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Hormone-epigenome interactions in behavioural regulation.

Baumbach JL, Zovkic IB.

Horm Behav. 2020 Jan 13;118:104680. doi: 10.1016/j.yhbeh.2020.104680. [Epub ahead of print] Review.


Molecular signature of different lesion types in the brain white matter of patients with progressive multiple sclerosis.

Elkjaer ML, Frisch T, Reynolds R, Kacprowski T, Burton M, Kruse TA, Thomassen M, Baumbach J, Illes Z.

Acta Neuropathol Commun. 2019 Dec 11;7(1):205. doi: 10.1186/s40478-019-0855-7.


Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.

Sturm G, Finotello F, Petitprez F, Zhang JD, Baumbach J, Fridman WH, List M, Aneichyk T.

Bioinformatics. 2019 Jul 15;35(14):i436-i445. doi: 10.1093/bioinformatics/btz363.


Evidence that a positive feedback loop drives centrosome maturation in fly embryos.

Alvarez-Rodrigo I, Steinacker TL, Saurya S, Conduit PT, Baumbach J, Novak ZA, Aydogan MG, Wainman A, Raff JW.

Elife. 2019 Sep 9;8. pii: e50130. doi: 10.7554/eLife.50130.


The effects of social instability stress and subsequent ethanol consumption in adolescence on brain and behavioral development in male rats.

Marcolin ML, Baumbach JL, Hodges TE, McCormick CM.

Alcohol. 2019 Aug 26;82:29-45. doi: 10.1016/j.alcohol.2019.08.003. [Epub ahead of print]


Retraction Note: Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis.

Elkjaer ML, Frisch T, Reynolds R, Kacprowski T, Burton M, Kruse TA, Thomassen M, Baumbach J, Illes Z.

Acta Neuropathol Commun. 2019 Aug 21;7(1):136. doi: 10.1186/s40478-019-0790-7.


The epigenetic factor BORIS (CTCFL) controls the androgen receptor regulatory network in ovarian cancer.

Salgado-Albarrán M, González-Barrios R, Guerra-Calderas L, Alcaraz N, Estefanía Sánchez-Correa T, Castro-Hernández C, Sánchez-Pérez Y, Aréchaga-Ocampo E, García-Carrancá A, Cantú de León D, Herrera LA, Baumbach J, Soto-Reyes E.

Oncogenesis. 2019 Aug 12;8(8):41. doi: 10.1038/s41389-019-0150-2.


Bedside Measurement of Volatile Organic Compounds in the Atmosphere of Neonatal Incubators Using Ion Mobility Spectrometry.

Steinbach J, Goedicke-Fritz S, Tutdibi E, Stutz R, Kaiser E, Meyer S, Baumbach JI, Zemlin M.

Front Pediatr. 2019 Jun 18;7:248. doi: 10.3389/fped.2019.00248. eCollection 2019.


Increased Levels of Genomic Instability and Mutations in Homologous Recombination Genes in Locally Advanced Rectal Carcinomas.

do Canto LM, Larsen SJ, Catin Kupper BE, Begnami MDFS, Scapulatempo-Neto C, Petersen AH, Aagaard MM, Baumbach J, Aguiar S Jr, Rogatto SR.

Front Oncol. 2019 May 14;9:395. doi: 10.3389/fonc.2019.00395. eCollection 2019.


DNA methylome profiling in identical twin pairs discordant for body mass index.

Li W, Zhang D, Wang W, Wu Y, Mohammadnejad A, Lund J, Baumbach J, Christiansen L, Tan Q.

Int J Obes (Lond). 2019 Dec;43(12):2491-2499. doi: 10.1038/s41366-019-0382-4. Epub 2019 May 31.


Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.

Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt HHHW, Pleschka S, Röttger R, Baumbach J.

Syst Med (New Rochelle). 2019 Mar 28;2(1):1-9. doi: 10.1089/sysm.2018.0013. eCollection 2019.


Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes.

da Costa AABA, do Canto LM, Larsen SJ, Ribeiro ARG, Stecca CE, Petersen AH, Aagaard MM, de Brot L, Baumbach J, Baiocchi G, Achatz MI, Rogatto SR.

BMC Cancer. 2019 May 6;19(1):422. doi: 10.1186/s12885-019-5622-4.


Statistical analysis of MCC-IMS data for two group comparisons-an exemplary study on two devices.

Horsch S, Baumbach JI, Rahnenführer J.

J Breath Res. 2019 Jun 4;13(3):036011. doi: 10.1088/1752-7163/ab1ee2.


Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis.

Elkjaer ML, Frisch T, Reynolds R, Kacprowski T, Burton M, Kruse TA, Thomassen M, Baumbach J, Illes Z.

Acta Neuropathol Commun. 2019 Apr 25;7(1):58. doi: 10.1186/s40478-019-0709-3. Retraction in: Acta Neuropathol Commun. 2019 Aug 21;7(1):136.


Author Correction: Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S.

Nat Genet. 2019 Apr;51(4):766. doi: 10.1038/s41588-019-0400-4.


From single drug targets to synergistic network pharmacology in ischemic stroke.

Casas AI, Hassan AA, Larsen SJ, Gomez-Rangel V, Elbatreek M, Kleikers PWM, Guney E, Egea J, López MG, Baumbach J, Schmidt HHHW.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):7129-7136. doi: 10.1073/pnas.1820799116. Epub 2019 Mar 20.


The Selection of a Hepatocyte Cell Line Susceptible to Plasmodium falciparum Sporozoite Invasion That Is Associated With Expression of Glypican-3.

Tweedell RE, Tao D, Hamerly T, Robinson TM, Larsen S, Grønning AGB, Norris AM, King JG, Law HCH, Baumbach J, Bergmann-Leitner ES, Dinglasan RR.

Front Microbiol. 2019 Feb 28;10:127. doi: 10.3389/fmicb.2019.00127. eCollection 2019.


PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome.

Naz K, Naz A, Ashraf ST, Rizwan M, Ahmad J, Baumbach J, Ali A.

BMC Bioinformatics. 2019 Mar 12;20(1):123. doi: 10.1186/s12859-019-2713-9.


Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S.

Nat Genet. 2019 Apr;51(4):716-727. doi: 10.1038/s41588-019-0359-1. Epub 2019 Mar 4. Erratum in: Nat Genet. 2019 Mar 25;:.


Age-dependent DNA methylation patterns on the Y chromosome in elderly males.

Lund JB, Li S, Christensen K, Mengel-From J, Soerensen M, Marioni RE, Starr J, Pattie A, Deary IJ, Baumbach J, Tan Q.

Aging Cell. 2019 Feb 21:e12907. doi: 10.1111/acel.12907. [Epub ahead of print]


Epidemiology of Invasive Group B Streptococcal Infections Among Nonpregnant Adults in the United States, 2008-2016.

Francois Watkins LK, McGee L, Schrag SJ, Beall B, Jain JH, Pondo T, Farley MM, Harrison LH, Zansky SM, Baumbach J, Lynfield R, Snippes Vagnone P, Miller LA, Schaffner W, Thomas AR, Watt JP, Petit S, Langley GE.

JAMA Intern Med. 2019 Apr 1;179(4):479-488. doi: 10.1001/jamainternmed.2018.7269.


DNA methylome profiling of all-cause mortality in comparison with age-associated methylation patterns.

Lund JB, Li S, Baumbach J, Svane AM, Hjelmborg J, Christiansen L, Christensen K, Redmond P, Marioni RE, Deary IJ, Tan Q.

Clin Epigenetics. 2019 Feb 8;11(1):23. doi: 10.1186/s13148-019-0622-4.


Enriched power of disease-concordant twin-case-only design in detecting interactions in genome-wide association studies.

Li W, Baumbach J, Mohammadnejad A, Brasch-Andersen C, Vandin F, Korbel JO, Tan Q.

Eur J Hum Genet. 2019 Apr;27(4):631-636. doi: 10.1038/s41431-018-0320-2. Epub 2019 Jan 18.


Parameter estimation of qualitative biological regulatory networks on high performance computing hardware.

Saeed MT, Ahmad J, Baumbach J, Pauling J, Shafi A, Paracha RZ, Hayat A, Ali A.

BMC Syst Biol. 2018 Dec 29;12(1):146. doi: 10.1186/s12918-018-0670-y.


E. coli gene regulatory networks are inconsistent with gene expression data.

Larsen SJ, Röttger R, Schmidt HHHW, Baumbach J.

Nucleic Acids Res. 2019 Jan 10;47(1):85-92. doi: 10.1093/nar/gky1176.


Adolescent social stress and social context influence the intake of ethanol and sucrose in male rats soon and long after the stress exposures.

Marcolin ML, Hodges TE, Baumbach JL, McCormick CM.

Dev Psychobiol. 2019 Jan;61(1):81-95. doi: 10.1002/dev.21800. Epub 2018 Nov 6.


Clinical Features and Outcomes of Immunocompromised Children Hospitalized With Laboratory-Confirmed Influenza in the United States, 2011-2015.

Collins JP, Campbell AP, Openo K, Farley MM, Cummings CN, Kirley PD, Herlihy R, Yousey-Hindes K, Monroe ML, Ladisky M, Lynfield R, Baumbach J, Spina N, Bennett N, Billing L, Thomas A, Schaffner W, Price A, Garg S, Anderson EJ.

J Pediatric Infect Dis Soc. 2019 Dec 27;8(6):539-549. doi: 10.1093/jpids/piy101.


Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes.

Martin NA, Nawrocki A, Molnar V, Elkjaer ML, Thygesen EK, Palkovits M, Acs P, Sejbaek T, Nielsen HH, Hegedus Z, Sellebjerg F, Molnar T, Barbosa EGV, Alcaraz N, Gallyas F Jr, Svenningsen AF, Baumbach J, Lassmann H, Larsen MR, Illes Z.

PLoS One. 2018 Aug 16;13(8):e0202530. doi: 10.1371/journal.pone.0202530. eCollection 2018.


Sex-specific effects of CB1 receptor antagonism and stress in adolescence on anxiety, corticosterone concentrations, and contextual fear in adulthood in rats.

Simone JJ, Baumbach JL, McCormick CM.

Int J Dev Neurosci. 2018 Oct;69:119-131. doi: 10.1016/j.ijdevneu.2018.07.011. Epub 2018 Jul 29.


DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data.

Frisch T, Gøttcke J, Röttger R, Tan Q, Baumbach J.

Methods Mol Biol. 2018;1807:51-62. doi: 10.1007/978-1-4939-8561-6_5.


Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas.

Lund J, Tan Q, Baumbach J.

Methods Mol Biol. 2018;1807:21-35. doi: 10.1007/978-1-4939-8561-6_3.


On the power of epigenome-wide association studies using a disease-discordant twin design.

Li W, Christiansen L, Hjelmborg J, Baumbach J, Tan Q.

Bioinformatics. 2018 Dec 1;34(23):4073-4078. doi: 10.1093/bioinformatics/bty532.


A case-only genome-wide association study on gene-sex interaction in allergic rhinitis.

Mohammadnejad A, Brasch-Andersen C, Li W, Haagerup A, Baumbach J, Tan Q.

Ann Allergy Asthma Immunol. 2018 Sep;121(3):366-367.e2. doi: 10.1016/j.anai.2018.07.001. Epub 2018 Jul 5. No abstract available.


Predictors of social instability stress effects on social interaction and anxiety in adolescent male rats.

Hodges TE, Baumbach JL, McCormick CM.

Dev Psychobiol. 2018 Sep;60(6):651-663. doi: 10.1002/dev.21626. Epub 2018 Jun 21.


Guiding biomedical clustering with ClustEval.

Wiwie C, Baumbach J, Röttger R.

Nat Protoc. 2018 Jun;13(6):1429-1444. doi: 10.1038/nprot.2018.038. Epub 2018 May 24.


CoNVaQ: a web tool for copy number variation-based association studies.

Larsen SJ, do Canto LM, Rogatto SR, Baumbach J.

BMC Genomics. 2018 May 18;19(1):369. doi: 10.1186/s12864-018-4732-8.


A homeostatic clock sets daughter centriole size in flies.

Aydogan MG, Wainman A, Saurya S, Steinacker TL, Caballe A, Novak ZA, Baumbach J, Muschalik N, Raff JW.

J Cell Biol. 2018 Apr 2;217(4):1233-1248. doi: 10.1083/jcb.201801014. Epub 2018 Mar 2.


The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets.

Hassan SS, Jamal SB, Radusky LG, Tiwari S, Ullah A, Ali J, Behramand, de Carvalho PVSD, Shams R, Khan S, Figueiredo HCP, Barh D, Ghosh P, Silva A, Baumbach J, Röttger R, Turjanski AG, Azevedo VAC.

Front Genet. 2018 Feb 13;9:44. doi: 10.3389/fgene.2018.00044. eCollection 2018.


Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine.

Zanin M, Chorbev I, Stres B, Stalidzans E, Vera J, Tieri P, Castiglione F, Groen D, Zheng H, Baumbach J, Schmid JA, Basilio J, Klimek P, Debeljak N, Rozman D, Schmidt HHHW.

Brief Bioinform. 2019 May 21;20(3):1057-1062. doi: 10.1093/bib/bbx160.


Multi-capillary Column Ion Mobility Spectrometry of Volatile Metabolites for Phenotyping of Microorganisms.

Halbfeld C, Baumbach JI, Blank LM, Ebert BE.

Methods Mol Biol. 2018;1671:229-258. doi: 10.1007/978-1-4939-7295-1_15.


An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae.

Jamal SB, Hassan SS, Tiwari S, Viana MV, Benevides LJ, Ullah A, Turjanski AG, Barh D, Ghosh P, Costa DA, Silva A, Röttger R, Baumbach J, Azevedo VAC.

PLoS One. 2017 Oct 19;12(10):e0186401. doi: 10.1371/journal.pone.0186401. eCollection 2017.


De novo pathway-based biomarker identification.

Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach J.

Nucleic Acids Res. 2017 Sep 19;45(16):e151. doi: 10.1093/nar/gkx642.


A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations.

Horsch S, Kopczynski D, Kuthe E, Baumbach JI, Rahmann S, Rahnenführer J.

PLoS One. 2017 Sep 14;12(9):e0184321. doi: 10.1371/journal.pone.0184321. eCollection 2017.


On the performance of pre-microRNA detection algorithms.

Saçar Demirci MD, Baumbach J, Allmer J.

Nat Commun. 2017 Aug 24;8(1):330. doi: 10.1038/s41467-017-00403-z.


Adhesion of volatile propofol to breathing circuit tubing.

Lorenz D, Maurer F, Trautner K, Fink T, Hüppe T, Sessler DI, Baumbach JI, Volk T, Kreuer S.

J Breath Res. 2017 Aug 21;11(3):036005. doi: 10.1088/1752-7163/aa795d.


The endogenous transposable element Tgm9 is suitable for generating knockout mutants for functional analyses of soybean genes and genetic improvement in soybean.

Sandhu D, Ghosh J, Johnson C, Baumbach J, Baumert E, Cina T, Grant D, Palmer RG, Bhattacharyya MK.

PLoS One. 2017 Aug 10;12(8):e0180732. doi: 10.1371/journal.pone.0180732. eCollection 2017.


Social instability stress in adolescent male rats reduces social interaction and social recognition performance and increases oxytocin receptor binding.

Hodges TE, Baumbach JL, Marcolin ML, Bredewold R, Veenema AH, McCormick CM.

Neuroscience. 2017 Sep 17;359:172-182. doi: 10.1016/j.neuroscience.2017.07.032. Epub 2017 Jul 21.


CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape.

Larsen SJ, Baumbach J.

J Integr Bioinform. 2017 Jul 21;14(2). pii: /j/jib.2017.14.issue-2/jib-2017-0014/jib-2017-0014.xml. doi: 10.1515/jib-2017-0014.


Calibration and validation of a MCC/IMS prototype for exhaled propofol online measurement.

Maurer F, Walter L, Geiger M, Baumbach JI, Sessler DI, Volk T, Kreuer S.

J Pharm Biomed Anal. 2017 Oct 25;145:293-297. doi: 10.1016/j.jpba.2017.06.052. Epub 2017 Jul 1.


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