A Boot, M Liu, N Stantial, V Shah, W Yu, KC Nitiss, JL Nitiss, S Jinks-Robertson, SG Rozen. "Recurrent mutations in topoisomerase IIα cause a novel mutator phenotype in human cancers", Proceedings of the National Academy of Sciences 1, 119 (2022) doi: 10.1073/pnas.2114024119 IF 11.205

Y Wu, EHZ Chua, AWT Ng, A Boot, SG Rozen. "Accuracy of mutational signature software on correlated signatures" Sci Rep 12 (2022) doi: 10.1038/s41598-021-04207-6 IF 4.379

NJ Nasir, A Corrias, H Heemskerk, ET Ang, JH Jenkins, S Sebastin, L Tucker-Kellogg. “The panniculus carnosus muscle: A missing link in the chronicity of heel pressure ulcers?” Journal of the Royal Society Interface, Feb;19(187):20210631. (IF: 4.118) DOI: 10.1098/rsif.2021.0631  (2022) 

Richard AJ, Hang H, Allerton TD, Zhao P, Mendoza T, Ghosh S, Elks CM, Stephens JM. Loss of Adipocyte STAT5 Confers Increased Depot-Specific Adiposity in Male and Female Mice That Is Not Associated With Altered Adipose Tissue Lipolysis. Front Endocrinol (Lausanne). 2022;13:812802. doi: 10.3389/fendo.2022.812802. eCollection 2022. PubMed PMID: 35464049; PubMed Central PMCID: PMC9022209.

Rajak S, Gupta P, Anjum B, Raza S, Tewari A, Ghosh S, Tripathi M, Singh BK, Sinha RA. Role of AKR1B10 and AKR1B8 in the pathogenesis of non-alcoholic steatohepatitis (NASH) in mouse. Biochim Biophys Acta Mol Basis Dis. 2022 Apr 1;1868(4):166319. doi: 10.1016/j.bbadis.2021.166319. Epub 2021 Dec 23. PubMed PMID: 34954342

Thibonnier M, Ghosh S, Blanchard A. Effects of a short-term cold exposure on circulating microRNAs and metabolic parameters in healthy adult subjects. J Cell Mol Med. 2022 Jan;26(2):548-562. doi: 10.1111/jcmm.17121. Epub 2021 Dec 17. PubMed PMID: 34921497; PubMed Central PMCID: PMC8743656.

A Grubman, XY Choo, G Chew, JF Ouyang, G Sun, NP Croft, FJ Rossello, R Simmons, S Buckberry, DV Landin, J Pflueger, TH Vandekolk, Z Abay, Y Zhou, X Liu, J Chen, M Larcombe, JM Haynes, C McLean, S Williams, SY Chai, T Wilson, R Lister, CW Pouton, AW Purcell, OJL Rackham, E Petretto & JM Polo. Transcriptional signature in microglia associated with Aβ plaque phagocytosis. Nature Communications 2021; 12(1):3015

KYY Huang & E Petretto. Cross-species integration of single-cell RNA-seq resolved alveolar-epithelial transitional states in idiopathic pulmonary fibrosis. American Journal of Physiology-Lung Cellular and Molecular Physiology 2021

N Padmanabhan, Huang KK, A Boot, K Lim, S Srivastava, S Chen, Z Wu, H-O Lee, VT. Mukundan, C Chan, YK Chan, Ong X, JJ. Pitt, ZFA Isa, M Xing, MH Lee, ALK Tan, S Ho WT, MA. Luftig, D Kappei, WD. Kruger, J Bian, YS Ho, M Teh, SG Rozen, P Tan. "Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation" Genome Biol 22, 167 (2021) doi: 10.1186/s13059-021-02375-2 IF 10.806

M Liu, A Boot, AWT Ng, R Gordân, SG Rozen. "Mutational processes in cancer preferentially affect binding of particular transcription factors" Sci Rep 11, 3339 (2021) doi: 10.1038/s41598-021-82910-0 IF 4.379

Y Bylstra, WK Lim, S Kam, KW Tham, R.R Wu, JX Teo, S Davila, JL Kuan, SH Chan, N Bertin, Cheng XY, S Rozen, BT Teh, KK Yeo, SA Cook, SS Jamuar, GS. Ginsburg, LA. Orlando & P Tan. "Family history assessment significantly enhances delivery of precision medicine in the genomics era" Genome Med 13, 3 (2021) doi: 10.1186/s13073-020-00819-1 IF 5.802

BR Campbell, Z Chen, DL Faden, N Agrawal, RJ Li, GJ Hanna, NG Iyer, A Boot, SG Rozen, AL Vettore, B Panda, NM Krishnan, CR Pickering, JN Myers, X Guo, KAL Kuhs "The mutational landscape of early- and typical-onset oral tongue squamous cell carcinoma" Cancer 127(4):544-553. (2021) doi: 10.1002/cncr.33309 IF 5.742

Lai FT, C Blöcker, HH Li, M Lo, M Wong, CL Tang, EK.W. Tan, SG. Rozen, PY Cheah. "Enhancer-derived long non-coding RNAs CCAT1 and CCAT2 at rs6983267 has limited predictability for early stage colorectal carcinoma metastasis" Sci Rep 11, 404 (2021) doi: 10.1038/s41598-020-79906-7 IF 4.379

NS Jagannathan, CWV Hogue, L Tucker-Kellogg. “Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2.” PLoS Computational Biology. PLoS Comput Biol. 6;17(1):e1008474. (IF: 4.475) DOI: 10.1371/journal.pcbi.1008474 (2021). 

A Surendran, CF Dewey Jr., BC Low, L Tucker-Kellogg. “A computational model of mutual antagonism in the mechano-signaling network of RhoA and Nitric Oxide.” BMC Cell Biology (changed its name to BMC Molecular and Cell Biology), Oct 12; 22(Suppl 1):47. (IF: 4.241) DOI: 10.1186/s12860-021-00383-5. (2021)

Ghosh S, Park CH, Lee J, Lee N, Zhang R, Huesing C, Reijnders D, Sones J, Münzberg H, Redman L, Chang JS. Maternal cold exposure induces distinct transcriptome changes in the placenta and fetal brown adipose tissue in mice. BMC Genomics. 2021 Jul 3;22(1):500. doi: 10.1186/s12864-021-07825-6

Fang H, Ghosh S, Sims L, Stone KP, Hill CM, Spires DR, Ilatovskaya DV, Morrison CD, Gettys T, Stadler K. FGF21 prevents low protein diet-induced renal inflammation in aged mice. Am J Physiol Renal Physiol. 2021 Jun 21;. doi: 10.1152/ajprenal.00107.2021

Robbins JM, Peterson B, Schranner D, Tahir UA, Rienmüller T, Deng S, Keyes MJ, Katz DH, Beltran PMJ, Barber JL, Baumgartner C, Carr SA, Ghosh S, Shen C, Jennings LL, Ross R, Sarzynski MA, Bouchard C, Gerszten RE. Human plasma proteomic profiles indicative of cardiorespiratory fitness. Nat Metab. 2021 Jun;3(6):786-797. doi: 10.1038/s42255-021-00400-z

Bi-Lin KW, Seshachalam PV, Tuoc T, Stoykova A, Ghosh S, Singh MK. Critical role of the BAF chromatin remodeling complex during murine neural crest development. PLoS Genet. 2021 Mar;17(3):e1009446. doi: 10.1371/journal.pgen.1009446

Fang, H., Stone, K.P., Forney, L.A., Sims, L.C., Gutierrez, G.C., Ghosh, S., and Gettys, T.W. Implementation of dietary methionine restriction using casein after selective oxidative deletion of methionine. iScience, 24, 102470, 2021. doi.org/10.1016/j.isci.2021.102470

 

LB Alexandrov, J Kim, NJ Haradhvala, MN Huang, AWT Ng, Y Wu, AB Boot, KR Covington, DA Gordenin, EN Bergstrom, SMA Islam, N Lopez-Bigas, LJ Klimczak, JR McPherson, S Morganella, R Sabarinathan, DA Wheeler, V Mustonen, PCAWG Mutational Signatures Working Group, G Getz, SG Rozen*, MR Stratton*, PCAWG Consortium. "The repertoire of mutational signatures in human cancer" Nature 578 94-101 doi.org/10.1038/s41586-020-1943-3 (2020) (*corresponding author) IF 42.778
Web link for this paper: https://www.nature.com/articles/s41586-020-1943-3

A Boot, AWT Ng, FT Chong, S-C Ho, W Yu, DSW Tan, NG Iyer, SG Rozen. "Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types" Genome Res, 30 803-813 doi: 10.1101/gr.255620.119 (2020) IF 11.093
Web link for this paper: https://genome.cshlp.org/content/30/6/803.full

SG Rozen, "Mutational selection in normal urothelium" Science, 370(6512):34-35 doi:10.1126/science.abe0955 (2020) IF 41.845
Web link for this paper: https://science.sciencemag.org/content/370/6512/34?rss=1

S Cheng, D Ray, RTH Lee, KB Naripogu, PA Bt Mohamed Yusoff, PBL Goh, Y Liu, Y Suzuki, K Das, HS Chan, WK Wong, WH Chan, PK-H Chow, HS Ong, P Raj, KC Soo, P Tan, DM Epstein, SG Rozen. "A functional network of gastric-cancer-associated splicing events controlled by dysregulated splicing factors" NAR Genomics and Bioinformatics, 2:2 lqaa013 doi: 10.1093/nargab/lqaa013 (2020)
Web link for this paper: https://academic.oup.com/nargab/article/2/2/lqaa013/5763101

J Guo, OJL Rackham, N Sandholm, B He, AM Österholm, E Valo, V Harjutsalo, C Forsblom, I Toppila, M Parkkonen, Q Li, W Zhu, N Harmston, S Chothani, MK Öhman, E Eng, Y Sun, E Petretto, PH Groop & K Tryggvason. "Whole-genome sequencing of Finnish type 1 diabetic siblings discordant for kidney disease reveals DNA variants associated with diabetic nephropathy" Journal of the American Society of Nephrology 2020; 31(2):309-323 IF 9.274
Web link for this paper: https://jasn.asnjournals.org/content/31/2/309

US Kamaraj, J Chen, K Katwadi, JF Ouyang, YB Yang Sun, Y Ming Lim, X Liu, L Handoko, JM Polo, E Petretto & OJL Rackham. “EpiMogrify models H3K4me3 data to identify signaling molecules that improve cell fate control and maintenance”. Cell Systems 2020; S2405-4712(20)30334-3
Web link for this paper: https://www.sciencedirect.com/science/article/pii/S2405471220303343

S Liu, N Harmston, TL Glaser, Y Wong, Z Zhong, B Madan, DM Virshup & E Petretto. "Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation" Genome Medicine 2020; 12(1):89 IF 5.631
Web link for this paper: https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00788-5

X Liu, JF Ouyang, FJ Rossello, JP Tan, KC Davidson, DS Valdes, J Schröder, YBY Sun, J Chen, AS Knaupp, G Sun, HS Chy, Z Huang, J Pflueger, J Firas, V Tano, S Buckberry, JM Paynter, MR Larcombe, D Poppe, XY Choo, CM O’Brien, WA Pastor, D Chen, AL Leichter, H Naeem, P Tripathi, PP Das, A Grubman, DR Powell, AL Laslett, LDavid, SK Nilsson, AT Clark, R Lister, CM Nefzger, LG Martelotto, OJL Rackham & JM Polo "Reprogramming roadmap reveals route to human induced trophoblast stem cells" Nature. 2020. Pubmed: 32939092.  (corresponding author) IF 42.779
Web link for this paper: https://www.nature.com/articles/s41586-020-2734-6

EY Cao, JF Ouyang, OJL Rackham "GeneSwitches: ordering gene expression and functional events in single-cell experiments" Bioinformatics. 2020. Pubmed: 32058565.  (corresponding author) IF 5.61
Web link for this paper: https://academic.oup.com/bioinformatics/article/36/10/3273/5736130

Q Zhou, Z Fu, Y Gong, VP Seshachalam, J Li, Y Ma, H Liang, W Guan, S Lin, S Ghosh, L Sun, and H Zhou "Metabolic health status contributes to transcriptome alternation in human visceral adipose tissue during obesity" Obesity, 2020 Sep doi.org/10.1002/oby.22950 (co-corresponding author) IF 3.742
Web link for this paper: https://onlinelibrary.wiley.com/doi/abs/10.1002/oby.22950

WS Dantas, H Roschel, IH Murai, S Gil, G Davuluri, CL Axelrod, S Ghosh, SS Newman, H Zhang, SK Shinjo, WD Neves, C Merege-Filho, WR Teodoro, VL Capelozzi, RM Pereira, FB Benatti, AL de Sá-Pinto, R de Cleva, MA Santo, JP Kirwan, B Gualano "Exercise-Induced Increases in Insulin Sensitivity After Bariatric surgery are Mediated by Muscle Extracellular Matrix Remodeling" Diabetes. 2020 May 14;. doi: 10.2337/db19-1180. IF 7.72
Web link for this paper: https://diabetes.diabetesjournals.org/content/69/8/1675

Mia, M.M., Cibi, D.M., Ghani, S., Song, W., Tee, N., Ghosh, S., Mao, J., Olson, E.N., and Singh, M.K. "YAP/TAZ deficiency reprograms macrophage phenotypeand improves infarct healing and cardiac function after myocardial infarction" PLoS Biology, 18, e3000941 (2020) doi.org/10.1371/journal.pbio.3000941  IF 7.076
Web link for this paper: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000941

Guo, A.K., Itahana, Y., Seshachalam, V.P., Chow, H.Y., Ghosh, S. and Itahana, K. "Mutant TP53 interacts with BCAR1 to contribute to cancer cell invasion" British Journal of Cancer, 124, 299-312 (2020) doi.org/10.1038/s41416-020-01124-9 (2020) IF 5.791
Web link for this paper: https://www.nature.com/articles/s41416-020-01124-9

NS Jagannathan, MO Ihsan, XX Kin, RE Welsch, MV Clément, L Tucker-Kellogg. "TRANSCOMPP: Understanding phenotypic plasticity by estimating Markov transition rates for cell state transitions" Bioinformatics May 1;36(9):2813-2820 (2020) IF 5.61
Web link for this paper: https://academic.oup.com/bioinformatics/article/36/9/2813/5714733

NS Jagannathan, CWV Hogue, L Tucker-Kellogg. "De novo ensemble modeling suggests that AP2-binding to disordered regions can increase steric volume of Epsin but not Eps15"Pac Symp Biocomput. 25:183-194 (2020).
Web link for this paper: https://www.worldscientific.com/doi/abs/10.1142/9789811215636_0017

BWS Soh, A Corrias, L Tucker-Kellogg. "Computational modeling of the thin muscle layer, panniculus carnosus, demonstrates principles of pressure injury and prophylactic dressings" Innovations and Emerging Technologies in Wound Care, Elsevier (2020) Note: peer-reviewed primary results.
Web link for this paper: https://www.sciencedirect.com/science/article/pii/B9780128150283000031

 

J Zavadil, SG Rozen. "Experimental Delineation of Mutational Signatures Is an Essential Tool in Cancer Epidemiology and Prevention" Chemical Research in Toxicology 2019, 32 (11), 2153-2155 doi.org/10.1021/acs.chemrestox.9b00339 (2019). IF 3.278
Web link for this paper: https://pubs.acs.org/doi/10.1021/acs.chemrestox.9b00339

EN Bergstrom, MN Huang, U Mahto, M Barnes, MR Stratton, SG Rozen, LB Alexandrov. "SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events" BMC Genomics 20,685 doi: 10.1186/s12864-019-6041-2 (2019) IF 3.730
Web link for this paper: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6041-2

H Chen, A Moreno-Moral, F Pesce, N Devapragash, M Mancini, E Ling Heng, M Rotival, P K Srivastava, N Harmston, K Shkura, OJL Rackham, W-P Yu, Xi-Ming Sun, N Gui Zhen Tee, E Tan, PJR Barton, LE Felkin, E Lara-Pezzi, G Angelini, C Beltrami, M Pravenec, S Schafer, L Bottolo, N Hubner, Costanza Emanueli, SA Cook & E Petretto "WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling" Nature Communications 2019; 10(1):3616 IF 12.121
Web link for this paper: https://www.nature.com/articles/s41467-019-11551-9

A Grubman, G Chew, JF Ouyang, G Sun, XY Choo, C McLean, RK Simmons, S Buckberry, DB Vargas-Landin, D Poppe, J Pflueger, R Lister, OJL Rackham, E Petretto & JM Polo. "A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation" Nature Neuroscience 2019; 22(12):2087-2097 IF 20.071
Web link for this paper: https://www.nature.com/articles/s41593-019-0539-4

S Chothani , S Schäfer , E Adami , S Viswanathan, AA Widjaja , SR Langley, J Tan, M Wang, NM Quaife , CJ Pua, G D'Agostino, SG Shekeran, BL George, S Lim, EY Cao , S van Heesch, F Witte, LE Felkin, EG Christodoulou, J Dong, S Blachut, G Patone, PJR Barton, N Hubner , SA Cook, OJL Rackham. "Widespread Translational Control of Fibrosis in the Human Heart by RNA-binding Proteins" Circulation, 2019. Pubmed: 31284728 (corresponding author) IF 23.603
Web link for this paper: https://pubmed.ncbi.nlm.nih.gov/31284728/

AX Sun, QYuan, M Fukuda, W Yu, H Yan, GGY Lim, MH Nai, GAD’Agostino, H Tran, Y Itahana, D Wang, H Lokman, K Itahana, SWL Lim, J Tang, YY Chang, M Zhang, SA Cook, OJL Rackham, CT Lim, EK Tan, HH Ng, KL Lim, YH Jiang, HS Je. "Potassium channel dysfunction in human neuronal models of Angelman syndrome" Science, 2019. Pubmed: 31857479 IF 41.845
Web link for this paper: https://science.sciencemag.org/content/366/6472/1486

C Li, KR Chng, JS Kwah, TV Av-Shalom, L Tucker-Kellogg, N Nagarajan. "An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data" Microbiome 7(1):118 (2019) IF 11.607
Web link for this paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0729-z

WK Lim, X Chai, S Ghosh, D Ray, M Wang, SAK Rasheed, PJ Casey. "Gα-13 induces CXC motif chemokine ligand 5 expression in prostate cancer cells by transactivating NF-κB" J Biol Chem. 2019 Nov 29;294(48):18192-18206 IF 4.238
Web link for this paper: https://www.jbc.org/article/S0021-9258(20)30685-2/fulltext

CYY Chan, JZH Low, ES Gan, EZ Ong, SL Zhang, HC Tan, X Chai, S Ghosh, EE Ooi, KR Chan. "Antibody-Dependent Dengue Virus Entry Modulates Cell Intrinsic Responses for Enhanced Infection" mSphere. 2019 Sep 18;4(5). doi: 10.1128/mSphere.00528-19
Web link for this paper: https://msphere.asm.org/content/4/5/e00528-19

DM Cibi, MM Mia, SG Shekeran, LS Yun, R Sandireddy, P Gupta, M Hota, L Sun, S Ghosh, and MK Singh "Neural-crest specific deletion of Rbfox2 in mice leads to craniofacial abnormalities including cleft palate" eLife, 8 (2019) IF7.080
Web link for this paper: https://elifesciences.org/articles/45418

LB Alexandrov, J Kim, NJ Haradhvala, MN Huang, Ng, Alvin WT, AB Boot, KR Covington, DA Gordenin, E Bergstrom, N Lopez-Bigas, LJ Klimczak, JR McPherson, S Morganella, Sabarinathan, Radhakrishnan , DA Wheeler, V Mustonen, G Getz, SG Rozen*, MR Stratton* on behalf of the PCAWG Mutational Signatures Working Group and the , ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. "The repertoire of mutational signatures in human cancer". Preprint on bioRxiv,  https://doi.org/10.1101/322859, in review at Nature (2018) * denotes corresponding author

Web link for this paper:  https://www.biorxiv.org/content/early/2018/05/15/322859

A Boot, M Huang, AWT Ng, S-C Ho, JQ Lim, Y Kawakami, K Chayama, BT Teh, H Nakagawa, SG  Rozen. "In-depth characterization of the cisplatin mutational signature in a human cell line and in esophageal and liver tumors" Genome Res 28(5):654-665 (2018) IF 11.92
Web link for this paper:  https://www.ncbi.nlm.nih.gov/pubmed/29632087

JP Chan, BH Wong, CF Chin, DLA Galam, JC Foo, LC Wong, S Ghosh, MR Wenk, A Cazenave-Gassiot, D Silver. "The lysolipid transporter Mfsd2a regulates lipogenesis in the developing brain" PLoS Biol. (2018) IF 9.163
Web link for this paper:  https://doi.org/10.1371/journal.pbio.2006443 

S Chothani, S Schafer, E Adami, S Viswanathan, AA Widjaja, SR Langley, J Tan, JP Chee, G D'Agostino, S van Heesch, F Witte, LE Felkin, EG Christodoulou, J Dong, S Blachut, G Patone, PJR Barton, N Hubner, SA Cook, OJL Rackham. "Translational control of cardiac fibrosis" bioRxiv, (2018) doi: https://doi.org/10.1101/451666
Web link for this paper:  https://www.biorxiv.org/content/10.1101/451666v1

S Gurley, S Ghosh, J Stacy, K Azushima, R Sakban, S George, M Maeda, T Meyer, T Coffman. "Inflammation and immunity pathways regulate genetic susceptibility to diabetic nephropathy" Diabetes 67, 2096-2106 (2018) IF 7.273
Web link for this paper: https://diabetesjournals.org/diabetes/article/67/10/2096/35309/Inflammation-and-Immunity-Pathways-Regulate

RNV Krishna Deepak, A Abdullah, P Talwar, H Fan, P Ravanan. "Identification of FDA-approved drugs as novel allosteric inhibitors of human executioner caspases" Proteins (2018) Sep. doi: 10.1002/prot.25601. PubMed PMID: 30194780. IF 2.499
Web link for this paper: https://www.ncbi.nlm.nih.gov/pubmed/30194780  

C Li, L Tucker-Kellogg, N Nagarajan. "System biology modeling with compositional microbiome data reveals personalized gut microbial dynamics and keystone species" bioRxiv, (2018) doi: https://doi.org/10.1101/288803
Web link for this paper:  https://www.biorxiv.org/content/early/2018/03/27/288803

VJY Lim, W Du, YZ Chen, H Fan. "A benchmarking study on virtual ligand screening against homology  models of human GPCRs" Proteins (2018) Jul. doi: 10.1002/prot.25533.
PubMed PMID: 30051928. IF 2.499
Web link for this paper:  https://www.ncbi.nlm.nih.gov/pubmed/30051928

A Moreno-Moral*, M Bagnati*, S Koturan, J-H Ko, C Fonseca, N Harmston, L Game,  J Martin, V Ong, DJ Abraham, C. Denton, J Behmoaras*, E Petretto*."Changes in macrophage transcriptome associate with systemic sclerosis and diate GSDMA contribution to disease risk"  Ann. Rheum. Dis. (2018) 77(4):596-601 (* = corresponding author) IF 12.8
web link to the paper:  Extended report: Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk

EC Saputra, L Huang, Y Chen, L Tucker-Kellogg. "Combination therapy and the evolution of resistance: the theoretical merits of synergism and antagonism in cancer" Cancer Res. (2018) DOI: 10.1158/0008-5472.CAN-17-1201 IF 9.130
Web link for this paper:  http://cancerres.aacrjournals.org/content/early/2018/04/23/0008-5472.CAN-17-1201.short

PK Srivastava, JV Eyll, P Godard, M Mazzuferi, A Delahaye-Duriez, JV Steenwinckel, P Gressens, B Danis, C Vandenplas, P Foerch, K Leclercq, G Mairet-Coello, A Cardenas, F Vanclef, L Laaniste, I Niespodziany, J Keaney, J Gasser, G Gillet, K Shkura, SA Chong, J Behmoaras, I Kadiu, E Petretto*, RM Kaminski*, MR Johnson*. "A systems-level framework for drug discovery identifies Csf1r as an anti-epileptic drug target" Nat. Commun. (2018) 9(1):3561 (* = corresponding author) IF 12.1
Web link to the paper: A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target | Nature Communications

A Tan Li Min, SR Langley, C Fan Tan, C Jin Fang, C Meng Khoo, M Khee-Shing Leow, E Yin Hao Khoo, A Moreno-Moral, M Pravenec, M Rotival, S Anand Sadananthan, S Sendhil Velan, K Venkataraman, Y Seng Chong, Y Seng Lee, S Xueling, W Stunkel, L Mei Hui, E Shyong Tai*, E  Petretto*. "Ethnicity-specific skeletal muscle transcriptional signatures and their relevance to insulin resistance in Singapore"  J. Clin. Endocrinol. Metab. 2018; jc.2018-00309 (* = corresponding author) IF 5.8
Web link for this paper: Ethnicity-specific skeletal muscle transcriptional signatures and their relevance to insulin resistance in Singapore | The Journal of Clinical Endocrinology & Metabolism | Oxford Academic

YC Tang, S-C Ho, E Tan, AWT Ng, JR McPherson, GYL Goh, BT Teh, F Bard, SG Rozen. "Functional Genomics Identifies Specific Vulnerabilities in PTEN-Deficient Breast Cancer" Breast Cancer Res, 20(1), 22 doi:10.1186/s13058-018-0949-3 (2018) IF 6.345
Web link for this paper:  https://www.ncbi.nlm.nih.gov/pubmed/29566768

J Wilkins, P Ghosh, J Vivar, B Chakraborty, S Ghosh. "Exploring the associations between systemic inflammation, obesity and healthy days: a health related quality of life (HRQOL) analysis of NHANES 2005-2008" BMC Obesity, 5:21(2018)
Web link for this paper:  https://www.ncbi.nlm.nih.gov/pubmed/30123515

T Yan, WF Ooi, A Qamra, A Cheung, D Ma, GM Sundaram, C Xu, M Xing, L Poon, J Wang, YP Loh, JHJ Ho, JJQ Ng, MK Ramlee, L Aswad, SG Rozen, S Ghosh, F Bard, P Sampath, V Tergaonkar, JOJ Davies, JR Hughes, E Goh, X Bi, MJ Fullwood, P Tan, S Li. "HoxC5 and miR-615-3p target newly evolving genomic regions to repress hTERT and inhibit tumorigenesis" Nat. Commun. 9, 100 (2018) IF 12.1
Web link for this paper:  https://www.nature.com/articles/s41467-017-02601-1

OJL Rackham, SR Langley, T Oates, E Vradi, N Harmston, PK Srivastava, J Behmoaras, P Dellaportas*, L Bottolo, E Petretto*. "A Bayesian approach for analysis of whole-genome bisulphite sequencing data identifies disease-associated changes in DNA methylation"  Genetics 205(4):1443-1458 (2017) (* = corresponding author) IF 5.69
Web link for this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378105/ 
Web link for editorial: http://www.genetics.org/content/205/4/NP 

AWT Ng, SL Poon, MN Huang, JQ Lim, A Boot, W Yu, Y Suzuki, S Thangaraju, CCY. Ng, P Tan, S-T Pang, H-Y Huang, M-Ch Yu, P-H Lee¹, S-Y Hsieh^1*, AY Chang^1*, BT Teh^*,SG Rozen^*."Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia" Sci Transl Med in press (2017) IF 16.79

S Ghosh, LA Forney, D Wanders, KP Stone, TW Gettys. "An integrative analysis of tissue-specific transcriptomic and metabolomics responses to short-term dietary methionine restriction in mice" PLOS ONE https://doi.org/10.1371/journal.pone.0177513 (2017) IF 2.80

H Li, L Venkatraman, BC  Narmada, JK White, H Yu , L Tucker-Kellogg. "Computational analysis reveals the coupling between bistability and the sign of a feedback loop in a TGF-β1 activation model" BMC Syst Biol, in press (2017) IF 2.30

Z Bai, X Chai, MJ Yoon, HJ Kim, KA Lo, Z Zhang, D Xu, DTC Siang, ACE Walet, S Xu, SY Chia, P Chen, H Yang, S Ghosh*, L Sun. "Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators" PLOS Biology 15(8):e2002176 doi: 10.1371/journal.pbio.2002176 (2017) (* = corresponding author) IF 9.79
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B Pontes, P Monzo, L Gole, AL Le Roux, AJ Kosmalska, ZY Tam, W Luo, S Kan, V Viasnoff, P Roca-Cusachs, L Tucker-Kellogg, N Gauthier.  "Membrane tension controls lamellipodial buckling and adhesion positioning at leading edge of cells" J of Cell Biol (ePub 7 July 2017). IF 9.78
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LD Ler, S Ghosh, X Chai, AA Thike, HL Heng, EY Siew, S Dey, LK Koh, JQ Lim, WK Lim, SS Myint, JL Loh, P Ong, XX Sam, D Huang, T Lim, PH Tan, S Nagarajan, CWS Cheng, H Ho, LG Ng, J Yuen, P-H Lin, C-K Chuang, Y-H Chang, W-H Weng, SG Rozen, P Tan, CL Creasy, S-T Pang, MT McCabe, SL Poon, BT Teh. "Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2" Sci Transl Med 9: eaai8312 (2017) IF  16.79
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C-C Hon, JA Ramilowski, J Harshbarger, N Bertin, OJL Rackham,…,ARR Forrest "An atlas of human long non-coding RNAs with accurate 5` ends". Nature 543:199-204 (2017) IF 40.13
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S Schafer, A De Marvao, E Adami, LR Fiedler, B Ng, E Khin, OJL Rackham,…, SA Cook "Titin truncating variants affect heart function in disease cohorts and the general population"Nat Genet, 49:46-53 (2017) IF 27.95
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MN Huang, W Yu, WW Teoh, M Ardin, A Jusakul, A Ng, A Boot, B Abedi-Ardekani, S Villar, SS Myint, R Othman, SL Poon, A Heguy, M Olivier, M Hollstein, P Tan, BT Teh, K Sabapathy, J Zavadil, S Rozen. "Genome-scale mutational signatures of aflatoxin in cells, mice and human tumors" Genome Res doi:10.1101/gr.220038.116 (2017) IF 11.35
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ML Krishnan, J Van Steenwincke, A-L Schang, J Yan, J Arnadottir, T Le Charpentier, Z Csaba, P Dournaud, S Cipriani, C Auvynet, L Titomanlio, J Pansiot, G Ball, JP Boardman, AJ Walley, A Saxena, G Mirza, B Fleiss, AD Edwards*, E Petretto*, P Gressens*. "Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants" Nat Commun 8 (2017) (* = corresponding author) IF 12.12
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A Jusakul, I Cutcutache, CH Yong, JQ Lim, MN Huang, N Padmanabhan, V Nellore, S Kongpetch, AWT Ng, LM Ng, SP Choo, SS Myint, R Thanan, S Nagarajan, WK Lim, CCY Ng, A Boot, M Liu, CK Ong, V Rajasegaran, S Lie, AS-T Lim, TH Lim, J Tan, MJ Liang, J Mcpherson, N Khuntikeo, V Bhudhisawasdi, P Yongvanit, S Wongkham, Y Totoki, H Nakamura, Y Arai, S Yamasaki, P Chow, AYF Chung, LLPJ Ooi, T Lim, S Dima, D Duda, I Popescu, P Broet, S-Y Hsieh, M-C Yu, A Scarpa, J Lai, D Luo, AL Carvalho, A Vettore, H Rhee, YN Park, L Alexandrov, R Gordan*, S Rozen*, T Shibata*, C Pairojkul*, BT Teh*, P Tan*. "Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma" Cancer Discov doi:10.1158/2159-8290.CD-17-0368 (2017) (* = corresponding author) IF 19.78
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PK Srivastava, M Bagnati, A Delahaye-Duriez, J-H Ko, M Rotival, SR Langley, K Shkura, M Mazzuferi, B Danis, J van Eyll, P Foerch, J Behmoaras, RM Kaminski, E Petretto*, MR Johnson*. "Genome-wide analysis of differential RNA editing in epilepsy" Genome Res 27(3):440-450 (2017) (* = corresponding author) IF 11.92
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Y. Suzuki, S.B. Ng, C. Chua, W.Q. Leow, J. Chng, S.Y. Liu, K. Ramnarayanan, A. Gan, D.L. Ho, R. Ten, Y. Su, A. Lezhava, J. H. Lai, D. Koh, K.H. Lim, P. Tan, S.G Rozen*, I.B. Tan* "Multiregion ultra-deep sequencing reveals early intermixing and variable levels of intratumoral heterogeneity in colorectal cancer" Mol Oncol doi:10.1002/1878-0261.12012 (2016) (* = corresponding author) IF 5.37
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T.H.M. Chan, A. Qamra, K.T. Tan, J. Guo, H. Yang, L. Qi, J.S. Lin, V.H.E. Ng, Y. Song, H. Hong, S.T. Tay, Y. Liu, J. Lee, S.Y. Rha, Z. Feng, J.B.Y. So, B.T. Teh, Y.K. Guan, S. Rozen, D.G. Tenen, P. Tan, L. Chen "ADAR-mediated RNA editing predicts progression and prognosis of gastric cancer" Gastroenterol 151:637-650 (2016) IF 16.71
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O.J.L. Rackham*, J. Firas, H. Fang, M.E. Oates, M.L. Holmes, A.S. Knaupp, the FANTOM consortium, H. Suzuki, C.M. Nefzger, C.O. Daub, J.W. Shin, E. Petretto, A.R.R. Forrest, Y. Hayashizaki, J.M. Polo*, J. Gough*. "A predictive computational framework for direct reprogramming between human cell types" Nat. Genet. 48, 331–335 (2016) IF 29.3
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M.R. Johnson*, K. Shkura, S.R. Langley, A. Delahaye-Duriez, P. Srivastava, W.D. Hill, O.J.L. Rackham, G. Davies, S.E. Harris, A. Moreno-Moral, M. Rotival, D. Speed, S. Petrovski, A. Katz, C.J. Steves, A. Visconti, M. Falchi, L. Bottolo, T. Rossetti, J.M. Starr, D.C. Liewald, B. Danis, M. Mazzuferi, P. Foerch, A. Grote, C. Helmstäedter, A.J. Becker, R.M. Kaminski, I.J. Deary, E Petretto*. "Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease" Nat. Neurosci. 19(2):223-232 (2016) (* = corresponding author) IF 16.1
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O.J.L. Rackham*, P. Dellaportas, E. Petretto, L. Bottolo. "WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools" Bioinformatics 31:14 2371-2373 (2015) (* = corresponding author) IF 5.76
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O.J Rackham, H.A Shihab, M.R Johnson, E. Petretto. "EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritisation " Nucleic Acids Res. 43(5):e33-e33 (2015) IF  9.1
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J. Tan, C.K. Ong, W.K. Lim, C.C.Y. Ng, A.A. Thike, L.M. Ng, V. Rajasegaran, S.S. Myint, S. Nagarajan, S. Thangaraju, S. Dey, N.D. Md Nasir, G.C. Wijaya, J.Q. Lim, D. Huang, Z. Li, B.H. Wong, J.Y.S. Chan, J.R. McPherson, I. Cutcutache, G. Poore, S.T. Tay, W.J. T. Tan, C. Putti, B.S. Ahmad, P. Iau, C.W. Chan, A.P.T. Tang, W.S. Yong, P. Madhukumar, G.H. Ho, V.K.M. Tan, C.Y. Wong, M. Hartman, K.W. Ong, B.K.T. Tan, S.G. Rozen*, P. Tan*, P.H. Tan*, B.T. Teh*. "Genomic landscapes of breast fibroepithelial tumors" Nat Genet 47:1341–1345 (2015) (* = corresponding author) IF 29.35
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I. Cutcutache, Y. Suzuki, I.B. Tan, S. Ramgopal, S. Zhang, K. Ramnarayana, A. Gan, H.H. Lee, S.T. Tay, A. Ooi, C.K. Ong, J.T. Bolthouse, B.R. Lane, J.G. Anema, R.J. Kahnoski, P. Tan*, B.T. Teh*, S.G. Rozen*. "Exome-wide sequencing shows low mutation rates and identifies novel mutated genes in seminomas" Eur. Urol. 68(1):77-83 (2015) (* = corresponding author) IF 13.9

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M.R. Johnson*, J. Behmoaras, L. Bottolo, M.L. Krishnan, K. Pernhorst, P.L Meza Santoscoy, T. Rossetti, D. Speed, P.K. Srivastava, M. Chadeau-Hyam, N. Hajji, A. Dabrowska, M. Rotival, B. Razzaghi, S. Kovac, K. Wanisch, F. Grillo, A. Slaviero, S.R. Langley, K. Shkura, P. Roncon, T. De, M. Mattheisen, P. Niehusmann, T.J. O'Brien, S. Petrovski, M. von Lehe, P. Hoffmann, J. Eriksson, A. Coffey, S. Cichon, M. Walker, M. Simonato, B. Danis, M. Mazzuferi, P. Foerch, S. Schoch, V. De Paola, R.M. Kaminski, V.T. Cunliffe, A.J. Becker, E. Petretto*. "Systems-genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus" Nature Commun. 6 (2015) (* = corresponding author) IF 11.4
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T. Rankinen, M.A. Sarzynski, S. Ghosh, C. Bouchard. "Are there genetic paths common to obesity, cardiovascular disease outcomes and cardiovascular risk factors? " Circ. Res. 116(5):909-922 (2015) IF 11.0
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T.H. Nim, L. Luo, J.K. White, M.-V. Clement, L. Tucker-Kellogg. "Non-canonical activation of Akt in serum-stimulated fibroblasts, revealed by comparative modeling of pathway dynamics" PLoS Comput. Biol. 11(11): e1004505 (2015) IF 4.8
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S.L Poon, M.N. Huang, Y. Choo, J.R McPherson, W. Yu, H.L Heng, A. Gan, S.S. Myint, E.Y. Siew, L.D. Ler, L.G. Ng, W.-H. Weng, C.-K. Chuang, J.S.P. Yuen, S.-T. Pang, P. Tan, B.T. Teh, S.G. Rozen. "Mutation signatures implicate aristolochic acid in bladder cancer development" Genome Med.7(1):38 (2015) IF 5.8
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S. Ghosh, J. Vivar, C.P. Nelson, C. Willenborg, A.V. Segre, V.P. Makinen, M. Nikpay, J. Erdmann, S. Blankenberg, C. O’Donnell, W. Marz, R. Laaksonen, A.F. Stewart, S.E. Epstein, S.H. Shah, C.B. Granger, S.L. Hazen, S. Kathiseran, M.P. Reilly, X. Yang, T. Quertermous, N.J. Samani, H. Schunkert, T.L. Assimes, R. McPherson. "Systems genetics analysis of genome-wide association study reveals novel associations between key biological processes and coronary artery disease" Arterioscl. Throm. Vas. Biol. 35(7):1712-22 (2015) doi 10.1161/ATVBAHA.115.305513 IF 5.5
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N.S. Jagannathan, L. Tucker-Kellogg. "Membrane permeability during pressure ulcer formation: A computational model of dynamic competition between cytoskeletal damage and repair" J Biomech (2015) Published online: December IF 2.75
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A.J. Sardar, M.E. Oates, H. Fang, A.R.R. Forrest, H. Kawaji, J. Gough, O.J.L. Rackham*, FANTOM Consortium. "The evolution of human cells in terms of protein innovation" Mol. Biol. Evol. 31:6 1364-1374 (2014) (* = corresponding author) IF 13.64
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H. Kang, A. Kerloc’h, M. Rotival, X. Xu, Q. Zhang, Z. D’Souza, M. Kim, J. Carlson Scholz, J.H. Ko, P.K. Srivastava, T. Rossetti, J.R. Genzen, W. Cui, T.J. Aitman, L. Game, J.E. Melvin, A. Hanidu, J. Dimock, J. Zheng, D. Souza, A. Behera, G. Nabozny, H.T. Cook, D. Bassett, G.R. Williams, J. Li, A. Vignery*, E. Petretto*, J. Behmoaras*. "Kcnn4 is a regulator of macrophage multinucleation in bone homeostasis and inflammatory disease" Cell Rep. 8(4):1210-1224 (2014) (* = corresponding author) IF 7.2
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S. Ghosh, D. Wanders, K.P. Stone, N.T. Van, C.C. Cortez, T.W. Gettys. "A systems biology analysis of the unique and overlapping transcriptional responses to caloric restriction and dietary methionine restriction in rats" FASEB J. 28(6):2577-2590 (2014) IF 5.5
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A. Kitsy, S. Carney, J.C. Vivar, M.S. Knight, M.A. Pointer, J.K. Gwathmey, S. Ghosh. "Effects of leucine supplementation and serum withdrawal on branched-chain amino acid pathway gene and protein expression in mouse adipocytes" PLOS One 9(7):e102615 (2014) IF 3.5
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S.L. Poon, J.R. McPherson, P. Tan, B.T. Teh, S.G. Rozen. "Genome wide carcinogen signatures promise new opportunities for cancer prevention" Genome Med. (review) 6:24 (2014) IF 4.9
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