Nature. 2021;595(7865):91-95.

Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases.

Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV.

Front Mol Biosci. 2021 Jan 18;7:603740.

Identifying determinants of bacterial fitness in a model of human gut microbial succession

Feng L, Raman AS, Hibberd MC, Cheng J, Griffin NW, Peng Y, Leyn SA, Rodionov DA, Osterman AL, Gordon JI

Proc Natl Acad Sci U S A. 2020 Feb 4;117(5):2622-2633

Formula with Added Sugar is Associated with a Distinct Gut Microbiota in Hispanic Infants.

Jones RB, Berger PK, Plows JF, Alderete TL, Millstein J, Iablokov SN, Rodionov DA, Knight R, Osterman Al, Bode L, Goran MI

Gut Microbes. 2020; 12(1):1813534

B-Vitamin Sharing Promotes Stability of Gut Microbial Communities.

Sharma V, Rodionov DA, Leyn SA, Tran D, Iablokov SN, Ding H, Peterson DA, Osterman AL, Peterson SN

Front Microbiol. 2019 Jul 2;10:1485

Extended list of publications

List of publications (by PhenoBiome's co-founders) on development, application, and experimental validation of various components of the PhenoBiome's technology.

D – description of methodology, which, for earlier (nonmicrobiome) papers implies underlying components of the current methodology (genomics-based reconstruction of metabolic pathways and associated regulatory mechanisms)

A – application of methodology to a specific biological or medical problem (likewise, before a new wave of microbiome papers, this means application to large groups of microbial species, but not communities)

V – experimental validation refers to a smaller category of papers (more in pre-microbiome) where bioinoformatics-based predictions were followed by experimental verification.

Genomics-based Predictive Metabolic Profiling of Microbial Communities

Development and homeostasis of infant gut microbiome (collaboration with Dr. J. Gordon)

Bifidobacterium infantis treatment promotes weight gain in Bangladeshi infants with severe acute malnutritionA

Barratt MJ, Nuzhat S, Ahsan K, Frese SA, Arzamasov AA, Sarker SA, Islam MM, Palit P, Islam MR, Hibberd MC, Nakshatri S, Cowardin CA, Guruge JL, Byrne AE, Venkatesh S, Sundaresan V, Henrick B, Duar RM, Mitchell RD, Casaburi G, Prambs J, Flannery R, Mahfuz M, Rodionov DA, Osterman AL, Kyle D, Ahmed T, Gordon JI.

Sci Transl Med. 2022 Apr 13;14(640):eabk1107.

Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans A

Han ND, Cheng J, Delannoy-Bruno O, Webber D, Terrapon N, Henrissat B, Rodionov DA, Arzamasov AA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Desai C, Marion S, Barratt MJ, Heath AC, Gordon JI.

Cell. 2022 Aug 4;185(16):3056-3057.

Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humansD

Nature. 2021;595(7865):91-95.

Duodenal Microbiota in Stunted Undernourished Children with EnteropathyA

Chen RY, Kung VL, Das S, Hossain MS, Hibberd MC, Guruge J, Mahfuz M, Begum SMKN, Rahman MM, Fahim SM, Gazi MA, Haque R, Sarker SA, Mazumder RN, Di Luccia B, Ahsan K, Kennedy E, Santiago-Borges J, Rodionov DA, Leyn SA, Osterman AL, Barratt MJ, Ahmed T, Gordon JI

N Engl J Med. 2020 Jul 23;383(4):321-333

Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood UndernutritionA

Di Luccia B, Ahern PP, Griffin NW, Cheng J, Guruge JL, Byrne AE, Rodionov DA, Leyn SA, Osterman AL, Ahmed T, Colonna M, Barratt MJ, Delahaye NF, Gordon JI

Cell Host Microbe. 2020 Jun 10;27(6):899-908.e5

Identifying determinants of bacterial fitness in a model of human gut microbial successionD

Feng L, Raman AS, Hibberd MC, Cheng J, Griffin NW, Peng Y, Leyn SA, Rodionov DA, Osterman AL, Gordon JI

Proc Natl Acad Sci U S A. 2020 Feb 4;117(5):2622-2633

Bioremediation of a Common Product of Food Processing by a Human Gut BacteriumA

Wolf AR, Wesener DA, Cheng J, Houston-Ludlam AN, Beller ZW, Hibberd MC, Giannone RJ, Peters SL, Hettich RL, Leyn SA, Rodionov DA, Osterman AL, Gordon JI

Cell Host Microbe. 2019 Oct 9;26(4):463-477.e8

A sparse covarying unit that describes healthy and impaired human gut microbiota developmentD

Raman AS, Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Subramanian S, Kang G, Bessong PO, Lima AAM, Kosek MN, Petri WA Jr, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Huq S, Mostafa I, Islam M, Mahfuz M, Haque R, Ahmed T, Barratt MJ, Gordon JI

Science. 2019 Jul 12;365(6449):eaau4735

Effects of microbiota-directed foods in gnotobiotic animals and undernourished childrenA

Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL, Cheng J, Chen RY, Subramanian S, Cowardin CA, Meier MF, O'Donnell D, Talcott M, Spears LD, Semenkovich CF, Henrissat B, Giannone RJ, Hettich RL, Ilkayeva O, Muehlbauer M, Newgard CB, Sawyer C, Head RD, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Hossain MI, Islam M, Choudhury N, Sarker SA, Huq S, Mahmud I, Mostafa I, Mahfuz M, Barratt MJ, Ahmed T, Gordon JI

Science. 2019 Jul 12;365(6449):eaau4732

The effects of micronutrient deficiencies on bacterial species from the human gut microbiotaA

Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI

Sci Transl Med. 2017 May 17;9(390):eaal4069

Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished childrenA

Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkaveya O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM, Fan YM, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Maleta KM, Newgard CB, Ashorn P, Dewey KG, Gordon JI.

Science. 2016 Feb 19;351(6275):10.1126/science.aad3311

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut BacteroidesV

Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N, Henrissat B, Osterman AL, Gordon JI.

Science. 2015 Oct 2;350(6256):aac5992

Nutrients effects on human gut microbiome (collaboration with Dr. S. Peterson and Prof. Michael Goran)

Alteration of Community Metabolism by Prebiotics and Medicinal HerbsA

Peterson CT, Perez Santiago J, Iablokov SN, Rodionov DA, Peterson SN.

Microorganisms. 2023 Mar 22;11(4):868.

Short-Chain Fatty Acids Modulate Healthy Gut Microbiota Composition and Functional PotentialA

Peterson CT, Perez Santiago J, Iablokov SN, Chopra D, Rodionov DA, Peterson SN.

Curr Microbiol. 2022 Mar 14;79(5):128.

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharidesD

Ojima MN, Jiang L, Arzamasov AA, Yoshida K, Odamaki T, Xiao J, Nakajima A, Kitaoka M, Hirose J, Urashima T, Katoh T, Gotoh A, van Sinderen D, Rodionov DA, Osterman AL, Sakanaka M, Katayama T.

ISME J. 2022 Sep;16(9):2265-2279.

Community Metabolic Interactions, Vitamin Production and Prebiotic Potential of Medicinal Herbs Used for ImmunomodulationA

Peterson CT, Iablokov SN, Uchitel S, Chopra D, Perez-Santiago J, Rodionov DA, Peterson SN.

Front Genet. 2021 Feb 3;12:584197.

Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human healthA

Coker JK, Moyne O, Rodionov DA, Zengler K.

Gut Microbes. 2021 Jan-Dec;13(1):1-18.

Formula with Added Sugar is Associated with a Distinct Gut Microbiota in Hispanic InfantsV

Jones RB, Berger PK, Plows JF, Alderete TL, Millstein J, Iablokov SN, Rodionov DA, Knight R, Osterman Al, Bode L, Goran MI

Gut Microbes. 2020; 12(1):1813534

Dietary Emulsifier Sodium Stearoyl Lactylate Alters Gut Microbiota in vitro and Inhibits Bacterial Butyrate ProducersV

Elmén L, Zlamal JE, Scott DA, Lee RB, Chen DJ, Colas AR, Rodionov DA, Peterson SN

Front Microbiol. 2020 May 15;11:892

B-Vitamin Sharing Promotes Stability of Gut Microbial CommunitiesV

Sharma V, Rodionov DA, Leyn SA, Tran D, Iablokov SN, Ding H, Peterson DA, Osterman AL, Peterson SN

Front Microbiol. 2019 Jul 2;10:1485

Prebiotic Potential of Culinary Spices Used to Support Digestion and BioabsorptionA

Peterson CT, Rodionov DA, Iablokov SN, Pung MA, Chopra D, Mills PJ, Peterson SN

Evid Based Complement Alternat Med. 2019 Jun 2;2019:8973704

16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropicsA

Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN

PLoS One. 2019 Mar 19;14(3):e0213869

Phenotype profiling and development of Binary Phenotype Matrix

Genomic reconstruction of short-chain fatty acid production by the human gut microbiotaD

Frolova MS, Suvorova IA, Iablokov SN, Petrov SN, Rodionov DA.

Front Mol Biosci. 2022 Aug 11;9:949563.

Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut MicrobiomeD

Ashniev GA, Petrov SN, Iablokov SN, Rodionov DA.

Microorganisms. 2022 Mar 30;10(4):740.

Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel DiseasesV

Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV.

Front Mol Biosci. 2021 Jan 18;7:603740.

Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial CommunitiesD

Iablokov SN, Novichkov PS, Osterman AL, Rodionov DA.

Front Microbiol. 2021 May 25;12:653314.

Micronutrient Requirements and Sharing Capabilities of the Human Gut MicrobiomeD

Rodionov DA, Arzamasov AA, Khoroshkin MS, Iablokov SN, Leyn SA, Peterson SN, Novichkov PS, Osterman AL

Front Microbiol. 2019 Jun 12;10:1316

Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived ConsortiaD

Leyn SA, Maezato Y, Romine MF, Rodionov DA

Front Microbiol. 2017 Jul 13;8:1304

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communitiesV

Romine MF, Rodionov DA, Maezato Y, Osterman AL, Nelson WC

ISME J. 2017 Jun;11(6):1434-1446

Genomics-based Reconstruction, Prediction and Validation of Metabolic Pathways/Phenotypes for diverse microbial species

The Subsystems approach for genome annotation and metabolic reconstruction

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomesD

Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V

Nucleic Acids Res. 2005 Oct 7;33(17):5691-702

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The Use of Subsystems to Encode Biosynthesis of Vitamins and CofactorsV

Osterman AL, Overbeek R, Rodionov DA

In Comprehensive Natural Products II Chemistry and Biology; Mander, L., Lui, H.-W., Eds.; Elsevier:Oxford, 2010; volume 7, pp.141–159

Application of subsystems approach for various metabolic pathways and microbial taxa

Novel Metabolic Pathways and Regulons for Hexuronate Utilization in ProteobacteriaA

Bouvier JT, Sernova NV, Ghasempur S, Rodionova IA, Vetting MW, Al-Obaidi NF, Almo SC, Gerlt JA, Rodionov DA

J Bacteriol. 2018 Dec 20;201(2):e00431-18

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylumA

Rodionova IA, Li X, Plymale AE, Motamedchaboki K, Konopka AE, Romine MF, Fredrickson JK, Osterman AL, Rodionov DA

Environ Microbiol Rep. 2015 Apr;7(2):204-10

Comparative genomics and functional analysis of rhamnose catabolic pathways and regulons in bacteriaV

Rodionova IA, Li X, Thiel V, Stolyar S, Stanton K, Fredrickson JK, Bryant DA, Osterman AL, Best AA, Rodionov DA

Front Microbiol. 2013 Dec 23;4:407

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron:comparative genomics reconstruction of metabolic and regulatory networksA

Ravcheev DA, Godzik A, Osterman AL, Rodionov DA

BMC Genomics. 2013 Dec 12;14:873

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritimaA

Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL

Front Microbiol. 2013 Aug 23;4:244

N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in ShewanellaV

Leyn SA, Gao F, Yang C, Rodionov DA

J Biol Chem. 2012 Aug 10;287(33):28047-56

Genomic encyclopedia of sugar utilization pathways in the Shewanella genusD,V

Rodionov DA, Yang C, Li X, Rodionova IA, Wang Y, Obraztsova AY, Zagnitko OP, Overbeek R, Romine MF, Reed S, Fredrickson JK, Nealson KH, Osterman AL

BMC Genomics. 2010 Sep 13;11:494

Reconstruction of xylose utilization pathway and regulons in FirmicutesA

Gu Y, Ding Y, Ren C, Sun Z, Rodionov DA, Zhang W, Yang S, Yang C, Jiang W

BMC Genomics. 2010 Apr 21;11:255

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensisV

Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, Osterman AL

J Biol Chem. 2006 Oct 6;281(40):29872-85

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteriaA

Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS

Genome Biol. 2004;5(11):R90

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systemsD

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS

Nucleic Acids Res. 2004 Jun 23;32(11):3340-53

Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotesA

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS

J Biol Chem. 2003 Oct 17;278(42):41148-59

Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanismsA

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS

J Biol Chem. 2002 Dec 13;277(50):48949-59

Genomics-based Prediction and Validation of Microbial Transporters and Transcriptional Regulatory Networks

Review on the comparative genomics approaches

Comparative genomic reconstruction of transcriptional regulatory networks in bacteriaD

Rodionov DA

Chem Rev. 2007 Aug;107(8):3467-97

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Comparative genomics and functional annotation of bacterial transportersA

Gelfand MS, Rodionov DA

Physics of Life Reviews. 2008: 5: 22-49

Research articles (applications)

Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagRD

Arzamasov AA, Nakajima A, Sakanaka M, Ojima MN, Katayama T, Rodionov DA, Osterman AL.

mSystems. 2022 Oct 26;7(5):e0034322.

LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio speciesA

Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A

PLoS One. 2019 Apr 9;14(4):e0214960

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transportA

Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE

Environ Microbiol. 2019 Feb;21(2):784-799

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide UtilizationD

Arzamasov AA, van Sinderen D, Rodionov DA

Front Microbiol. 2018 Apr 24;9:776

Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifsA

Garber ME, Rajeev L, Kazakov AE, Trinh J, Masuno D, Thompson MG, Kaplan N, Luk J, Novichkov PS, Mukhopadhyay A

Mol Microbiol. 2018 Mar;107(6):704-717

Comparative genomics and evolution of transcriptional regulons in ProteobacteriaA

Leyn SA, Suvorova IA, Kazakov AE, Ravcheev DA, Stepanova VV, Novichkov PS, Rodionov DA

Microb Genom. 2016 Jul 11;2(7):e000061

Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium GenusA

Khoroshkin MS, Leyn SA, Van Sinderen D, Rodionov DA

Front Microbiol. 2016 Feb 9;7:120

Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons in BacteriaA

Suvorova IA, Rodionov DA

Microb Genom. 2016 Jan 18;2(1):e000047

σ54-dependent regulome in Desulfovibrio vulgaris HildenboroughA

Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS

BMC Genomics. 2015 Nov 10;16:919

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing BacteriumA

Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov PS, Wall JD, Mukhopadhyay A

J Bacteriol. 2015 Nov;197(21):3400-8

Comparative genomics of transcriptional regulation of methionine metabolism in ProteobacteriaA

Leyn SA, Suvorova IA, Kholina TD, Sherstneva SS, Novichkov PS, Gelfand MS, Rodionov DA

PLoS One. 2014 Nov 20;9(11):e113714

Control of methionine metabolism by the SahR transcriptional regulator in ProteobacteriaA

Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA

Environ Microbiol. 2014 Jan;16(1):1-8

Comparative genomics and evolution of regulons of the LacI-family transcription factorsD

Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA

Front Microbiol. 2014 Jun 11;5:294

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteriaA

Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS

J Bacteriol. 2013 Oct;195(19):4466-75

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteriaA

Sun EI, Leyn SA, Kazanov MD, Saier MH Jr, Novichkov PS, Rodionov DA

BMC Genomics. 2013 Sep 2;14:597

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilisD

Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA

J Bacteriol. 2013 Jun;195(11):2463-73

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteriaA

Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA

BMC Genomics. 2013 Feb 12;14:94

Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor RexA

Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA

J Bacteriol. 2012 Mar;194(5):1145-57

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genusA,V

Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS

BMC Genomics. 2011 Jun 15;12 Suppl 1(Suppl 1):S3

Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidenceD

Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov PS, Rodionov DA

J Bacteriol. 2011 Jul;193(13):3228-40

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotesD

Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA

Nucleic Acids Res. 2010 Jan;38(Database issue):D111-8

Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulatorsV

Rodionov DA, De Ingeniis J, Mancini C, Cimadamore F, Zhang H, Osterman AL, Raffaelli N

Nucleic Acids Res. 2008 Apr;36(6):2047-59

Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulonV

Rodionov DA, Li X, Rodionova IA, Yang C, Sorci L, Dervyn E, Martynowski D, Zhang H, Gelfand MS, Osterman AL

Nucleic Acids Res. 2008 Apr;36(6):2032-46

A novel class of modular transporters for vitamins in prokaryotesV

Rodionov DA, Hebbeln P, Eudes A, ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T.J

Bacteriol. 2009 Jan;191(1):42-51

Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transportersA

Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T.J

Bacteriol. 2006 Jan;188(1):317-27

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?A

Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS

Nucleic Acids Res. 2003 Dec 1;31(23):6748-57

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and ArchaeaD

Rodionov DA, Mironov AA, Gelfand MS

Genome Res. 2002 Oct;12(10):1507-16

Data mining

— In collaboration with GBA —

Identification of multidimensional Boolean patterns in microbial communities

Golovko G, Kamil K, Albayrak L, Nia AM, Duarte RSA, Chumakov S, Fofanov Y.

Microbiome. 2020 Sep 11;8(1):131

Detection of multi-dimensional co-exclusion patterns in microbial communities.

Albayrak L, Khanipov K, Golovko G, Fofanov Y.

Bioinformatics. 2018 Nov 1;34(21):3695-3701.

Multidimensional Boolean Patterns in Multi-omics Data

Golovko G, Reyes V, Pinchuk I, Fofanov Y

https://www.biorxiv.org/content/10.1101/2021.01.12.426358v1

Epigenetics

— In collaboration with FOXO Technologies —

Blood DNA methylation sites predict death risk in a longitudinal study of 12, 300 individuals.

Colicino E, Marioni R, Ward-Caviness C, Gondalia R, Guan W, Chen B, Tsai PC, Huan T, Xu G, Golareh A, Schwartz J, Vokonas P, Just A, Starr JM, McRae AF, Wray NR, Visscher PM, Bressler J, Zhang W, Tanaka T, Moore AZ, Pilling LC, Zhang G, Stewart JD, Li Y, Hou L, Castillo-Fernandez J, Spector T, Kiel DP, Murabito JM, Liu C, Mendelson M, Assimes T, Absher D, Tsaho PS, Lu AT, Ferrucci L, Wilson R, Waldenberger M, Prokisch H, Bandinelli S, Bell JT, Levy D, Deary IJ, Horvath S, Pankow J, Peters A, Whitsel EA, Baccarelli A.

Aging (Albany NY). 2020 Jul 22;12

Novel age-associated DNA methylation changes and epigenetic age acceleration in middle-aged African Americans and whites.

Tajuddin SM, Hernandez DG, Chen BH, Noren Hooten N, Mode NA, Nalls MA, Singleton AB, Ejiogu N, Chitrala KN, Zonderman AB, Evans MK.

Clinical Epigenetics. 2019 Aug 19;11(1):119.

Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease.

Agha G, Mendelson MM, Ward-Caviness CK, Joehanes R, Huan T, Gondalia R, Salfati E, Brody JA, Fiorito G, Bressler J, Chen BH, Ligthart S, Guarrera S, Colicino E, Just AC, Wahl S, Gieger C, Vandiver AR, Tanaka T, Hernandez DG, Pilling LC, Singleton AB, Sacerdote C, Krogh V, Panico S, Tumino R, Li Y, Zhang G, Stewart JD, Floyd JS, Wiggins KL, Rotter JI, Multhaup M, Bakulski K, Horvath S, Tsao PS, Absher DM, Vokonas P, Hirschhorn J, Fallin MD, Liu C, Bandinelli S, Boerwinkle E, Dehghan A, Schwartz JD, Psaty BM, Feinberg AP, Hou L, Ferrucci L, Sotoodehnia N, Matullo G, Peters A, Fornage M, Assimes TL, Whitsel EA, Levy D, Baccarelli AA.

Circulation. 2019 Aug 20; 140(8):645-657.

The Role of Epigenetic Aging in Education and Racial/Ethnic Mortality Disparities Among Older U.S. Women.

Liu Z, Chen BH, Assimes TL, Ferrucci L, Horvath S, Levine ME.

Psychoneuroendocrinology. 2019 Jun;104:18-24.

Epigenetic age is a cell-intrinsic property in transplanted human hematopoietic cells.

Søraas A, Matsuyama M, de Lima M, Wald D, Buechner J, Gedde-Dahl T, Søraas CL, Chen B, Ferrucci L, Dahl JA, Horvath S, Matsuyama S.

Aging Cell. 2019 Feb 2:e12897.

Tracking the Epigenetic Clock Across the Human Life Course: A Meta-analysis of Longitudinal Cohort Data.

Marioni RE, Suderman M, Chen BH, Horvath S, Bandinelli S, Morris T, Beck S, Ferrucci L, Pedersen NL, Relton CL, Deary IJ, Hägg S.

J Gerontol A Biol Sci Med Sci. 2019 Jan 1;74(1):57-61.

An epigenetic biomarker of aging for lifespan and healthspan.

Levine ME, Lu AT, Quach A, Chen BH, Assimes TL, Bandinelli S, Hou L, Baccarelli AA, Stewart JD, Li Y, Whitsel EA, Wilson JG, Reiner AP, Aviv A, Lohman K, Liu Y, Ferrucci L, Horvath S.

Aging. 2018 Apr 18;10(4):573-591.

Analysis of repeated leukocyte DNA methylation assessments reveals persistent epigenetic alterations after an incident myocardial infarction.

Ward-Caviness CK, Agha G, Chen BH, Pfeiffer L, Wilson R, Wolf P, Gieger C, Schwartz J, Vokonas PS, Hou L, Just AC, Bandinelli S, Hernandez DG, Singleton AB, Prokisch H, Meitinger T, Kastenmüller G, Ferrucci L, Baccarelli AA, Waldenberger M, Peters A.

Clinical Epigenetics. 2018 Dec 27;10(1):161.

GWAS of epigenetic aging rates in blood reveals a critical role for TERT.

Lu AT, Xue L, Salfati EL, Chen BH, Ferrucci L, Levy D, Joehanes R, Murabito JM, Kiel DP, Tsai PC, Yet I, Bell JT, Mangino M, Tanaka T, McRae AF, Marioni RE, Visscher PM, Wray NR, Deary IJ, Levine ME, Quach A, Assimes T, Tsao PS, Absher D, Stewart JD, Li Y, Reiner AP, Hou L, Baccarelli AA, Whitsel EA, Aviv A, Cardona A, Day FR, Wareham NJ, Perry JRB, Ong KK, Raj K, Lunetta KL, Horvath S.

Nature Communications. 2018 Jan 26;9(1):387.

Age-associated microRNA expression in human peripheral blood is associated with all-cause mortality and age-related traits.

Huan T, Chen G, Liu C, Bhattacharya A, Rong J, Chen BH, Seshadri S, Tanriverdi K, Freedman JE, Larson MG, Murabito JM, Levy D.

Aging Cell. 2017 Oct 17.

Leukocyte telomere length, T cell composition and DNA methylation age.

Chen BH, Carty CL, Kimura M, Kark JD, Chen W, Li S, Zhang T, Kooperberg C, Levy D, Assimes T, Absher D, Horvath S, Reiner AP, Aviv A.

Aging (Albany NY). 2017 Sep 20;9(9):1983-1995.

Epigenetic clock analysis of diet, exercise, education, and lifestyle factors.

Quach A, Levine ME, Tanaka T, Lu AT, Chen BH, Ferrucci L, Ritz B, Bandinelli S, Neuhouser ML, Beasley JM, Snetselaar L, Wallace RB, Tsao PS, Absher D, Assimes TL, Stewart JD, Li Y, Hou L, Baccarelli AA, Whitsel EA, Horvath S.

Aging (Albany NY). 2017 Feb 14;9(2):419-446.

DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases.

Ligthart S, Marzi C, Aslibekyan S, Mendelson MM, Conneely KN, Tanaka T, Colicino E, Waite LL, Joehanes R, Guan W, Brody JA, Elks C, Marioni R, Jhun MA, Agha G, Bressler J, Ward-Caviness CK, Chen BH, Huan T, Bakulski K, Salfati EL; WHI-EMPC Investigators., Fiorito G; CHARGE epigenetics of Coronary Heart Disease., Wahl S, Schramm K, Sha J, Hernandez DG, Just AC, Smith JA, Sotoodehnia N, Pilling LC, Pankow JS, Tsao PS, Liu C, Zhao W, Guarrera S, Michopoulos VJ, Smith AK, Peters MJ, Melzer D, Vokonas P, Fornage M, Prokisch H, Bis JC, Chu AY, Herder C, Grallert H, Yao C, Shah S, McRae AF, Lin H, Horvath S, Fallin D, Hofman A, Wareham NJ, Wiggins KL, Feinberg AP, Starr JM, Visscher PM, Murabito JM, Kardia SL, Absher DM, Binder EB, Singleton AB, Bandinelli S, Peters A, Waldenberger M, Matullo G, Schwartz JD, Demerath EW, Uitterlinden AG, van Meurs JB, Franco OH, Chen YI, Levy D, Turner ST, Deary IJ, Ressler KJ, Dupuis J, Ferrucci L, Ong KK, Assimes TL, Boerwinkle E, Koenig W, Arnett DK, Baccarelli AA, Benjamin EJ, Dehghan A.

Genome Biology. 2016 Dec 12;17(1):255

Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.

Mendelson MM, Marioni RE, Joehanes R, Liu C, Hedman AK, Aslibekyan S, Demerath EW, Guan W, Zhi D, Yao C, Huan T, Willinger C, Chen B, Courchesne P, Multhaup M, Irvin MR, Cohain A, Schadt EE, Grove ML, Bressler J, North K, Sundström J, Gustafsson S, Shah S, McRae AF, Harris SE, Gibson J, Redmond P, Corley J, Murphy L, Starr JM, Kleinbrink E, Lipovich L, Visscher PM, Wray NR, Krauss RM, Fallin D, Feinberg A, Absher DM, Fornage M, Pankow JS, Lind L, Fox C, Ingelsson E, Arnett DK, Boerwinkle E, Liang L, Levy D, Deary IJ.

PLoS Medicine. 2017 Jan 17;14(1):e1002215

DNA methylation-based measures of biological age: meta-analysis predicting time to death.

Chen BH, Marioni RE, Colicino E, Peters MJ, Ward-Caviness CK, Tsai P, Roetker NS, Just AC, Demerath EW, Guan W, Bressler J, Fornage M, Studenski S, Vandiver AR, Moore AZ, Tanaka T, Kiel DP, Liang L, Vokonas P, Schwartz J, Lunetta KL, Murabito JM, Bandinelli S, Hernandez DG, Melzer D, Nalls M, Pilling LC, Price TR, Singleton AB, Gieger C, Holle R, Kretschmer A, Kronenberg F, Kunze S, Linseisen J, Meisinger C, Rathmann W, Waldenberger M, Visscher PM, Shah S, Wray NR, McRae AF, Franco OH, Hofman A, Uitterlinden AG, Absher D, Assimes T, Levine ME, Lu AT, Tsao PS, Hou L, Manson JE, Carty CL, LaCroix AZ, Reiner AP, Spector TD, Feinberg AP, Levy D, Baccarelli A, van Meurs J, Bell JT, Peters A, Deary IJ, Pankow JS, Ferrucci L, Horvath S.

Aging. 2016 Sep 28;8(9):1844-1865

An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease.

Horvath S, Gurven M, Levine ME, Trumble BC, Kaplan H, Allayee H, Ritz BR, Chen B, Lu AT, Rickabaugh TM, Jamieson BD, Sun D, Li S, Chen W, Quintana-Murci L, Fagny M, Kobor MS, Tsao PS, Reiner AP, Edlefsen KL, Absher D, Assimes TL

Genome Biology. 2016 Aug 11;17(1):171

Menopause accelerates biological aging.

Levine ME, Lu AT, Chen BH, Hernandez DG, Singleton AB, Ferrucci L, Bandinelli S, Salfati E, Manson JE, Quach A, Kusters CD, Kuh D, Wong A, Teschendorff AE, Widschwendter M, Ritz BR, Absher D, Assimes TL, Horvath S.

Proc Natl Acad Sci. 2016 Aug 16;113(33):9327-32.

DNA methylation age of blood predicts future onset of lung cancer in the women's health initiative

Levine ME, Hosgood HD, Chen B, Absher D, Assimes T, Horvath S.

Aging. 2015 Sep; 7(9):690-700

Genome-wide identification of microRNA expression quantitative trait loci.

Huan T, Rong J, Liu C, Zhang X, Tanriverdi K, Joehanes R, Chen BH, Murabito JM, Yao C, Courchesne P, Munson PJ, O'Donnell CJ, Cox N, Johnson AD, Larson MG, Levy D, Freedman JE.

Nature Communications. 2015 Mar 20;6:6601.

DNA methylation age of blood predicts all-cause mortality in later life.

Marioni RE, Shah S, McRae AF, Chen BH, Colicino E, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, Martin NG, Montgomery GW, Feinberg AP, M. Fallin D, Multhaup ML, Jaffe AE, Joehanes R, Schwartz J, Just AC, Lunetta KL, Murabito JM, Starr JM, Horvath S, Baccarelli AA, Levy D, Visscher PM, Wray NR, Deary IJ.

Genome Biology. 2015 Jan 30;16:25

Epigenome-wide association study of fasting blood lipids in the Genetics of Lipid Lowering Drugs and Diet Network Study.

Irvin MR, Zhi D, Joehanes R, Mendelson M, Aslibekyan S, Claas SA, Thibeault KS, Patel N, Day K, Waite Jones L, Liang L, Chen BH, Yao C, Tiwari HK, Ordovas JM, Levy D, Absher D, Arnett DK.

Circulation. 2014 Jun 11