Cristian Coarfa, Ph.D. - Publications

Affiliations: 
2007 Rice University, Houston, TX 
Area:
Computer Science

75 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Ware MJ, Keshishian V, Law JJ, Ho JC, Favela CA, Rees P, Smith B, Mohammad S, Hwang RF, Rajapakshe K, Coarfa C, Huang S, Edwards DP, Corr SJ, Godin B, et al. Generation of an in vitro 3D PDAC stroma rich spheroid model. Biomaterials. 108: 129-142. PMID 27627810 DOI: 10.1016/j.biomaterials.2016.08.041  0.8
2016 Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, et al. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nature Communications. 7: 12601. PMID 27574101 DOI: 10.1038/ncomms12601  0.8
2016 Ochsner SA, Tsimelzon A, Dong J, Coarfa C, McKenna NJ. Research Resource: A reference transcriptome for constitutive androstane receptor and pregnane X receptor xenobiotic signaling. Molecular Endocrinology (Baltimore, Md.). me20161095. PMID 27409825 DOI: 10.1210/me.2016-1095  0.8
2016 Napoli M, Venkatanarayan A, Raulji P, Meyers BA, Norton W, Mangala LS, Sood AK, Rodriguez-Aguayo C, Lopez-Berestein G, Vin H, Duvic M, Tetzlaff MB, Curry JL, Rook AH, Abbas HA, ... Coarfa C, et al. ΔNp63/DGCR8-Dependent MicroRNAs Mediate Therapeutic Efficacy of HDAC Inhibitors in Cancer. Cancer Cell. 29: 874-888. PMID 27300436 DOI: 10.1016/j.ccell.2016.04.016  0.8
2016 Shivanna B, Maity S, Zhang S, Patel A, Jiang W, Wang L, Welty SE, Belmont J, Coarfa C, Moorthy B. Gene Expression Profiling Identifies Cell Proliferation and Inflammation as the Predominant Pathways Regulated by Aryl hydrocarbon Receptor in Primary Human Fetal Lung Cells Exposed to Hyperoxia. Toxicological Sciences : An Official Journal of the Society of Toxicology. PMID 27103661 DOI: 10.1093/toxsci/kfw071  0.8
2016 Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, ... ... Coarfa C, et al. miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. PMID 27036018 DOI: 10.18632/oncotarget.8412  0.8
2016 Eclarinal JD, Zhu S, Baker MS, Piyarathna DB, Coarfa C, Fiorotto ML, Waterland RA. Maternal exercise during pregnancy promotes physical activity in adult offspring. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 27033262 DOI: 10.1096/fj.201500018R  0.8
2016 Lopez SM, Agoulnik AI, Zhang M, Peterson LE, Suarez E, Gandarillas GA, Frolov A, Li R, Rajapakshe K, Coarfa C, Ittmann M, Weigel N, Agoulnik IU. Nuclear Receptor Corepressor 1 expression and output declines with prostate cancer progression. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 26968201 DOI: 10.1158/1078-0432.CCR-15-1983  0.8
2016 Park JH, Vithayathil S, Kumar S, Sung PL, Dobrolecki LE, Putluri V, Bhat VB, Bhowmik SK, Gupta V, Arora K, Wu D, Tsouko E, Zhang Y, Maity S, Donti TR, ... ... Coarfa C, et al. Fatty Acid Oxidation-Driven Src Links Mitochondrial Energy Reprogramming and Oncogenic Properties in Triple-Negative Breast Cancer. Cell Reports. PMID 26923594 DOI: 10.1016/j.celrep.2016.02.004  0.8
2016 von Rundstedt FC, Kimal R, Ma J, Arnold J, Gohlke J, Putluri V, Krishnapuram R, Piyarathna DB, Lotan Y, Gödde D, Roth S, Störkel S, Levitt JM, Michailidis G, Sreekumar A, ... ... Coarfa C, et al. Integrative pathway analysis of metabolic signature in bladder cancer - a linkage to the Cancer Genome Atlas Project and prediction of survival. The Journal of Urology. PMID 26802582 DOI: 10.1016/j.juro.2016.01.039  0.8
2015 Zhang S, Wei JS, Li SQ, Badgett TC, Song YK, Agarwal S, Coarfa C, Tolman C, Hurd L, Liao H, He J, Wen X, Liu Z, Thiele CJ, Westermann F, et al. MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma. Cancer Letters. PMID 26683771 DOI: 10.1016/j.canlet.2015.11.045  0.8
2015 Holdman XB, Welte T, Rajapakshe K, Pond A, Coarfa C, Mo Q, Huang S, Hilsenbeck SG, Edwards DP, Zhang X, Rosen JM. Upregulation of EGFR signaling is correlated with tumor stroma remodeling and tumor recurrence in FGFR1-driven breast cancer. Breast Cancer Research : Bcr. 17: 141. PMID 26581390 DOI: 10.1186/s13058-015-0649-1  0.8
2015 Kessler NJ, Van Baak T, Baker MS, Laritsky E, Coarfa C, Waterland RA. CpG methylation differences between neurons and glia are highly conserved from mouse to human. Human Molecular Genetics. PMID 26566671 DOI: 10.1093/hmg/ddv459  0.8
2015 Jonsson P, Coarfa C, Mesmar F, Raz T, Rajapakshe K, Thompson JF, Gunaratne PH, Williams C. Single-molecule sequencing reveals estrogen-regulated clinically relevant lncRNAs in breast cancer. Molecular Endocrinology (Baltimore, Md.). me20151153. PMID 26426411 DOI: 10.1210/me.2015-1153  0.8
2015 Shafi AA, Putluri V, Arnold JM, Tsouko E, Maity S, Roberts JM, Coarfa C, Frigo DE, Putluri N, Sreekumar A, Weigel NL. Differential regulation of metabolic pathways by androgen receptor (AR) and its constitutively active splice variant, AR-V7, in prostate cancer cells. Oncotarget. PMID 26378018 DOI: 10.18632/oncotarget.5585  0.8
2015 Coarfa C, Fiskus W, Eedunuri VK, Rajapakshe K, Foley C, Chew SA, Shah SS, Geng C, Shou J, Mohamed JS, O'Malley BW, Mitsiades N. Comprehensive proteomic profiling identifies the androgen receptor axis and other signaling pathways as targets of microRNAs suppressed in metastatic prostate cancer. Oncogene. PMID 26364608 DOI: 10.1038/onc.2015.295  0.8
2015 Blessing AM, Ganesan S, Rajapakshe K, Ying Sung Y, Reddy Bollu L, Shi Y, Cheung E, Coarfa C, Chang JT, McDonnell DP, Frigo DE. Identification of a Novel Coregulator, SH3YL1, That Interacts With the Androgen Receptor N-Terminus. Molecular Endocrinology (Baltimore, Md.). 29: 1426-39. PMID 26305679 DOI: 10.1210/me.2015-1079  0.8
2015 Chang CH, Zhang M, Rajapakshe K, Coarfa C, Edwards D, Huang S, Rosen JM. Mammary Stem Cells and Tumor-Initiating Cells Are More Resistant to Apoptosis and Exhibit Increased DNA Repair Activity in Response to DNA Damage. Stem Cell Reports. PMID 26300228 DOI: 10.1016/j.stemcr.2015.07.009  0.8
2015 Sun B, Shah B, Fiskus W, Qi J, Rajapakshe K, Coarfa C, Li L, Devaraj SG, Sharma S, Zhang L, Wang ML, Saenz DT, Krieger S, Bradner JE, Bhalla KN. Synergistic activity of BET protein antagonist-based combinations in mantle cell lymphoma cells sensitive or resistant to ibrutinib. Blood. PMID 26254443 DOI: 10.1182/blood-2015-04-639542  0.8
2015 Silver MJ, Kessler NJ, Hennig BJ, Dominguez-Salas P, Laritsky E, Baker MS, Coarfa C, Hernandez-Vargas H, Castelino JM, Routledge MN, Gong YY, Herceg Z, Lee YS, Lee K, Moore SE, et al. Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment. Genome Biology. 16: 118. PMID 26062908 DOI: 10.1186/s13059-015-0660-y  0.8
2015 Bhardwaj A, Ganesan N, Tachibana K, Rajapakshe K, Albarracin CT, Gunaratne PH, Coarfa C, Bedrosian I. Annexin A1 Preferentially Predicts Poor Prognosis of Basal-Like Breast Cancer Patients by Activating mTOR-S6 Signaling. Plos One. 10: e0127678. PMID 26000884 DOI: 10.1371/journal.pone.0127678  0.8
2015 Lin F, Marcelo KL, Rajapakshe K, Coarfa C, Dean A, Wilganowski N, Robinson H, Sevick E, Bissig KD, Goldie LC, Means AR, York B. The camKK2/camKIV relay is an essential regulator of hepatic cancer. Hepatology (Baltimore, Md.). 62: 505-20. PMID 25847065 DOI: 10.1002/hep.27832  0.8
2015 Kannan K, Coarfa C, Chao PW, Luo L, Wang Y, Brinegar AE, Hawkins SM, Milosavljevic A, Matzuk MM, Yen L. Recurrent BCAM-AKT2 fusion gene leads to a constitutively activated AKT2 fusion kinase in high-grade serous ovarian carcinoma. Proceedings of the National Academy of Sciences of the United States of America. 112: E1272-7. PMID 25733895 DOI: 10.1073/pnas.1501735112  0.8
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Coarfa C, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/nature14248  0.8
2015 Amin V, Harris RA, Onuchic V, Jackson AR, Charnecki T, Paithankar S, Lakshmi Subramanian S, Riehle K, Coarfa C, Milosavljevic A. Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs. Nature Communications. 6: 6370. PMID 25691256 DOI: 10.1038/ncomms7370  0.8
2015 Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nature Communications. 6: 6363. PMID 25691127 DOI: 10.1038/ncomms7363  0.8
2015 Venkatanarayan A, Raulji P, Norton W, Chakravarti D, Coarfa C, Su X, Sandur SK, Ramirez MS, Lee J, Kingsley CV, Sananikone EF, Rajapakshe K, Naff K, Parker-Thornburg J, Bankson JA, et al. IAPP-driven metabolic reprogramming induces regression of p53-deficient tumours in vivo. Nature. 517: 626-30. PMID 25409149 DOI: 10.1038/nature13910  0.8
2015 Bliss-Moreau M, Coarfa C, Gunaratne PH, Guitart J, Krett NL, Rosen ST. Identification of p38β as a therapeutic target for the treatment of Sézary syndrome. The Journal of Investigative Dermatology. 135: 599-608. PMID 25148579 DOI: 10.1038/jid.2014.367  0.8
2015 Kannan K, Kordestani GK, Galagoda A, Coarfa C, Yen L. Aberrant MUC1-TRIM46-KRTCAP2 Chimeric RNAs in High-grade serous ovarian carcinoma Cancers. 7: 2083-2093. DOI: 10.3390/cancers7040878  0.8
2014 Menon DU, Coarfa C, Xiao W, Gunaratne PH, Meller VH. siRNAs from an X-linked satellite repeat promote X-chromosome recognition in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 111: 16460-5. PMID 25368194 DOI: 10.1073/pnas.1410534111  0.8
2014 Geng C, Rajapakshe K, Shah SS, Shou J, Eedunuri VK, Foley C, Fiskus W, Rajendran M, Chew SA, Zimmermann M, Bond R, He B, Coarfa C, Mitsiades N. Androgen receptor is the key transcriptional mediator of the tumor suppressor SPOP in prostate cancer. Cancer Research. 74: 5631-43. PMID 25274033 DOI: 10.1158/0008-5472.CAN-14-0476  0.8
2014 Coarfa C, Pichot C, Jackson A, Tandon A, Amin V, Raghuraman S, Paithankar S, Lee AV, McGuire SE, Milosavljevic A. Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools. Bmc Bioinformatics. 15: S2. PMID 25080362 DOI: 10.1186/1471-2105-15-S7-S2  0.8
2014 Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, et al. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proceedings of the National Academy of Sciences of the United States of America. 111: 11467-72. PMID 25049417 DOI: 10.1073/pnas.1317751111  0.8
2014 Ma J, Coarfa C, Qin X, Bonnen PE, Milosavljevic A, Versalovic J, Aagaard K. mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities. Bmc Genomics. 15: 257. PMID 24694284 DOI: 10.1186/1471-2164-15-257  0.8
2014 Kannan K, Coarfa C, Rajapakshe K, Hawkins SM, Matzuk MM, Milosavljevic A, Yen L. CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. Plos Genetics. 10: e1004216. PMID 24675677 DOI: 10.1371/journal.pgen.1004216  0.8
2014 Chakravarti D, Su X, Cho MS, Bui NH, Coarfa C, Venkatanarayan A, Benham AL, Flores González RE, Alana J, Xiao W, Leung ML, Vin H, Chan IL, Aquino A, Müller N, et al. Induced multipotency in adult keratinocytes through down-regulation of ΔNp63 or DGCR8. Proceedings of the National Academy of Sciences of the United States of America. 111: E572-81. PMID 24449888 DOI: 10.1073/pnas.1319743111  0.8
2014 Kunde-Ramamoorthy G, Coarfa C, Laritsky E, Kessler NJ, Harris RA, Xu M, Chen R, Shen L, Milosavljevic A, Waterland RA. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. Nucleic Acids Research. 42: e43. PMID 24391148 DOI: 10.1093/nar/gkt1325  0.8
2013 Hamilton MP, Rajapakshe K, Hartig SM, Reva B, McLellan MD, Kandoth C, Ding L, Zack TI, Gunaratne PH, Wheeler DA, Coarfa C, McGuire SE. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nature Communications. 4: 2730. PMID 24220575 DOI: 10.1038/ncomms3730  0.8
2013 Tennakoon JB, Wang H, Coarfa C, Cooney AJ, Gunaratne PH. Chromatin changes in dicer-deficient mouse embryonic stem cells in response to retinoic acid induced differentiation. Plos One. 8: e74556. PMID 24040281 DOI: 10.1371/journal.pone.0074556  0.8
2013 Seo E, Basu-Roy U, Gunaratne PH, Coarfa C, Lim DS, Basilico C, Mansukhani A. SOX2 regulates YAP1 to maintain stemness and determine cell fate in the osteo-adipo lineage. Cell Reports. 3: 2075-87. PMID 23791527 DOI: 10.1016/j.celrep.2013.05.029  0.8
2013 Hsu DM, Agarwal S, Benham A, Coarfa C, Trahan DN, Chen Z, Stowers PN, Courtney AN, Lakoma A, Barbieri E, Metelitsa LS, Gunaratne P, Kim ES, Shohet JM. G-CSF receptor positive neuroblastoma subpopulations are enriched in chemotherapy-resistant or relapsed tumors and are highly tumorigenic. Cancer Research. 73: 4134-46. PMID 23687340 DOI: 10.1158/0008-5472.CAN-12-4056  0.8
2013 Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. Plos Genetics. 9: e1003333. PMID 23468659 DOI: 10.1371/journal.pgen.1003333  0.8
2013 Yu F, Coarfa C. Sequence alignment, analysis, and bioinformatic pipelines Next Generation Sequencing: Translation to Clinical Diagnostics. 59-77. DOI: 10.1007/978-1-4614-7001-4_4  0.8
2012 Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A. The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. Bmc Bioinformatics. 13: S11. PMID 23320832 DOI: 10.1186/1471-2105-13-S13-S11  0.8
2012 Plé H, Landry P, Benham A, Coarfa C, Gunaratne PH, Provost P. The repertoire and features of human platelet microRNAs. Plos One. 7: e50746. PMID 23226537 DOI: 10.1371/journal.pone.0050746  0.8
2012 Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Jakkamsetti A, Pham P, Coarfa C, Milosavljevic A, Yu F. Atlas2 Cloud: a framework for personal genome analysis in the cloud Bmc Genomics. 13. PMID 23134663  0.8
2012 Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. Plos One. 7: e36466. PMID 22719832 DOI: 10.1371/journal.pone.0036466  0.8
2012 Davies MN, Volta M, Pidsley R, Lunnon K, Dixit A, Lovestone S, Coarfa C, Harris RA, Milosavljevic A, Troakes C, Al-Sarraj S, Dobson R, Schalkwyk LC, Mill J. Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biology. 13: R43. PMID 22703893 DOI: 10.1186/gb-2012-13-6-r43  0.8
2012 Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. Plos Genetics. 8: e1002692. PMID 22615578 DOI: 10.1371/journal.pgen.1002692  0.8
2012 Challis D, Yu J, Evani US, Jackson AR, Paithankar S, Coarfa C, Milosavljevic A, Gibbs RA, Yu F. An integrative variant analysis suite for whole exome next-generation sequencing data Bmc Bioinformatics. 13. PMID 22239737 DOI: 10.1186/1471-2105-13-8  0.8
2012 Gunaratne PH, Coarfa C, Soibam B, Tandon A. miRNA data analysis: next-gen sequencing. Methods in Molecular Biology (Clifton, N.J.). 822: 273-88. PMID 22144206 DOI: 10.1007/978-1-61779-427-8_19  0.8
2011 Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 141: 1782-91. PMID 21741921 DOI: 10.1053/j.gastro.2011.06.072  0.8
2011 Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S, Clayton DF. Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. Bmc Genomics. 12: 277. PMID 21627805 DOI: 10.1186/1471-2164-12-277  0.8
2011 Shohet JM, Ghosh R, Coarfa C, Ludwig A, Benham AL, Chen Z, Patterson DM, Barbieri E, Mestdagh P, Sikorski DN, Milosavljevic A, Kim ES, Gunaratne PH. A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma. Cancer Research. 71: 3841-51. PMID 21498633 DOI: 10.1158/0008-5472.CAN-10-4391  0.8
2011 Miller CA, Hampton O, Coarfa C, Milosavljevic A. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. Plos One. 6: e16327. PMID 21305028 DOI: 10.1371/journal.pone.0016327  0.8
2011 Evani US, Challis D, Yu J, Jackson AR, Paithankar S, Bainbridge MN, Coarfa C, Milosavljevic A, Yu F. Enabling Atlas2 personal genome analysis on the cloud Proceedings - Ieee International Workshop On Genomic Signal Processing and Statistics. 117-120.  0.8
2010 Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM. Analysis of microRNA expression in the prepubertal testis. Plos One. 5: e15317. PMID 21206922 DOI: 10.1371/journal.pone.0015317  0.8
2010 Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. Bmc Bioinformatics. 11: 572. PMID 21092284 DOI: 10.1186/1471-2105-11-572  0.8
2010 Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/nbt.1682  0.8
2010 Polikepahad S, Knight JM, Naghavi AO, Oplt T, Creighton CJ, Shaw C, Benham AL, Kim J, Soibam B, Harris RA, Coarfa C, Zariff A, Milosavljevic A, Batts LM, Kheradmand F, et al. Proinflammatory role for let-7 microRNAS in experimental asthma. The Journal of Biological Chemistry. 285: 30139-49. PMID 20630862 DOI: 10.1074/jbc.M110.145698  0.8
2010 Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Molecular Human Reproduction. 16: 463-71. PMID 20215419 DOI: 10.1093/molehr/gaq017  0.8
2010 Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Research. 20: 273-80. PMID 20019143 DOI: 10.1101/gr.096388.109  0.8
2009 Ma L, Buchold GM, Greenbaum MP, Roy A, Burns KH, Zhu H, Han DY, Harris RA, Coarfa C, Gunaratne PH, Yan W, Matzuk MM. GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. Plos Genetics. 5: e1000635. PMID 19730684 DOI: 10.1371/journal.pgen.1000635  0.8
2009 Hampton OA, Den Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Research. 19: 167-77. PMID 19056696 DOI: 10.1101/gr.080259.108  0.8
2008 Coarfa C, Milosavljevic A. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 102-13. PMID 18229679  0.8
2007 Coarfa C, Mellor-Crummey J, Froyd N, Dotsenko Y. Scalability analysis of SPMD codes using expectations Proceedings of the International Conference On Supercomputing. 13-22. DOI: 10.1145/1274971.1274976  0.8
2006 Dotsenko Y, Coarfa C, Nakhleh L, Mellor-Crummey J, Roshan U. PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. International Journal of Bioinformatics Research and Applications. 2: 407-19. PMID 18048181 DOI: 10.1504/IJBRA.2006.011039  0.8
2006 Coarfa C, Dotsenko Y, Mellor-Crummey J. Experiences with Sweep3D implementations in Co-array Fortran Journal of Supercomputing. 36: 101-121. DOI: 10.1007/s11227-006-7952-7  0.8
2006 Coarfa C, Druschel P, Wallach DS. Performance analysis of TLS web servers Acm Transactions On Computer Systems. 24: 39-69.  0.8
2005 Coarfa C, Dotsenko Y, Mellor-Crummey J, Cantonnet F, Ei-Ghazawi T, Mohanti A, Yao Y, Chavarría-Miranda D. An evaluation of global address space languages: Co-array fortran and Unified Parallel C Proceedings of the Acm Sigplan Symposium On Principles and Practice of Parallel Programming, Ppopp. 36-47. DOI: 10.1145/1065944.1065950  0.8
2005 Coarfa C, Dotsenko Y, Mellor-Crummey J, Nakhleh L, Roshan U. PRec-I-DCM3: A parallel framework for fast and accurate large scale phylogeny reconstruction Proceedings of the International Conference On Parallel and Distributed Systems - Icpads. 2: 346-350. DOI: 10.1109/ICPADS.2005.240  0.8
2005 Dotsenko Y, Coarfa C, Mellor-Crummey J, Chavarría-Miranda D. Experiences with Co-array Fortran on hardware shared memory platforms Lecture Notes in Computer Science. 3602: 332-347.  0.8
2004 Dotsenko Y, Coarfa C, Mellor-Crummey J. A multi-platform Co-array Fortran compiler Parallel Architectures and Compilation Techniques - Conference Proceedings, Pact. 29-40. DOI: 10.1109/PACT.2004.1342539  0.8
2004 Coarfa C, Dotsenko Y, Eckhardt J, Mellor-Crummey J. Co-array fortran performance and potential: An NPB experimental study Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2958: 177-193.  0.8
2003 Coarfa C, Demopoulos DD, Aguirre ASM, Subramanian D, Vardi MY. Random 3-SAT: The Plot Thickens Constraints. 8: 243-261. DOI: 10.1023/A:1025671026963  0.8
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