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Items: 1 to 50 of 100

1.

Systems biology approaches towards predictive microbial ecology.

Otwell AE, López García de Lomana A, Gibbons SM, Orellana MV, Baliga NS.

Environ Microbiol. 2018 Aug 14. doi: 10.1111/1462-2920.14378. [Epub ahead of print]

PMID:
30106224
2.

The BCGΔBCG1419c Vaccine Candidate Reduces Lung Pathology, IL-6, TNF-α, and IL-10 During Chronic TB Infection.

Flores-Valdez MA, Pedroza-Roldán C, Aceves-Sánchez MJ, Peterson EJR, Baliga NS, Hernández-Pando R, Troudt J, Creissen E, Izzo L, Bielefeldt-Ohmann H, Bickett T, Izzo AA.

Front Microbiol. 2018 Jun 12;9:1281. doi: 10.3389/fmicb.2018.01281. eCollection 2018.

3.

Ocean acidification conditions increase resilience of marine diatoms.

Valenzuela JJ, López García de Lomana A, Lee A, Armbrust EV, Orellana MV, Baliga NS.

Nat Commun. 2018 Jun 13;9(1):2328. doi: 10.1038/s41467-018-04742-3.

4.

Transcriptional regulatory networks underlying gene expression changes in Huntington's disease.

Ament SA, Pearl JR, Cantle JP, Bragg RM, Skene PJ, Coffey SR, Bergey DE, Wheeler VC, MacDonald ME, Baliga NS, Rosinski J, Hood LE, Carroll JB, Price ND.

Mol Syst Biol. 2018 Mar 26;14(3):e7435. doi: 10.15252/msb.20167435.

5.

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations.

Qin W, Amin SA, Lundeen RA, Heal KR, Martens-Habbena W, Turkarslan S, Urakawa H, Costa KC, Hendrickson EL, Wang T, Beck DA, Tiquia-Arashiro SM, Taub F, Holmes AD, Vajrala N, Berube PM, Lowe TM, Moffett JW, Devol AH, Baliga NS, Arp DJ, Sayavedra-Soto LA, Hackett M, Armbrust EV, Ingalls AE, Stahl DA.

ISME J. 2018 Feb;12(2):508-519. doi: 10.1038/ismej.2017.186. Epub 2017 Oct 20.

PMID:
29053148
6.

Adaptive Prediction Emerges Over Short Evolutionary Time Scales.

López García de Lomana A, Kaur A, Turkarslan S, Beer KD, Mast FD, Smith JJ, Aitchison JD, Baliga NS.

Genome Biol Evol. 2017 Jun 1;9(6):1616-1623. doi: 10.1093/gbe/evx116.

7.

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.

Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND.

PLoS Comput Biol. 2017 May 17;13(5):e1005489. doi: 10.1371/journal.pcbi.1005489. eCollection 2017 May.

8.

Robustness of a model microbial community emerges from population structure among single cells of a clonal population.

Thompson AW, Turkarslan S, Arens CE, López García de Lomana A, Raman AV, Stahl DA, Baliga NS.

Environ Microbiol. 2017 Aug;19(8):3059-3069. doi: 10.1111/1462-2920.13764. Epub 2017 May 29.

PMID:
28419704
9.

Mechanism for microbial population collapse in a fluctuating resource environment.

Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS.

Mol Syst Biol. 2017 Mar 20;13(3):919. doi: 10.15252/msb.20167058.

10.

The State of Systems Genetics in 2017.

Baliga NS, Björkegren JL, Boeke JD, Boutros M, Crawford NP, Dudley AM, Farber CR, Jones A, Levey AI, Lusis AJ, Mak HC, Nadeau JH, Noyes MB, Petretto E, Seyfried NT, Steinmetz LM, Vonesch SC.

Cell Syst. 2017 Jan 25;4(1):7-15. doi: 10.1016/j.cels.2017.01.005.

11.

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.

Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell BS, Kendziorski C, Attie AD.

PLoS Genet. 2016 Dec 9;12(12):e1006466. doi: 10.1371/journal.pgen.1006466. eCollection 2016 Dec.

12.

A genome wide dosage suppressor network reveals genomic robustness.

Patra B, Kon Y, Yadav G, Sevold AW, Frumkin JP, Vallabhajosyula RR, Hintze A, Østman B, Schossau J, Bhan A, Marzolf B, Tamashiro JK, Kaur A, Baliga NS, Grayhack EJ, Adami C, Galas DJ, Raval A, Phizicky EM, Ray A.

Nucleic Acids Res. 2017 Jan 9;45(1):255-270. doi: 10.1093/nar/gkw1148. Epub 2016 Nov 29.

13.

MiR-155-regulated molecular network orchestrates cell fate in the innate and adaptive immune response to Mycobacterium tuberculosis.

Rothchild AC, Sissons JR, Shafiani S, Plaisier C, Min D, Mai D, Gilchrist M, Peschon J, Larson RP, Bergthaler A, Baliga NS, Urdahl KB, Aderem A.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6172-E6181. Epub 2016 Sep 28.

14.

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis.

Peterson EJR, Ma S, Sherman DR, Baliga NS.

Nat Microbiol. 2016 Jun 6;1(8):16078. doi: 10.1038/nmicrobiol.2016.78.

15.

Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis.

Plaisier CL, O'Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga NS.

Cell Syst. 2016 Aug;3(2):172-186. doi: 10.1016/j.cels.2016.06.006. Epub 2016 Jul 14.

16.

Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.

Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, Lee E, Corrin P, Hart T, Bolouri H, Davison J, Zhang Q, Hardcastle J, Aronow BJ, Plaisier CL, Baliga NS, Moffat J, Lin Q, Li XN, Nam DH, Lee J, Pollard SM, Zhu J, Delrow JJ, Clurman BE, Olson JM, Paddison PJ.

Cell Rep. 2015 Dec 22;13(11):2425-2439. doi: 10.1016/j.celrep.2015.11.021. Epub 2015 Dec 7.

17.

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.

López García de Lomana A, Schäuble S, Valenzuela J, Imam S, Carter W, Bilgin DD, Yohn CB, Turkarslan S, Reiss DJ, Orellana MV, Price ND, Baliga NS.

Biotechnol Biofuels. 2015 Dec 2;8:207. doi: 10.1186/s13068-015-0391-z. eCollection 2015.

18.

Pan-transcriptomic analysis identifies coordinated and orthologous functional modules in the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum.

Ashworth J, Turkarslan S, Harris M, Orellana MV, Baliga NS.

Mar Genomics. 2016 Apr;26:21-8. doi: 10.1016/j.margen.2015.10.011. Epub 2015 Nov 10.

PMID:
26560047
19.

A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses.

Imam S, Schäuble S, Valenzuela J, López García de Lomana A, Carter W, Price ND, Baliga NS.

Plant J. 2015 Dec;84(6):1239-56. doi: 10.1111/tpj.13059. Epub 2015 Nov 30.

20.

A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities.

Thompson AW, Crow MJ, Wadey B, Arens C, Turkarslan S, Stolyar S, Elliott N, Petersen TW, van den Engh G, Stahl DA, Baliga NS.

J Microbiol Methods. 2015 Oct;117:74-7. doi: 10.1016/j.mimet.2015.07.009. Epub 2015 Jul 14.

21.

Data-driven integration of genome-scale regulatory and metabolic network models.

Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND.

Front Microbiol. 2015 May 5;6:409. doi: 10.3389/fmicb.2015.00409. eCollection 2015. Review.

22.

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.

Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga NS.

Sci Data. 2015 Mar 31;2:150010. doi: 10.1038/sdata.2015.10. eCollection 2015.

23.

Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.

Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS.

BMC Syst Biol. 2015;9 Suppl 2:S1. doi: 10.1186/1752-0509-9-S2-S1. Epub 2015 Apr 15.

24.

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.

Reiss DJ, Plaisier CL, Wu WJ, Baliga NS.

Nucleic Acids Res. 2015 Jul 27;43(13):e87. doi: 10.1093/nar/gkv300. Epub 2015 Apr 14.

25.

Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea.

Gomes-Filho JV, Zaramela LS, Italiani VC, Baliga NS, Vêncio RZ, Koide T.

RNA Biol. 2015;12(5):490-500. doi: 10.1080/15476286.2015.1019998.

26.

The universe under a microscope.

Raman AV, Baliga NS.

Environ Microbiol Rep. 2015 Feb;7(1):11-2. doi: 10.1111/1758-2229.12225. No abstract available.

PMID:
25721591
27.

The DNA-binding network of Mycobacterium tuberculosis.

Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR.

Nat Commun. 2015 Jan 12;6:5829. doi: 10.1038/ncomms6829.

28.

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.

Muller EE, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA, Roume H, Lin J, May P, Hicks ND, Heintz-Buschart A, Wampach L, Liu CM, Price LB, Gillece JD, Guignard C, Schupp JM, Vlassis N, Baliga NS, Moritz RL, Keim PS, Wilmes P.

Nat Commun. 2014 Nov 26;5:5603. doi: 10.1038/ncomms6603.

29.

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.

Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS.

BMC Syst Biol. 2014 Nov 14;8:122. doi: 10.1186/s12918-014-0122-2.

30.

Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.

Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS, Sherman DR.

Genome Biol. 2014;15(11):502.

31.

Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers.

Ashworth J, Bernard B, Reynolds S, Plaisier CL, Shmulevich I, Baliga NS.

Nucleic Acids Res. 2014 Dec 1;42(21):12973-83. doi: 10.1093/nar/gku1031. Epub 2014 Nov 5.

32.

Erosion of functional independence early in the evolution of a microbial mutualism.

Hillesland KL, Lim S, Flowers JJ, Turkarslan S, Pinel N, Zane GM, Elliott N, Qin Y, Wu L, Baliga NS, Zhou J, Wall JD, Stahl DA.

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14822-7. doi: 10.1073/pnas.1407986111. Epub 2014 Sep 29.

33.

Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

Ashworth J, Plaisier CL, Lo FY, Reiss DJ, Baliga NS.

PLoS One. 2014 Sep 25;9(9):e107863. doi: 10.1371/journal.pone.0107863. eCollection 2014. Erratum in: PLoS One. 2014;9(11):e114450.

34.

Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.

Zaramela LS, Vêncio RZ, ten-Caten F, Baliga NS, Koide T.

PLoS One. 2014 Sep 19;9(9):e107680. doi: 10.1371/journal.pone.0107680. eCollection 2014.

35.

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.

Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga NS.

Nucleic Acids Res. 2014 Oct;42(18):11291-303. doi: 10.1093/nar/gku777. Epub 2014 Sep 17.

36.

A system-level model for the microbial regulatory genome.

Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS.

Mol Syst Biol. 2014 Jul 15;10:740. doi: 10.15252/msb.20145160.

37.

An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.

Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS.

Mol Microbiol. 2014 Apr;92(2):369-82. doi: 10.1111/mmi.12564. Epub 2014 Mar 19.

38.

Intracytoplasmic copper homeostasis controls cytochrome c oxidase production.

Ekici S, Turkarslan S, Pawlik G, Dancis A, Baliga NS, Koch HG, Daldal F.

MBio. 2014 Jan 14;5(1):e01055-13. doi: 10.1128/mBio.01055-13.

39.

Model organisms retain an "ecological memory" of complex ecologically relevant environmental variation.

Beer KD, Wurtmann EJ, Pinel N, Baliga NS.

Appl Environ Microbiol. 2014 Mar;80(6):1821-31. doi: 10.1128/AEM.03280-13. Epub 2014 Jan 10.

40.

Network portal: a database for storage, analysis and visualization of biological networks.

Turkarslan S, Wurtmann EJ, Wu WJ, Jiang N, Bare JC, Foley K, Reiss DJ, Novichkov P, Baliga NS.

Nucleic Acids Res. 2014 Jan;42(Database issue):D184-90. doi: 10.1093/nar/gkt1190. Epub 2013 Nov 23.

41.

Molecular mechanisms of system responses to novel stimuli are predictable from public data.

Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD.

Nucleic Acids Res. 2014 Feb;42(3):1442-60. doi: 10.1093/nar/gkt938. Epub 2013 Oct 31.

42.

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen.

Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie TJ, Slagel J, Moritz RL, Hackett M, Leigh JA, Baliga NS.

Genome Res. 2013 Nov;23(11):1839-51. doi: 10.1101/gr.153916.112. Epub 2013 Oct 2.

43.

Modeling the evolution of C4 photosynthesis.

Beer KD, Orellana MV, Baliga NS.

Cell. 2013 Jun 20;153(7):1427-9. doi: 10.1016/j.cell.2013.05.058.

44.

A role for programmed cell death in the microbial loop.

Orellana MV, Pang WL, Durand PM, Whitehead K, Baliga NS.

PLoS One. 2013 May 8;8(5):e62595. doi: 10.1371/journal.pone.0062595. Print 2013.

45.

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana.

Ashworth J, Coesel S, Lee A, Armbrust EV, Orellana MV, Baliga NS.

Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7518-23. doi: 10.1073/pnas.1300962110. Epub 2013 Apr 17.

46.

Metallochaperones regulate intracellular copper levels.

Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS.

PLoS Comput Biol. 2013;9(1):e1002880. doi: 10.1371/journal.pcbi.1002880. Epub 2013 Jan 17.

47.

Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis.

Costa KC, Yoon SH, Pan M, Burn JA, Baliga NS, Leigh JA.

J Bacteriol. 2013 Apr;195(7):1456-62. doi: 10.1128/JB.02141-12. Epub 2013 Jan 18.

48.

Architecture for interoperable software in biology.

Bare JC, Baliga NS.

Brief Bioinform. 2014 Jul;15(4):626-36. doi: 10.1093/bib/bbs074. Epub 2012 Dec 11.

49.

Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant.

Muller EE, Pinel N, Gillece JD, Schupp JM, Price LB, Engelthaler DM, Levantesi C, Tandoi V, Luong K, Baliga NS, Korlach J, Keim PS, Wilmes P.

J Bacteriol. 2012 Dec;194(23):6670-1. doi: 10.1128/JB.01765-12.

50.

Global analysis of mRNA stability in Mycobacterium tuberculosis.

Rustad TR, Minch KJ, Brabant W, Winkler JK, Reiss DJ, Baliga NS, Sherman DR.

Nucleic Acids Res. 2013 Jan 7;41(1):509-17. doi: 10.1093/nar/gks1019. Epub 2012 Nov 3.

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