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.