URMC / Labs / Oltvai Lab / Publications

Publications

1. Nkosi D
2. Crowe WE
3. Altman BJ
4. Oltvai ZN
5. Giampoli EJ
6. Velez MJ
SATB2 is an Emergent Biomarker of Anaplastic Thyroid Carcinoma: A Series with Comprehensive Biomarker and Molecular Studies.; Endocrine pathology. 2024 Nov 05.
1. Kohram M
2. Sanderson AE
3. Loui A
4. Thompson PV
5. Vashistha H
6. Shomar A
7. Oltvai ZN
8. Salman H
Nonlethal deleterious mutation-induced stress accelerates bacterial aging.; Proceedings of the National Academy of Sciences of the United States of America; Vol 121(20), pp. e2316271121. 2024 May 06.
1. George GV
2. Liu H
3. Jajosky AN
4. Oltvai ZN
Resolving Discrepancies in Idylla BRAF Mutational Assay Results Using Targeted Next-Generation Sequencing.; Genes; Vol 15(5). 2024 Apr 23.
1. Irie N
2. Mizoguchi K
3. Warita T
4. Nakano M
5. Sasaki K
6. Tashiro J
7. Osaki T
8. Ishikawa T
9. Oltvai ZN
10. Warita K
Repurposing of the Cardiovascular Drug Statin for the Treatment of Cancers: Efficacy of Statin-Dipyridamole Combination Treatment in Melanoma Cell Lines.; Biomedicines; Vol 12(3). 2024 Mar 21.
1. Cox AJ
2. Crowe WE
3. Yang Q
4. Zhang B
5. Oltvai ZN
6. Liao X
Clinicopathologic and Molecular Characterization of Anorectal Neuroendocrine Carcinomas Reveals Human Papillomavirus, p53 and c-Myc as Alternative Mechanisms of Carcinogenesis.; Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc. 2023 Jul 28.
1. Nkosi D
2. George GV
3. Liu H
4. Buldo M
5. Velez MJ
6. Oltvai ZN
Efficient Lung Cancer Molecular Diagnostics by Combining Next Generation Sequencing with Reflex Idylla Genefusion Assay Testing.; Genes; Vol 14(8). 2023 Jul 28.
1. Zhou Y
2. Tashiro J
3. Kamatani S
4. Irie N
5. Suzuki A
6. Ishikawa T
7. Warita K
8. Oltvai ZN
9. Warita T
HMG-CoA reductase degrader, SR-12813, counteracts statin-induced upregulation of HMG-CoA reductase and augments the anticancer effect of atorvastatin.; Biochemical and biophysical research communications; Vol 677, pp. 13-19. 2023 Jul 27.
1. Irie N
2. Warita K
3. Tashiro J
4. Zhou Y
5. Ishikawa T
6. Oltvai ZN
7. Warita T
Expression of housekeeping genes varies depending on mevalonate pathway inhibition in cancer cells.; Heliyon; Vol 9(7), pp. e18017. 2023 Jul 08.
1. El Hussein S
2. Evans AG
3. Fitzsimmons JM
4. Leong N
5. Buldo M
6. Segal JP
7. Jajosky AN
8. Rothberg PG
9. Liesveld JL
10. Oltvai ZN
Clonal cytopenia of undetermined significance (CCUS)-associated reversion of donor-derived, transient αβ T-cell large granular clonal lymphocytosis, emerging post-transplant in a patient with a history of γδ T-cell large granular lymphocytic leukemia.; Cold Spring Harbor molecular case studies; Vol 9(2). 2023 May 09.
1. Nkosi D
2. Miller CA
3. Jajosky AN
4. Oltvai ZN
Incidental discovery of acute myeloid leukemia during liquid biopsy of a lung cancer patient.; Cold Spring Harbor molecular case studies; Vol 8(4). 2022 Jun.
1. Nkosi D
2. Casler VL
3. Syposs CR
4. Oltvai ZN
Utility of Select Gene Mutation Detection in Tumors by the Idylla Rapid Multiplex PCR Platform in Comparison to Next-Generation Sequencing.; Genes; Vol 13(5). 2022 Apr 29.
1. Warita T
2. Irie N
3. Zhou Y
4. Tashiro J
5. Sugiura A
6. Oltvai ZN
7. Warita K
Alterations in the omics profiles in mevalonate pathway-inhibited cancer cells.; Life sciences. 2022 Jan 28.
1. Warita K
2. Ishikawa T
3. Sugiura A
4. Tashiro J
5. Shimakura H
6. Hosaka YZ
7. Ohta KI
8. Warita T
9. Oltvai ZN
Concomitant attenuation of HMGCR expression and activity enhances the growth inhibitory effect of atorvastatin on TGF-β-treated epithelial cancer cells.; Scientific reports; Vol 11(1). 2021 Jun 17.
1. Oltvai ZN
2. Harley SE
3. Koes D
4. Michel S
5. Warlick ED
6. Nelson AC
7. Yohe S
8. Mroz P
Assessing acquired resistance to IDH1 inhibitor therapy by full-exon IDH1 sequencing and structural modeling.; Cold Spring Harbor molecular case studies; Vol 7(2). 2021 Apr.
1. Oltvai ZN
2. Smith EA
3. Wiens K
4. Nogee LM
5. Luquette M
6. Nelson AC
7. Wikenheiser-Brokamp KA
Neonatal respiratory failure due to novel compound heterozygous mutations in the ABCA3 lipid transporter.; Cold Spring Harbor molecular case studies; Vol 6(3). 2020 Jun.
1. Ponzoni L
2. Peñaherrera DA
3. Oltvai ZN
4. Bahar I
Rhapsody: predicting the pathogenicity of human missense variants.; Bioinformatics (Oxford, England); Vol 36(10). 2020 May 01.
1. Rashid S
2. Long Z
3. Singh S
4. Kohram M
5. Vashistha H
6. Navlakha S
7. Salman H
8. Oltvai ZN
9. Bar-Joseph Z
Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains.; Proceedings of the National Academy of Sciences of the United States of America; Vol 116(24). 2019 Jun 11.
1. Ishikawa T
2. Hosaka YZ
3. Beckwitt C
4. Wells A
5. Oltvai ZN
6. Warita K
Concomitant attenuation of HMG-CoA reductase expression potentiates the cancer cell growth-inhibitory effect of statins and expands their efficacy in tumor cells with epithelial characteristics.; Oncotarget; Vol 9(50). 2018 Jun 29.
1. Singh M
2. Warita K
3. Warita T
4. Faeder JR
5. Lee REC
6. Sant S
7. Oltvai ZN
Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors.; Scientific reports; Vol 8(1). 2018 Jun 20.
1. Beckwitt CH
2. Brufsky A
3. Oltvai ZN
4. Wells A
Statin drugs to reduce breast cancer recurrence and mortality.; Breast cancer research : BCR; Vol 20(1). 2018 Jan 20.
1. Beckwitt CH
2. Clark AM
3. Ma B
4. Whaley D
5. Oltvai ZN
6. Wells A
Statins attenuate outgrowth of breast cancer metastases.; British journal of cancer; Vol 119(9). 2018 Jan.
1. Raghu VK
2. Beckwitt CH
3. Warita K
4. Wells A
5. Benos PV
6. Oltvai ZN
Biomarker identification for statin sensitivity of cancer cell lines.; Biochemical and biophysical research communications; Vol 495(1). 2018 Jan 01.
1. Liu B
2. Oltvai ZN
3. Bayır H
4. Silverman GA
5. Pak SC
6. Perlmutter DH
7. Bahar I
Quantitative assessment of cell fate decision between autophagy and apoptosis.; Scientific reports; Vol 7(1). 2017 Jan 14.
1. Long Z
2. Quaife B
3. Salman H
4. Oltvai ZN
Cell-cell communication enhances bacterial chemotaxis toward external attractants.; Scientific reports; Vol 7(1). 2017 Jan 09.
1. Vazquez A
2. Oltvai ZN
Macromolecular crowding explains overflow metabolism in cells.; Scientific reports; Vol 6. 2016 Aug 03.
1. Cobanoglu MC
2. Oltvai ZN
3. Taylor DL
4. Bahar I
BalestraWeb: efficient online evaluation of drug-target interactions.; Bioinformatics (Oxford, England); Vol 31(1). 2015 Jan 01.
1. Warita K
2. Warita T
3. Beckwitt CH
4. Schurdak ME
5. Vazquez A
6. Wells A
7. Oltvai ZN
Statin-induced mevalonate pathway inhibition attenuates the growth of mesenchymal-like cancer cells that lack functional E-cadherin mediated cell cohesion.; Scientific reports; Vol 4. 2014 Dec 23.
1. Liu B
2. Bhatt D
3. Oltvai ZN
4. Greenberger JS
5. Bahar I
Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies.; Scientific reports; Vol 4. 2014 Sep 01.
1. Cobanoglu MC
2. Liu C
3. Hu F
4. Oltvai ZN
5. Bahar I
Predicting drug-target interactions using probabilistic matrix factorization.; Journal of chemical information and modeling; Vol 53(12). 2013 Dec 23.
1. Zhou Y
2. Vazquez A
3. Wise A
4. Warita T
5. Warita K
6. Bar-Joseph Z
7. Oltvai ZN
Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells.; BMC systems biology; Vol 7. 2013 Dec 12.
1. Dolfi SC
2. Chan LL
3. Qiu J
4. Tedeschi PM
5. Bertino JR
6. Hirshfield KM
7. Oltvai ZN
8. Vazquez A
The metabolic demands of cancer cells are coupled to their size and protein synthesis rates.; Cancer & metabolism; Vol 1(1). 2013 Nov 07.
1. Wells A
2. Oltvai ZN
Ongoing technological revolution. Preface.; Clinics in laboratory medicine; Vol 32(4). 2012 Dec.
1. Park S
2. Pantanowitz L
3. Parwani AV
4. Wells A
5. Oltvai ZN
Workflow organization in pathology.; Clinics in laboratory medicine; Vol 32(4). 2012 Dec.
1. Wise A
2. Oltvai ZN
3. Bar-Joseph Z
Matching experiments across species using expression values and textual information.; Bioinformatics (Oxford, England); Vol 28(12). 2012 Jun 15.
1. Isin B
2. Tirupula KC
3. Oltvai ZN
4. Klein-Seetharaman J
5. Bahar I
Identification of motions in membrane proteins by elastic network models and their experimental validation.; Methods in molecular biology (Clifton, N.J.); Vol 914. 2012.
1. Isin B
2. Estiu G
3. Wiest O
4. Oltvai ZN
Identifying ligand binding conformations of the β2-adrenergic receptor by using its agonists as computational probes.; PloS one; Vol 7(12). 2012.
1. Vazquez A
2. Oltvai ZN
Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology.; PloS one; Vol 6(4). 2011 Apr 29.
1. Vazquez A
2. Markert EK
3. Oltvai ZN
Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation.; PloS one; Vol 6(11). 2011.
1. Le HS
2. Oltvai ZN
3. Bar-Joseph Z
Cross-species queries of large gene expression databases.; Bioinformatics (Oxford, England); Vol 26(19). 2010 Oct 01.
1. Vazquez A
2. Liu J
3. Zhou Y
4. Oltvai ZN
Catabolic efficiency of aerobic glycolysis: the Warburg effect revisited.; BMC systems biology; Vol 4. 2010 May 06.
1. Tegnér JN
2. Compte A
3. Auffray C
4. An G
5. Cedersund G
6. Clermont G
7. Gutkin B
8. Oltvai ZN
9. Stephan KE
10. Thomas R
11. Villoslada P
Computational disease modeling - fact or fiction?; BMC systems biology; Vol 3. 2009 Jun 04.
1. Lee DS
2. Burd H
3. Liu J
4. Almaas E
5. Wiest O
6. Barabási AL
7. Oltvai ZN
8. Kapatral V
Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets.; Journal of bacteriology; Vol 191(12). 2009 Jun.
1. Vazquez A
2. de Menezes MA
3. Barabási AL
4. Oltvai ZN
Impact of limited solvent capacity on metabolic rate, enzyme activities, and metabolite concentrations of S. cerevisiae glycolysis.; PLoS computational biology; Vol 4(10). 2008 Oct.
1. Ernst J
2. Beg QK
3. Kay KA
4. Balázsi G
5. Oltvai ZN
6. Bar-Joseph Z
A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli.; PLoS computational biology; Vol 4(3). 2008 Mar 28.
1. Vazquez A
2. Beg QK
3. Demenezes MA
4. Ernst J
5. Bar-Joseph Z
6. Barabási AL
7. Boros LG
8. Oltvai ZN
Impact of the solvent capacity constraint on E. coli metabolism.; BMC systems biology; Vol 2. 2008 Jan 23.
1. Albert R
2. Oltvai ZN
Shaping specificity in signaling networks.; Nature genetics; Vol 39(3). 2007 Mar.
1. Balázsi G
2. Oltvai ZN
A pitfall in series of microarrays: the position of probes affects the cross-correlation of gene expression profiles.; Methods in molecular biology (Clifton, N.J.); Vol 377. 2007.
1. Farkas IJ
2. Wu C
3. Chennubhotla C
4. Bahar I
5. Oltvai ZN
Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae.; BMC bioinformatics; Vol 7. 2006 Oct 28.
1. Farkas IJ
2. Beg QK
3. Oltvai ZN
Exploring transcriptional regulatory networks in the worm.; Cell; Vol 125(6). 2006 Jun 16.
1. Almaas E
2. Oltvai ZN
3. Barabási AL
The activity reaction core and plasticity of metabolic networks.; PLoS computational biology; Vol 1(7). 2005 Dec.
1. Balázsi G
2. Oltvai ZN
Sensing your surroundings: how transcription-regulatory networks of the cell discern environmental signals.; Science's STKE : signal transduction knowledge environment; Vol 2005(282). 2005 May 03.
1. Tong X
2. Campbell JW
3. Balázsi G
4. Kay KA
5. Wanner BL
6. Gerdes SY
7. Oltvai ZN
Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays.; Biochemical and biophysical research communications; Vol 322(1). 2004 Sep 10.
1. Yook SH
2. Oltvai ZN
3. Barabási AL
Functional and topological characterization of protein interaction networks.; Proteomics; Vol 4(4). 2004 Apr.
1. Barabási AL
2. Oltvai ZN
Network biology: understanding the cell's functional organization.; Nature reviews. Genetics; Vol 5(2). 2004 Feb.
1. Dobrin R
2. Beg QK
3. Barabási AL
4. Oltvai ZN
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network.; BMC bioinformatics; Vol 5. 2004 Jan 30.
1. Dezso Z
2. Oltvai ZN
3. Barabási AL
Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae.; Genome research; Vol 13(11). 2003 Nov.
1. Balázsi G
2. Kay KA
3. Barabási AL
4. Oltvai ZN
Spurious spatial periodicity of co-expression in microarray data due to printing design.; Nucleic acids research; Vol 31(15). 2003 Aug 01.
1. Tombor B
2. Rundell K
3. Oltvai ZN
Bcl-2 promotes premature senescence induced by oncogenic Ras.; Biochemical and biophysical research communications; Vol 303(3). 2003 Apr 11.
1. Oltvai ZN
2. Barabási AL
Systems biology. Life's complexity pyramid.; Science (New York, N.Y.); Vol 298(5594). 2002 Oct 25.