Publications

Author ID

Herranz D, Ambesi-Impiombato A, Palomero T, Schnell SA, Belver L, Wendorff AA, Xu L, Castillo-Martin M, Llobet-Navas D, Cordon-Cardo C, Clappier E, Soulier J, Ferrando AA. 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, Deng S, Liddelow SA, Zhang C, Daneman R, Maniatis T, Barres BA, Wu JQian. 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, Sims PA. 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, Bustamante CD. 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, Dovas A, Teich AF, Sheth SA, McKhann GM, Sisti MB, Bruce JN, Sims PA, Canoll P. 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, Chan Y, Salem RM, Lek M, Flannick J, Sim X, Manning A, Ladenvall C, Bumpstead S, Hämäläinen E, Aalto K, Maksimow M, Salmi M, Blankenberg S, Ardissino D, Shah S, Horne B, McPherson R, Hovingh GK, Reilly MP, Watkins H, Goel A, Farrall M, Girelli D, Reiner AP, Stitziel NO, Kathiresan S, Gabriel S, Barrett JC, Lehtimäki T, Laakso M, Groop L, Kaprio J, Perola M, McCarthy MI, Boehnke M, Altshuler DM, Lindgren CM, Hirschhorn JN, Metspalu A, Freimer NB, Zeller T, Jalkanen S, Koskinen S, Raitakari O, Durbin R, MacArthur DG, Salomaa V, Ripatti S, Daly MJ, Palotie A. 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, Hartzema AG, Khayter M, Voss EA, Lambert CG, Huser V, Dumontier M. 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, Graziano JH, Shapiro L, Mancia F. 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, Mpindi J-P, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. 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, Stockwell BR. 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, Mejia-Santana H, Mirelman A, Raymond D, Saunders-Pullman R, Desnick RJ, Atzmon G, Burns ER, Ostrer H, Hakonarson H, Bergman, iv A, Barzilai N, Darvasi A, Peter I, Guha S, Lencz T, Giladi N, Marder K, Pe'er I, Bressman SB, Orr-Urtreger A. 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, Celebi JTok. 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, Dinowitz N, Levin S, Landan G, Goldstein I, Goldfinger N, Pe'er D, Radlwimmer B, Lichter P, Rotter V, Aloni-Grinstein R. 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, Califano A, Abate-Shen C. 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, Showers C, Rothcock R, O J, Califano A, Canoll P, Bruce JN. 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, Villagrasa P, Chan JMinhow, Sanchez-Garcia F, Pe'er D, Rabadan R, Iavarone A, Cordon-Cardo C, Califano A, López-Otín C, Ezhkova E, Silva J. 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, Krainer AR, Darnell RB, Zhang C. 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, Stockwell BR. 2014. Ferrostatins inhibit oxidative lipid damage and cell death in diverse disease models.. J Am Chem Soc. ▶ Go to Pubmed

Trifonov V, Pasqualucci L, Tiacci E, Falini B, Rabadan R. 2013. SAVI: a statistical algorithm for variant frequency identification.. BMC Syst Biol. 7 Suppl 2:S2.▶ Go to Pubmed

Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes A, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foá R. 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, Friedman R, Kim JK, Ramasamy R, Ferrante AW, Schmidt AMarie. 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

Jang ISock, Margolin A, Califano A. 2013. hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests.. Interface Focus. 3(4):20130011.▶ Go to Pubmed

Rossi D, Khiabanian H, Spina V, Ciardullo C, Bruscaggin A, Famà R, Rasi S, Monti S, Deambrogi C, De Paoli L, Wang J, Gattei V, Guarini A, Foá R, Rabadan R, Gaidano G. 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, Lehto H, Laakso A, Kivisaari R, Koivisto T, Ronkainen A, Rinne J, Kiemeney LAL, Vermeulen SH, Kaunisto MA, Eriksson JG, Aromaa A, Perola M, Lehtimäki T, Raitakari OT, Salomaa V, Gunel M, Dermitzakis ET, Ruigrok YM, Rinkel GJE, Niemelä M, Hernesniemi J, Ripatti S, de Bakker PIW, Palotie A, Jääskeläinen JE. 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, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. 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, Brown LM, Girotti AW, Cornish VW, Schreiber SL, Stockwell BR. 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, Brum A, Park D, Galili N, Mukherjee S, Teruya-Feldstein J, Raza A, Rabadan R, Berman E, Kousteni S. 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, Jiang X, Lossos IS, Nicolas C, Balbin M, Bastard C, Bhagat G, Piris MA, Campo E, Bernard OA, Rabadan R, Ferrando A. 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, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P. 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, Ponzoni M, Chadburn A, Murty VV, Bhagat G, Gaidano G, Inghirami G, Malek SN, Rabadan R, Dalla-Favera R. 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, Potoka D, Warner BW, Bucher B, Lim F-Y, Pietsch J, Stolar C, Aspelund G, Arkovitz MS, Mefford H, Chung WK. 2014. Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia.. J Med Genet. ▶ Go to Pubmed

Dixon SJ, Stockwell BR. 2013. The Role of Iron and Reactive Oxygen Secies in Cell Death.. Nat Chem Biol. 10(1):9-17.▶ Go to Pubmed

Liu L, Kim H, Casta A, Kobayashi Y, Shapiro L, Christiano AM. 2013. Hairless Is a Histone H3K9 Demethylase.. FASEB J. ▶ Go to Pubmed

Harton MD, Wingler LM, Cornish VW. 2013. Transcriptional regulation improves the throughput of three-hybrid counter selections in Saccharomyces cerevisiae.. Biotechnol J. 8(12):1485-91.▶ Go to Pubmed

Freddolino PL, Goodarzi H, Tavazoie S. 2013. Revealing the Genetic Basis of Natural Bacterial Phenotypic Divergence.. J Bacteriol. ▶ Go to Pubmed

Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva ACarolina, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo-Martin M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink J, Cordon-Cardo C, Califano A, Ferrando A. 2013. Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia.. Cancer Cell. 24(6):766-76.▶ Go to Pubmed

Plata G, Vitkup D. 2013. Genetic Robustness and Functional Evolution of Gene Duplicates.. Nucleic Acids Res. ▶ 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, Reymond A, Dermitzakis ET, Deplancke B. 2014. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.. Bioinformatics. 30(2):165-71.▶ Go to Pubmed

Lencz T, Guha S, Liu C, Rosenfeld J, Mukherjee S, Derosse P, John M, Cheng L, Zhang C, Badner JA, Ikeda M, Iwata N, Cichon S, Rietschel M, Nöthen MM, Cheng ATA, Hodgkinson C, Yuan Q, Kane JM, Lee AT, Pisanté A, Gregersen PK, Pe'er I, Malhotra AK, Goldman D, Darvasi A. 2013. Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder.. Nat Commun. 4:2739.▶ Go to Pubmed

Becker-Weimann S, Xiong G, Furuta S, Han J, Kuhn I, Akavia UDavid, Pe'er D, Bissell MJ, Xu R. 2013. NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals.. Oncotarget. ▶ Go to Pubmed

Behr ER, Ritchie MD, Tanaka T, Kääb S, Crawford DC, Nicoletti P, Floratos A, Sinner MF, Kannankeril PJ, Wilde AAM, Bezzina CR, Schulze-Bahr E, Zumhagen S, Guicheney P, Bishopric NH, Marshall V, Shakir S, Dalageorgou C, Bevan S, Jamshidi Y, Bastiaenen R, Myerburg RJ, Schott J-J, A Camm J, Steinbeck G, Norris K, Altman R, Tatonetti N, Jeffery S, Kubo M, Nakamura Y, Shen Y, George AL, Roden DM. 2013. Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes.. PLoS One. 8(11):e78511.▶ Go to Pubmed

Lippert RA, Predescu C, Ierardi DJ, Mackenzie KM, Eastwood MP, Dror RO, Shaw DE. 2013. Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure.. J Chem Phys. 139(16):164106.▶ Go to Pubmed

Abate-Shen C, Pandolfi PP. 2013. Effective utilization and appropriate selection of genetically engineered mouse models for translational integration of mouse and human trials.. Cold Spring Harb Protoc. 2013(11)▶ Go to Pubmed

Chan JMinhow, Carlsson G, Rabadan R. 2013. Topology of viral evolution.. Proc Natl Acad Sci U S A. 110(46):18566-71.▶ Go to Pubmed

Ansari S, Binder J, Boue S, Di Fabio A, Hayes W, Hoeng J, Iskandar A, Kleiman R, Norel R, O'Neel B, Peitsch M, Poussin C, Pratt D, Rhrissorrakrai K, Schlage WK, Stolovitzky G, Talikka M. 2013. On crowd-verification of biological networks.. Bioinform Biol Insights. 7:307-25.▶ Go to Pubmed

Fabbri G, Khiabanian H, Holmes A, Wang J, Messina M, Mullighan CG, Pasqualucci L, Rabadan R, Dalla-Favera R. 2013. Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome.. J Exp Med. 210(11):2273-88.▶ Go to Pubmed

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