Search Publications

2014 Publications

Khiabanian H, Carpenter Z, Kugelman J, Chan J, Trifonov V, Nagle E, Warren T, Iversen P, Bavari S, Palacios G et al.  2014.  Viral diversity and clonal evolution from unphased genomic data. BMC Genomics. 15(Suppl 6):S17. Go to Pubmed
Abate F, Todaro M, van der Krogt J-A, Boi M, Landra I, Machiorlatti R, Tabbò F, Messana K, Abele C, Barreca A et al.  2014.  A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation. Leukemia. Go to Pubmed
Chang J, Gilman SR, Chiang AH, Sanders SJ, Vitkup D.  2014.  Genotype to phenotype relationships in autism spectrum disorders. Nat Neurosci. Go to Pubmed
Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B.  2014.  The Cyni framework for network inference in Cytoscape. Bioinformatics. Go to Pubmed
Wang J, Khiabanian H, Rossi D, Fabbri G, Gattei V, Forconi F, Laurenti L, Marasca R, Del Poeta G, Foá R et al.  2014.  Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia. Elife. 3 Go to Pubmed
Rampal R, Alkalin A, Madzo J, Vasanthakumar A, Pronier E, Patel J, Li Y, Ahn J, Abdel-Wahab O, Shih A et al.  2014.  DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia. Cell Rep. Go to Pubmed
Popadin KY, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, Nikolaev SI, Lukowski SW, Bazykin GA, Seplyarskiy VB, Ioannidis P et al.  2014.  Gene age predicts the strength of purifying selection acting on gene expression variation in humans. Am J Hum Genet. 95(6):660-74. Go to Pubmed
Buil A, Brown AAnand, Lappalainen T, Viñuela A, Davies MN, Zheng H-F, J Richards B, Glass D, Small KS, Durbin R et al.  2014.  Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. Nat Genet. Go to Pubmed
Sanchez-Garcia F, Villagrasa P, Matsui J, Kotliar D, Castro V, Akavia U-D, Chen B-J, Saucedo-Cuevas L, Barrueco RRodriguez, Llobet-Navas D et al.  2014.  Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers. Cell. Go to Pubmed
Vilar S, Uriarte E, Santana L, Friedman C, Tatonetti NP.  2014.  State of the Art and Development of a Drug-Drug Interaction Large Scale Predictor Based on 3D Pharmacophoric Similarity. Curr Drug Metab. 15(5):490-501. Go to Pubmed
Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H, Xiao G, Li Y, Allen J, Zhong R et al.  2014.  A community computational challenge to predict the activity of pairs of compounds. Nat Biotechnol. Go to Pubmed
Califano A.  2014.  Predicting protein networks in cancer. Nat Genet. 46(12):1252-3. Go to Pubmed
Thome JJC, Yudanin N, Ohmura Y, Kubota M, Grinshpun B, Sathaliyawala T, Kato T, Lerner H, Shen Y, Farber DL.  2014.  Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life. Cell. 159(4):814-28. Go to Pubmed
Gao Z, Przeworski M, Sella G.  2014.  Footprints of ancient balanced polymorphisms in genetic variation data from closely related species. Evolution. Go to Pubmed
Angeli JPedro Frie, Schneider M, Proneth B, Tyurina YY, Tyurin VA, Hammond VJ, Herbach N, Aichler M, Walch A, Eggenhofer E et al.  2014.  Inactivation of the ferroptosis regulator Gpx4 triggers acute renal failure in mice. Nat Cell Biol. 16(12):1180-91. Go to Pubmed
Munck C, Gumpert HK, Wallin AINilsson, Wang HH, Sommer MOA.  2014.  Prediction of resistance development against drug combinations by collateral responses to component drugs. Sci Transl Med. 6(262):262ra156. Go to Pubmed
Linkermann A, Skouta R, Himmerkus N, Mulay SR, Dewitz C, De Zen F, Prokai A, Zuchtriegel G, Krombach F, Welz P-S et al.  2014.  Synchronized renal tubular cell death involves ferroptosis. Proc Natl Acad Sci U S A. Go to Pubmed
Chiu H-S, Llobet-Navas D, Yang X, Chung W-J, Ambesi-Impiombato A, Iyer A, Kim HRyan, Seviour EG, Luo Z, Sehgal V et al.  2014.  Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Res. Go to Pubmed
Mingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C.  2014.  Single-cell mass cytometry of TCR signaling: Amplification of small initial differences results in low ERK activation in NOD mice. Proc Natl Acad Sci U S A. Go to Pubmed
Mendes CS, Rajendren SV, Bartos I, Márka S, Mann RS.  2014.  Kinematic Responses to Changes in Walking Orientation and Gravitational Load in Drosophila melanogaster. PLoS One. 9(10):e109204. Go to Pubmed
Parfitt D-E, Shen MM.  2014.  From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis. Philos Trans R Soc Lond B Biol Sci. 369(1657) Go to Pubmed
Yang K-A, Barbu M, Halim M, Pallavi P, Kim B, Kolpashchikov DM, Pecic S, Taylor S, Worgall TS, Stojanovic MN.  2014.  Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors. Nat Chem. 6(11):1003-8. Go to Pubmed
Krishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP.  2014.  Conditional density-based analysis of T cell signaling in single-cell data. Science. Go to Pubmed
Kushwaha R, Jagadish N, Kustagi M, Tomishima MJ, Mendiratta G, Bansal M, Kim HR, Sumazin P, Alvarez MJ, Lefebvre C et al.  2014.  Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells. Go to Pubmed
Linkermann A, Stockwell BR, Krautwald S, Anders H-J.  2014.  Regulated cell death and inflammation: an auto-amplification loop causes organ failure. Nat Rev Immunol. Go to Pubmed
Machado ACarolina D, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R.  2014.  Evolving insights on how cytosine methylation affects protein-DNA binding. Brief Funct Genomics. Go to Pubmed
Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G.  2014.  Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biol. 15(9):462. Go to Pubmed
Giorgi FM, Lopez G, Woo JH, Bisikirska B, Califano A, Bansal M.  2014.  Inferring protein modulation from gene expression data using conditional mutual information. PLoS One. 9(10):e109569. Go to Pubmed
Oren Y, Smith MB, Johns NI, Zeevi MKaplan, Biran D, Ron EZ, Corander J, Wang HH, Alm EJ, Pupko T.  2014.  Transfer of noncoding DNA drives regulatory rewiring in bacteria. Proc Natl Acad Sci U S A. Go to Pubmed
Chen JC, Alvarez MJ, Talos F, Dhruv H, Rieckhof GE, Iyer A, Diefes KL, Aldape K, Berens M, Shen MM et al.  2014.  Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks. Cell. 159(2):402-14. Go to Pubmed
Lee A, Khiabanian H, Kugelman J, Elliott O, Nagle E, Yu G-Y, Warren T, Palacios G, Rabadan R.  2014.  Transcriptome reconstruction and annotation of cynomolgus and African green monkey. BMC Genomics. 15(1):846. Go to Pubmed
Batra R, Charizanis K, Manchanda M, Mohan A, Li M, Finn DJ, Goodwin M, Zhang C, Sobczak K, Thornton CA et al.  2014.  Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease. Mol Cell. Go to Pubmed
Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR et al.  2014.  Unraveling the mechanism of cell death induced by chemical fibrils. Nat Chem Biol. Go to Pubmed
Hoffman KB, Demakas AR, Dimbil M, Tatonetti NP, Erdman CB.  2014.  Stimulated Reporting: The Impact of US Food and Drug Administration-Issued Alerts on the Adverse Event Reporting System (FAERS). Drug Saf. Go to Pubmed
Vendome J, Felsovalyi K, Song H, Yang Z, Jin X, Brasch J, Harrison OJ, Ahlsen G, Bahna F, Kaczynska A et al.  2014.  Structural and energetic determinants of adhesive binding specificity in type I cadherins. Proc Natl Acad Sci U S A. Go to Pubmed
Vilar S, Ryan PB, Madigan D, Stang PE, Schuemie MJ, Friedman C, Tatonetti NP, Hripcsak G.  2014.  Similarity-based modeling applied to signal detection in pharmacovigilance. CPT Pharmacometrics Syst Pharmacol. 3:e137. Go to Pubmed
Yang T-HOu, Cheng W-Y, Zheng T, Maurer MA, Anastassiou D.  2014.  Breast Cancer Prognostic Biomarker Using Attractor Metagenes and the FGD3-SUSD3 Metagene. Cancer Epidemiol Biomarkers Prev. Go to Pubmed
Chua CWai, Shibata M, Lei M, Toivanen R, Barlow LJ, Bergren SK, Badani KK, McKiernan JM, Benson MC, Hibshoosh H et al.  2014.  Single luminal epithelial progenitors can generate prostate organoids in culture. Nat Cell Biol. Go to Pubmed
Panousis NI, Gutierrez-Arcelus M, Dermitzakis ET, Lappalainen T.  2014.  Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies. Genome Biol. 15(9):467. Go to Pubmed
Kreimer A, Pe'er I.  2014.  Co-regulated Transcripts Associated to Cooperating eSNPs Define Bi-fan Motifs in Human Gene Networks. PLoS Genet. 10(9):e1004587. Go to Pubmed
Glessner J, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika EJ, Vardarajan B, Italia MJ, Leipzig J et al.  2014.  Increased Frequency of De Novo Copy Number Variations in Congenital Heart Disease by Integrative Analysis of SNP Array and Exome Sequence Data. Circ Res. Go to Pubmed
Carmi S, Hui KY, Kochav E, Liu X, Xue J, Grady F, Guha S, Upadhyay K, Ben-Avraham D, Mukherjee S et al.  2014.  Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins. Nat Commun. 5:4835. Go to Pubmed
Herranz D, Ambesi-Impiombato A, Palomero T, Schnell SA, Belver L, Wendorff AA, Xu L, Castillo-Martin M, Llobet-Navas D, Cordon-Cardo C et al.  2014.  A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia. Nat Med. 20(10):1130-7. Go to Pubmed
Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O'Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N et al.  2014.  An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex. J Neurosci. 34(36):11929-47. Go to Pubmed
Abate F, Zairis S, Ficarra E, Acquaviva A, Wiggins CH, Frattini V, Lasorella A, Iavarone A, Inghirami G, Rabadan R.  2014.  Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. BMC Syst Biol. 8(1):97. Go to Pubmed
Wang ZA, Toivanen R, Bergren SK, Chambon P, Shen MM.  2014.  Luminal Cells Are Favored as the Cell of Origin for Prostate Cancer. Cell Rep. Go to Pubmed
Thu CAye, Chen WV, Rubinstein R, Chevee M, Wolcott HN, Felsovalyi KO, Tapia JCarlos, Shapiro L, Honig B, Maniatis T.  2014.  Single-Cell Identity Generated by Combinatorial Homophilic Interactions between α, β, and γ Protocadherins. Cell. 158(5):1045-59. Go to Pubmed
van Arensbergen J, van Steensel B, Bussemaker HJ.  2014.  In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol. Go to Pubmed
Agelopoulos M, McKay DJ, Mann RS.  2014.  cgChIP: A Cell Type- and Gene-Specific Method for Chromatin Analysis. Methods Mol Biol. 1196:291-306. Go to Pubmed
Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ.  2014.  SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes. Methods Mol Biol. 1196:255-78. Go to Pubmed
Carr A, Pe'er D.  2014.  Broadening horizons: holistic viewpoints from the Biology of Genomes. Genome Biol. 15(7):416. Go to Pubmed
Greger L, Su J, Rung J, Ferreira PG, Lappalainen T, Dermitzakis ET, Brazma A.  2014.  Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants. PLoS One. 9(8):e104567. Go to Pubmed
Gonzalez C, Sims JS, Hornstein N, Mela A, Garcia F, Lei L, Gass DA, Amendolara B, Bruce JN, Canoll P et al.  2014.  Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors. J Neurosci. 34(33):10924-36. Go to Pubmed
Martin AR, Costa HA, Lappalainen T, Henn BM, Kidd JM, Yee M-C, Grubert F, Cann HM, Snyder M, Montgomery SB et al.  2014.  Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture. PLoS Genet. 10(8):e1004549. Go to Pubmed
Johnson S, van de Meent J-W, Phillips R, Wiggins CH, Lindén M.  2014.  Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion. Nucleic Acids Res. 42(16):10265-77. Go to Pubmed
Pefanis E, Wang J, Rothschild G, Lim J, Chao J, Rabadan R, Economides AN, Basu U.  2014.  Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature. Go to Pubmed
Gill BJ, Pisapia DJ, Malone HR, Goldstein H, Lei L, Sonabend A, Yun J, Samanamud J, Sims JS, Banu M et al.  2014.  MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma. Proc Natl Acad Sci U S A. 111(34):12550-5. Go to Pubmed
Wang J, Abate-Shen C.  2014.  Analyses of tumor-suppressor genes in germline mouse models of cancer. Cold Spring Harb Protoc. 2014(8):pdb.top069773. Go to Pubmed
Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T, Rehnström K, Esko T, Mägi R, Inouye M, Lappalainen T et al.  2014.  Distribution and medical impact of loss-of-function variants in the Finnish founder population. PLoS Genet. 10(7):e1004494. Go to Pubmed
Wolpaw AJ, Stockwell BR.  2014.  Multidimensional profiling in the investigation of small-molecule-induced cell death. Methods Enzymol. 545:265-302. Go to Pubmed
Matos MJoão, Vilar S, Kachler S, Fonseca A, Santana L, Uriarte E, Borges F, Tatonetti NP, Klotz K-N.  2014.  Insight into the Interactions between Novel Coumarin Derivatives and Human A3 Adenosine Receptors. ChemMedChem. Go to Pubmed
Goodarzi H, Zhang S, Buss CG, Fish L, Tavazoie S, Tavazoie SF.  2014.  Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins. Nature. Go to Pubmed
Overby CLynnette, Hripcsak G, Shen Y.  2014.  Estimating heritability of drug-induced liver injury from common variants and implications for future study designs. Sci Rep. 4:5762. Go to Pubmed
Woods DP, Ream TS, Minevich G, Hobert O, Amasino RM.  2014.  PHYTOCHROME C Is an Essential Light Receptor for Photoperiodic Flowering in the Temperate Grass, Brachypodium distachyon. Genetics. 198(1):397-408. Go to Pubmed
Oh H, Slattery M, Ma L, White KP, Mann RS, Irvine KD.  2014.  Yorkie Promotes Transcription by Recruiting a Histone Methyltransferase Complex. Cell Rep. Go to Pubmed
Segurel L, Wyman MJ, Przeworski M.  2014.  Determinants of Mutation Rate Variation in the Human Germline. Annu Rev Genomics Hum Genet. Go to Pubmed
Higgins CA, Petukhova L, Harel S, Ho YY, Drill E, Shapiro L, Wajid M, Christiano AM.  2014.  FGF5 is a crucial regulator of hair length in humans. Proc Natl Acad Sci U S A. Go to Pubmed
Boyce RD, Ryan PB, G Norén N, Schuemie MJ, Reich C, Duke J, Tatonetti NP, Trifirò G, Harpaz R, J Overhage M et al.  2014.  Bridging Islands of Information to Establish an Integrated Knowledge Base of Drugs and Health Outcomes of Interest. Drug Saf. Go to Pubmed
Repunte-Canonigo V, Lefebvre C, George O, Kawamura T, Morales M, Koob GF, Califano A, Masliah E, Sanna PPaolo.  2014.  Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats. Mol Neurodegener. 9:26. Go to Pubmed
Ghosh HS, Ceribelli M, Matos I, Lazarovici A, Bussemaker HJ, Lasorella A, Hiebert SW, Liu K, Staudt LM, Reizis B.  2014.  ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2. J Exp Med. Go to Pubmed
The Genome of the Netherlands Consortium.  2014.  Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet. Go to Pubmed
Ward LD, Wang J, Bussemaker HJ.  2014.  Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. BMC Genomics. 15(1):494. Go to Pubmed
Mukherjee S, Guha S, Ikeda M, Iwata N, Malhotra A, Pe'er I, Darvasi A, Lencz T.  2014.  Excess of homozygosity in the major histocompatibility complex in schizophrenia. Hum Mol Genet. Go to Pubmed
Fazlollahi M, Lee E, Muroff I, Lu X-J, Gomez-Alcala P, Causton HC, Bussemaker HJ.  2014.  Harnessing Natural Sequence Variation to Dissect Post-Transcriptional Regulatory Networks in Yeast. G3 (Bethesda). Go to Pubmed
Sciara G, Clarke OB, Tomasek D, Kloss B, Tabuso S, Byfield R, Cohn R, Banerjee S, Rajashankar KR, Slavkovic V et al.  2014.  Structural basis for catalysis in a CDP-alcohol phosphotransferase. Nat Commun. 5:4068. Go to Pubmed
Shan Y, Gnanasambandan K, Ungureanu D, Kim ET, Hammarén H, Yamashita K, Silvennoinen O, Shaw DE, Hubbard SR.  2014.  Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase. Nat Struct Mol Biol. Go to Pubmed
Petrey D, Honig B.  2014.  Structural bioinformatics of the interactome. Annu Rev Biophys. 43:193-210. Go to Pubmed
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-Ud-Din M, Hintsanen P, Khan SA et al.  2014.  A community effort to assess and improve drug sensitivity prediction algorithms. Nat Biotechnol. Go to Pubmed
Stojanovic MN, Stefanovic D, Rudchenko S.  2014.  Exercises in Molecular Computing. Acc Chem Res. Go to Pubmed
Iliadis A, Anastassiou D, Wang X.  2014.  A sequential Monte Carlo framework for haplotype inference in CNV/SNP genotype data. EURASIP J Bioinform Syst Biol. 2014(1):7. Go to Pubmed
Bonde MT, Kosuri S, Genee HJ, Sarup-Lytzen K, Church GM, Sommer MOA, Wang HH.  2014.  Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides. ACS Synth Biol. Go to Pubmed
Dixon SJ, Patel DN, Welsch M, Skouta R, Lee ED, Hayano M, Thomas AG, Gleason CE, Tatonetti N, Slusher BS et al.  2014.  Pharmacological inhibition of cystine-glutamate exchange induces endoplasmic reticulum stress and ferroptosis. Elife. :e02523. Go to Pubmed
Vacic V, Ozelius LJ, Clark LN, Bar-Shira A, Gana-Weisz M, Gurevich T, Gusev A, Kedmi M, Kenny EE, Liu X et al.  2014.  Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes. Hum Mol Genet. Go to Pubmed
Yaung SJ, Church GM, Wang HH.  2014.  Recent progress in engineering human-associated microbiomes. Methods Mol Biol. 1151:3-25. Go to Pubmed
Aydin IT, Melamed R, Adams SJ, Castillo-Martin M, Demir A, Bryk D, Brunner G, Cordon-Cardo C, Osman I, Rabadan R et al.  2014.  FBXW7 Mutations in Melanoma and a New Therapeutic Paradigm. J Natl Cancer Inst. 106(6) Go to Pubmed
Bonde MT, Klausen MS, Anderson MV, Wallin AIN, Wang HH, Sommer MOA.  2014.  MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res. Go to Pubmed
Shetzer Y, Kagan S, Koifman G, Sarig R, Kogan-Sakin I, Charni M, Kaufman T, Zapatka M, Molchadsky A, Rivlin N et al.  2014.  The onset of p53 loss of heterozygosity is differentially induced in various stem cell types and may involve the loss of either allele. Cell Death Differ. Go to Pubmed
Aytes A, Mitrofanova A, Lefebvre C, Alvarez MJ, Castillo-Martin M, Zheng T, Eastham JA, Gopalan A, Pienta KJ, Shen MM et al.  2014.  Cross-Species Regulatory Network Analysis Identifies a Synergistic Interaction between FOXM1 and CENPF that Drives Prostate Cancer Malignancy. Cancer Cell. 25(5):638-51. Go to Pubmed
Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti N, Dudley JT, Butte AJ.  2014.  Disease risk factors identified through shared genetic architecture and electronic medical records. Sci Transl Med. 6(234):234ra57. Go to Pubmed
Califano A, Kellis M, Stolovitzky G.  2014.  RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue. J Comput Biol. 21(5):371-2. Go to Pubmed
Delogu G, Serra S, Quezada E, Uriarte E, Vilar S, Tatonetti N, Viña D.  2014.  Monoamine Oxidase (MAO) Inhibitory Activity: 3-Phenylcoumarins versus 4-Hydroxy-3-phenylcoumarins. ChemMedChem. Go to Pubmed
Mee MT, Collins JJ, Church GM, Wang HH.  2014.  Syntrophic exchange in synthetic microbial communities. Proc Natl Acad Sci U S A. Go to Pubmed
Brown AAnand, Buil A, Viñuela A, Lappalainen T, Zheng H-F, J Richards B, Small KS, Spector TD, Dermitzakis ET, Durbin R.  2014.  Genetic interactions affecting human gene expression identified by variance association mapping. Elife. 3:e01381. Go to Pubmed
Backenroth D, Homsy J, Murillo LR, Glessner J, Lin E, Brueckner M, Lifton R, Goldmuntz E, Chung WK, Shen Y.  2014.  CANOES: detecting rare copy number variants from whole exome sequencing data. Nucleic Acids Res. Go to Pubmed
Bendall SC, Davis KL, Amir E-ADavid, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D.  2014.  Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell. 157(3):714-25. Go to Pubmed
Miller CP, Thorpe JD, Kortum AN, Coy CM, Cheng W-Y, Yang T-HOu, Anastassiou D, J Beatty D, Urban ND, C Blau A.  2014.  JAK2 expression is associated with tumor-infiltrating lymphocytes and improved breast cancer outcomes: implications for evaluating JAK2 inhibitors. Cancer Immunol Res. 2(4):301-6. Go to Pubmed
Matos MJoão, Vilar S, García-Morales V, Tatonetti N, Uriarte E, Santana L, Viña D.  2014.  Insight into the Functional and Structural Properties of 3-Arylcoumarin as an Interesting Scaffold in Monoamine Oxidase B Inhibition. ChemMedChem. Go to Pubmed
Lee E, de Ridder J, Kool J, Wessels LFA, Bussemaker H.  2014.  Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis. Proc Natl Acad Sci U S A. 111(15):5747-52. Go to Pubmed
Mann RS.  2014.  Neuroscience. The Michael Jackson fly. Science. 344(6179):48-9. Go to Pubmed
Kermany AR, Segurel L, Oliver TR, Przeworski M.  2014.  TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception. Bioinformatics. Go to Pubmed
Oikonomou P, Goodarzi H, Tavazoie S.  2014.  Systematic Identification of Regulatory Elements in Conserved 3' UTRs of Human Transcripts. Cell Rep. Go to Pubmed
van de Meent J-W, Bronson JE, Wiggins C, Gonzalez RL.  2014.  Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule FRET Experiments. Biophys J. 106(6):1327-37. Go to Pubmed
Hoffman KB, Dimbil M, Erdman CB, Tatonetti N, Overstreet BM.  2014.  The Weber Effect and the United States Food and Drug Administration's Adverse Event Reporting System (FAERS): Analysis of Sixty-Two Drugs Approved from 2006 to 2010. Drug Saf. Go to Pubmed
Sonabend AM, Carminucci A, Amendolara B, Bansal M, Leung R, Lei L, Realubit R, Li H, Karan C, Yun J et al.  2014.  Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma. Neuro Oncol. Go to Pubmed
Llobet-Navas D, Rodriguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martin M, Putcha P, Marshall N et al.  2014.  The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes Dev. Go to Pubmed
Matos MJoão, Janeiro P, Franco RMaría Gon, Vilar S, Tatonetti N, Santana L, Uriarte E, Borges F, Fontenla JAngel, Viña D.  2014.  Synthesis, pharmacological study and docking calculations of new benzo[f]coumarin derivatives as dual inhibitors of enzymatic systems involved in neurodegenerative diseases. Future Med Chem. 6(4):371-83. Go to Pubmed
Sundling C, Zhang Z, Phad GE, Sheng Z, Wang Y, Mascola JR, Li Y, Wyatt RT, Shapiro L, Hedestam GBKarlsson.  2014.  Single-Cell and Deep Sequencing of IgG-Switched Macaque B Cells Reveal a Diverse Ig Repertoire following Immunization. J Immunol. Go to Pubmed
Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ et al.  2014.  HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism. Cell Rep. Go to Pubmed
Skouta R, Dixon SJ, Wang J, Dunn DE, Orman M, Shimada K, Rosenberg P, Lo D, Weinberg J, Linkermann A et al.  2014.  Ferrostatins inhibit oxidative lipid damage and cell death in diverse disease models. J Am Chem Soc. Go to Pubmed
Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes A, Marinelli M, Fabbri G et al.  2014.  Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness. Blood. Go to Pubmed
Song F, Del Pozo CHurtado, Rosario R, Zou YShan, Ananthakrishnan R, Xu X, Patel PR, Benoit VM, Yan SFang, Li H et al.  2014.  RAGE Regulates the Metabolic and Inflammatory Response to High Fat Feeding in Mice. Diabetes. Go to Pubmed
Karczewski KJ, Snyder M, Altman R, Tatonetti N.  2014.  Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association. PLoS Genet. 10(2):e1004122. Go to Pubmed
Rossi D, Khiabanian H, Spina V, Ciardullo C, Bruscaggin A, Famà R, Rasi S, Monti S, Deambrogi C, De Paoli L et al.  2014.  Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia. Blood. Go to Pubmed
Kurki MI, Gaál EIlona, Kettunen J, Lappalainen T, Menelaou A, Anttila V, Hof FNG van 't, Fraunberg Mvon Und Zu, Helisalmi S, Hiltunen M et al.  2014.  High risk population isolate reveals low frequency variants predisposing to intracranial aneurysms. PLoS Genet. 10(1):e1004134. Go to Pubmed
Piana S, Klepeis JL, Shaw DE.  2014.  Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Curr Opin Struct Biol. 24C:98-105. Go to Pubmed
Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray M-A, Gopal S, Theisen MA, Bilodeau S, Thiru P et al.  2014.  ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State. Cell Rep. Go to Pubmed
Yang WSeok, Sriramaratnam R, Welsch ME, Shimada K, Skouta R, Viswanathan VS, Cheah JH, Clemons PA, Shamji AF, Clish CB et al.  2014.  Regulation of Ferroptotic Cancer Cell Death by GPX4. Cell. 156(1-2):317-31. Go to Pubmed
Kode A, Manavalan JS, Mosialou I, Bhagat G, Rathinam CV, Luo N, Khiabanian H, Lee A, Murty VV, Friedman R et al.  2014.  Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts. Nature. Go to Pubmed
Palomero T, Couronné L, Khiabanian H, Kim M-Y, Ambesi-Impiombato A, Perez-Garcia A, Carpenter Z, Abate F, Allegretta M, J Haydu E et al.  2014.  Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat Genet. Go to Pubmed
Moore MJ, Zhang C, Gantman EConn, Mele A, Darnell JC, Darnell RB.  2014.  Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc. 9(2):263-93. Go to Pubmed
Tepper RG, Murphy CT, Bussemaker H.  2014.  DAF-16 and PQM-1: Partners in longevity. Aging (Albany NY). Go to Pubmed
Sonabend AM, Bansal M, Guarnieri P, Lei L, Amendolara B, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J et al.  2014.  The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected During Tumor Progression. Cancer Res. Go to Pubmed
Pasqualucci L, Khiabanian H, Fangazio M, Vasishtha M, Messina M, Holmes A, Ouillette P, Trifonov V, Rossi D, Tabbò F et al.  2014.  Genetics of follicular lymphoma transformation. Cell Rep. 6(1):130-40. Go to Pubmed
Yu L, Bennett JT, Wynn J, Carvill GL, Cheung YHim, Shen Y, Mychaliska GB, Azarow KS, Crombleholme TM, Chung DH et al.  2014.  Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia. J Med Genet. Go to Pubmed
Shazman S, Lee H, Socol Y, Mann RS, Honig B.  2014.  OnTheFly: a Database of Drosophila melanogaster Transcription Factors and Their Binding Sites. Nucleic Acids Res. 42(1):D167-71. Go to Pubmed
Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N et al.  2014.  Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics. 30(2):165-71. Go to Pubmed