Search Publications

2016 Publications

Wang K, Leong KW, Yang Y.  2016.  Expanding Nanopatterned Substrates Using Stitch Technique for Nanotopographical Modulation of Cell Behavior. J Vis Exp. (118) Go to Pubmed
Lee J, Jackman JG, Kwun J, Manook M, Moreno A, Elster EA, Kirk AD, Leong KW, Sullenger BA.  2016.  Nucleic acid scavenging microfiber mesh inhibits trauma-induced inflammation and thrombosis. Biomaterials. 120:94-102. Go to Pubmed
Xu K, Rosenstiel P, Paragas N, Hinze C, Gao X, Shen THuai, Werth M, Forster C, Deng R, Bruck E et al.  2016.  Unique Transcriptional Programs Identify Subtypes of AKI. J Am Soc Nephrol. Go to Pubmed
van Arensbergen J, FitzPatrick VD, de Haas M, Pagie L, Sluimer J, Bussemaker HJ, van Steensel B.  2016.  Genome-wide mapping of autonomous promoter activity in human cells. Nat Biotechnol. Go to Pubmed
Kelsic ED, Chung H, Cohen, iv N, Park J, Wang HH, Kishony R.  2016.  RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Syst. 3(6):563-571.e6. Go to Pubmed
Manrai AK, Patel CJ, Gehlenborg N, Tatonetti NP, Ioannidis JPA, Kohane IS.  2016.  METHODS TO ENHANCE THE REPRODUCIBILITY OF PRECISION MEDICINE. Pac Symp Biocomput. 21:180-182. Go to Pubmed
Koşaloğlu Z, Zörnig I, Halama N, Kaiser I, Buchhalter I, Grabe N, Eils R, Schlesner M, Califano A, Jäger D.  2016.  Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases. Oncoimmunology. 5(11):e1213931. Go to Pubmed
Elmas A, Yang T-HOu, Wang X, Anastassiou D.  2016.  Discovering Genome-Wide Tag SNPs Based on the Mutual Information of the Variants. PLoS One. 11(12):e0167994. Go to Pubmed
Califano A, Alvarez MJ.  2016.  The recurrent architecture of tumour initiation, progression and drug sensitivity. Nat Rev Cancer. Go to Pubmed
Stockman VB, Ghamsari L, Lasso G, Honig B, Shapira SD, Wang HH.  2016.  A High-Throughput Strategy for Dissecting Mammalian Genetic Interactions. PLoS One. 11(12):e0167617. Go to Pubmed
Udyavar AR, Wooten DJ, Hoeksema MD, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V.  2016.  Novel hybrid phenotype revealed in Small Cell Lung Cancer by a transcription factor network model that can explain tumor heterogeneity. Cancer Res. Go to Pubmed
Udyavar AR, Wooten DJ, Hoeksema MD, Bansal M, Califano A, Estrada L, Schnell S, Irish JM, Massion PP, Quaranta V.  2016.  Novel hybrid phenotype revealed in Small Cell Lung Cancer by a transcription factor network model that can explain tumor heterogeneity. Cancer Res. Go to Pubmed
Rosenbloom DIS, Camara PG, Chu T, Rabadan R.  2016.  Evolutionary scalpels for dissecting tumor ecosystems. Biochim Biophys Acta. Go to Pubmed
Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T et al.  2016.  Free Energy Perturbation Calculation of Relative Binding Free energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1. J Mol Biol. Go to Pubmed
Shameer K, Johnson KW, Yahi A, Miotto R, Li LI, Ricks D, Jebakaran J, Kovatch P, Sengupta PP, Gelijns S et al.  2016.  Predictive modelling of hospital readmission rates using electronic medical record-wide machine learning: a case-study using Mount Sinai heart failure cohort Pac Symp Biocomput. 22:276-287. Go to Pubmed
Karczewski KJ, Tatonetti NP, Manrai AK, Patel CJ, C Brown T, Ioannidis JPA.  2016.  Methods to ensure the reproducibility of biomedical research Pac Symp Biocomput. 22:117-119. Go to Pubmed
Melamed RD, Aydin IT, Rajan GSusan, Phelps R, Silvers DN, Emmett KJ, Brunner G, Rabadan R, Celebi JTok.  2016.  Genomic Characterization of Dysplastic Nevi Unveils Implications for Diagnosis of Melanoma. J Invest Dermatol. Go to Pubmed
Hobert O, Glenwinkel L, White J.  2016.  Revisiting Neuronal Cell Type Classification in Caenorhabditis elegans. Curr Biol. 26(22):R1197-R1203. Go to Pubmed
Kim-Hellmuth S, Lappalainen T.  2016.  Concerted Genetic Function in Blood Traits. Cell. 167(5):1167-1169. Go to Pubmed
Zhang C, Shen Y.  2016.  A Cell Type-Specific Expression Signature Predicts Haploinsufficient Autism-Susceptibility Genes. Hum Mutat. Go to Pubmed
Huang J, Kang BH, Ishida E, Zhou T, Griesman T, Sheng Z, Wu F, Doria-Rose NA, Zhang B, McKee K et al.  2016.  Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth. Immunity. 45(5):1108-1121. Go to Pubmed
Cruz FSDela, Diolaiti D, Turk AT, Rainey AR, Ambesi-Impiombato A, Andrews SJ, Mansukhani MM, Nagy PL, Alvarez MJ, Califano A et al.  2016.  A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma. Genome Med. 8(1):116. Go to Pubmed
Shah A, Qian Y, Weyn-Vanhentenryck SM, Zhang C.  2016.  CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. Bioinformatics. Go to Pubmed
Jiang W, Li M, Chen Z, Leong KW.  2016.  Cell-laden microfluidic microgels for tissue regeneration. Lab Chip. 16(23):4482-4506. Go to Pubmed
Deng C, Lipstein MR, Scotto L, Serrano XOJirau, Mangone MA, Li S, Vendome J, Hao Y, Xu X, Deng S-X et al.  2016.  Silencing c-Myc translation as a therapeutic strategy through targeting PI3K delta and CK1 epsilon in hematological malignancies. Blood. Go to Pubmed
Goodman KMarie, Rubinstein R, Thu CAye, Mannepalli S, Bahna F, Ahlsen G, Rittenhouse C, Maniatis T, Honig B, Shapiro L.  2016.  γ-Protocadherin structural diversity and functional implications. Elife. 5 Go to Pubmed
Garzón JIgnacio, Deng L, Murray D, Shapira S, Petrey D, Honig B.  2016.  A computational interactome and functional annotation for the human proteome. Elife. 5 Go to Pubmed
Moorjani P, Gao Z, Przeworski M.  2016.  Human Germline Mutation and the Erratic Evolutionary Clock. PLoS Biol. 14(10):e2000744. Go to Pubmed
Simons YB, Sella G.  2016.  The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. Curr Opin Genet Dev. 41:150-158. Go to Pubmed
Jackman JG, Juwarker H, Poveromo LP, Levinson H, Leong KW, Sullenger BA.  2016.  Polycationic Nanofibers for Nucleic Acid Scavenging. Biomacromolecules. Go to Pubmed
Gendrel M, Atlas EG, Hobert O.  2016.  A cellular and regulatory map of the GABAergic nervous system of C. elegans. Elife. 5 Go to Pubmed
Kuo S-H, Lin C-Y, Wang J, Sims PA, Pan M-K, Liou J-Y, Lee D, Tate WJ, Kelly GC, Louis ED et al.  2016.  Climbing fiber-Purkinje cell synaptic pathology in tremor and cerebellar degenerative diseases. Acta Neuropathol. Go to Pubmed
Yuan J, Sims PA.  2016.  An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. Sci Rep. 6:33883. Go to Pubmed
McKean DM, Homsy J, Wakimoto H, Patel N, Gorham J, DePalma SR, Ware JS, Zaidi S, Ma W, Patel N et al.  2016.  Loss of RNA expression and allele-specific expression associated with congenital heart disease. Nat Commun. 7:12824. Go to Pubmed
Oshima K, Khiabanian H, da Silva-Almeida AC, Tzoneva G, Abate F, Ambesi-Impiombato A, Sanchez-Martin M, Carpenter Z, Penson A, Perez-Garcia A et al.  2016.  Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia. Proc Natl Acad Sci U S A. Go to Pubmed
Goodman KM, Yamagata M, Jin X, Mannepalli S, Katsamba PS, Ahlsen G, Sergeeva AP, Honig B, Sanes JR, Shapiro L.  2016.  Molecular basis of sidekick-mediated cell-cell adhesion and specificity. Elife. 5 Go to Pubmed
Wang D, Kon N, Lasso G, Jiang L, Leng W, Zhu W-G, Qin J, Honig B, Gu W.  2016.  Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode. Nature. Go to Pubmed
Li L, Boland MRegina, Miotto R, Tatonetti NP, Dudley JT.  2016.  Replicating Cardiovascular Condition-Birth Month Associations. Sci Rep. 6:33166. Go to Pubmed
Tavana O, Li D, Dai C, Lopez G, Banerjee D, Kon N, Chen C, Califano A, Yamashiro DJ, Sun H et al.  2016.  HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma. Nat Med. Go to Pubmed
Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, Rosenstiel P, Strom TM et al.  2016.  Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Sci Rep. 6:32406. Go to Pubmed
Tian M, Cheng C, Chen X, Duan H, Cheng H-L, Dao M, Sheng Z, Kimble M, Wang L, Lin S et al.  2016.  Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires. Cell. 166(6):1471-1484.e18. Go to Pubmed
Mayers JR, Torrence ME, Danai LV, Papagiannakopoulos T, Davidson SM, Bauer MR, Lau AN, Ji BW, Dixit PD, Hosios AM et al.  2016.  Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. Science. 353(6304):1161-5. Go to Pubmed
Castel SE, Mohammadi P, Chung WK, Shen Y, Lappalainen T.  2016.  Rare variant phasing and haplotypic expression from RNA sequencing with phASER. Nat Commun. 7:12817. Go to Pubmed
Moorjani P, Amorim CEduardo G, Arndt PF, Przeworski M.  2016.  Variation in the molecular clock of primates. Proc Natl Acad Sci U S A. Go to Pubmed
Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG et al.  2016.  DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome. Am J Hum Genet. 99(3):555-66. Go to Pubmed
Chen Y, Clarke OB, Kim J, Stowe S, Kim Y-K, Assur Z, Cavalier M, Godoy-Ruiz R, von Alpen DC, Manzini C et al.  2016.  Structure of the STRA6 receptor for retinol uptake. Science. 353(6302) Go to Pubmed
Reid RJD, Du X, Sunjevaric I, Rayannavar V, Dittmar J, Bryant E, Maurer M, Rothstein R.  2016.  A Yeast Synthetic Dosage Lethal Screen Identifies a Conserved Interaction between PLK1 and CKS1B Affecting Cancer Cell Viability. Genetics. Go to Pubmed
Bain JM, Cho MT, Telegrafi A, Wilson A, Brooks S, Botti C, Gowans G, Autullo LAnne, Krishnamurthy V, Willing MC et al.  2016.  Variants in HNRNPH2 on the X Chromosome Are Associated with a Neurodevelopmental Disorder in Females. Am J Hum Genet. Go to Pubmed
Elyashiv E, Sattath S, Hu TT, Strutsovsky A, McVicker G, Andolfatto P, Coop G, Sella G.  2016.  A Genomic Map of the Effects of Linked Selection in Drosophila. PLoS Genet. 12(8):e1006130. Go to Pubmed
Camara PG, Levine AJ, Rabadan R.  2016.  Inference of Ancestral Recombination Graphs through Topological Data Analysis. PLoS Comput Biol. 12(8):e1005071. Go to Pubmed
Black JB, Adler AF, Wang H-G, D'Ippolito AM, Hutchinson HA, Reddy TE, Pitt GS, Leong KW, Gersbach CA.  2016.  Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells. Cell Stem Cell. Go to Pubmed
Hao Y, Tatonetti NP.  2016.  Predicting G Protein-Coupled Receptor Downstream Signaling by Tissue Expression. Bioinformatics. Go to Pubmed
M Joyce G, Wheatley AK, Thomas PV, Chuang G-Y, Soto C, Bailer RT, Druz A, Georgiev IS, Gillespie RA, Kanekiyo M et al.  2016.  Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses. Cell. 166(3):609-23. Go to Pubmed
Belver L, Ferrando A.  2016.  The genetics and mechanisms of T cell acute lymphoblastic leukaemia. Nat Rev Cancer. 16(8):494-507. Go to Pubmed
Chang JB, Quinnies KM, Realubit R, Karan C, Rand JH, Tatonetti NP.  2016.  A novel, rapid method to compare the therapeutic windows of oral anticoagulants using the Hill coefficient. Sci Rep. 6:29387. Go to Pubmed
Moskovitch R, Choi H, Hripcsak G, Tatonetti N.  2016.  Prognosis of Clinical Outcomes with Temporal Patterns and Experiences with One Class Feature Selection. IEEE/ACM Trans Comput Biol Bioinform. Go to Pubmed
Olsen T, Zhu J, Kim J, Pei R, Stojanovic MN, Lin Q.  2016.  An Integrated Microfluidic SELEX Approach Using Combined Electrokinetic and Hydrodynamic Manipulation. J Lab Autom. Go to Pubmed
Saez-Rodriguez J, Costello JC, Friend SH, Kellen MR, Mangravite L, Meyer P, Norman T, Stolovitzky G.  2016.  Crowdsourcing biomedical research: leveraging communities as innovation engines. Nat Rev Genet. 17(8):470-86. Go to Pubmed
Gerhard DS, Clemons PA, Shamji AF, Hon C, Wagner BK, Schreiber SL, Krasnitz A, Sordella R, Sander C, Lowe SW et al.  2016.  Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. Mol Cancer Res. Go to Pubmed
Boland MR, Tatonetti NP.  2016.  Investigation of 7-dehydrocholesterol reductase pathway to elucidate off-target prenatal effects of pharmaceuticals: a systematic review. Pharmacogenomics J. Go to Pubmed
Berko ER, Cho MT, Eng C, Shao Y, Sweetser DA, Waxler J, Robin NH, Brewer F, Donkervoort S, Mohassel P et al.  2016.  De novo missense variants in HECW2 are associated with neurodevelopmental delay and hypotonia. J Med Genet. Go to Pubmed
Hornstein N, Torres D, Sharma SDas, Tang G, Canoll P, Sims PA.  2016.  Ligation-free ribosome profiling of cell type-specific translation in the brain. Genome Biol. 17(1):149. Go to Pubmed
Chuang L-S, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Ng SMeng Evely, Zhang W, Hsu N-Y et al.  2016.  A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF. Gastroenterology. 151(4):710-723.e2. Go to Pubmed
Anzalone AV, Chen Z, Cornish VW.  2016.  Synthesis of photoactivatable azido-acyl caged oxazine fluorophores for live-cell imaging. Chem Commun (Camb). Go to Pubmed
Li H, Kuwajima T, Oakley D, Nikulina E, Hou J, Yang WSeok, Lowry ERhodes, Lamas NJorge, Amoroso MWeygandt, Croft GF et al.  2016.  Protein Prenylation Constitutes an Endogenous Brake on Axonal Growth. Cell Rep. Go to Pubmed
Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S et al.  2016.  Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun. 7:12065. Go to Pubmed
Camara PG, Rosenbloom DIS, Emmett KJ, Levine AJ, Rabadan R.  2016.  Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination. Cell Syst. 3(1):83-94. Go to Pubmed
Zhao X, Yang K, Zhao R, Ji T, Wang X, Yang X, Zhang Y, Cheng K, Liu S, Hao J et al.  2016.  Inducing enhanced immunogenic cell death with nanocarrier-based drug delivery systems for pancreatic cancer therapy. Biomaterials. 102:187-197. Go to Pubmed
Dutta A, Le Magnen C, Mitrofanova A, Ouyang X, Califano A, Abate-Shen C.  2016.  Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation. Science. 352(6293):1576-80. Go to Pubmed
Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M et al.  2016.  The genetics of nodal marginal zone lymphoma. Blood. Go to Pubmed
Sheng R, Jung D-J, Silkov A, Kim H, Singaram I, Wang Z-G, Xin Y, Kim E, Park M-J, Thiagarajan-Rosenkranz P et al.  2016.  Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain. J Biol Chem. 291(34):17639-50. Go to Pubmed
Alvarez MJ, Shen Y, Giorgi FM, Lachmann A, B Ding B, B Ye H, Califano A.  2016.  Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet. Go to Pubmed
Palmer C, Pe'er I.  2016.  Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation. PLoS Genet. 12(6):e1006091. Go to Pubmed
Yamamoto K, Wang J, Sprinzen L, Xu J, Haddock CJ, Li C, Lee BJ, Loredan DG, Jiang W, Vindigni A et al.  2016.  Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors. Elife. 5 Go to Pubmed
Harrison OJ, Brasch J, Lasso G, Katsamba PS, Ahlsen G, Honig B, Shapiro L.  2016.  Structural basis of adhesive binding by desmocollins and desmogleins. Proc Natl Acad Sci U S A. Go to Pubmed
Pulko V, Davies JS, Martinez C, Lanteri MC, Busch MP, Diamond MS, Knox K, Bush EC, Sims PA, Sinari S et al.  2016.  Human memory T cells with a naive phenotype accumulate with aging and respond to persistent viruses. Nat Immunol. Go to Pubmed
Wang J, Cazzato E, Ladewig E, Frattini V, Rosenbloom DIS, Zairis S, Abate F, Liu Z, Elliott O, Shin Y-J et al.  2016.  Clonal evolution of glioblastoma under therapy. Nat Genet. Go to Pubmed
Gayvert KM, Dardenne E, Cheung C, Boland MRegina, Lorberbaum T, Wanjala J, Chen Y, Rubin MA, Tatonetti NP, Rickman DS et al.  2016.  A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors. Cell Rep. 15(11):2348-56. Go to Pubmed
Sims JS, Grinshpun B, Feng Y, Ung TH, Neira JA, Samanamud JL, Canoll P, Shen Y, Sims PA, Bruce JN.  2016.  Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. Proc Natl Acad Sci U S A. Go to Pubmed
Soria-Valles C, Gutiérrez-Fernández A, Osorio FG, Carrero D, Ferrando AA, Colado E, M Fernández-García S, Bonzon-Kulichenko E, Vázquez J, Fueyo A et al.  2016.  MMP-25 Metalloprotease Regulates Innate Immune Response through NF-κB Signaling. J Immunol. Go to Pubmed
Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L et al.  2016.  The Genome Project-Write. Science. Go to Pubmed
Kim J, Olsen TR, Zhu J, Hilton JP, Yang K-A, Pei R, Stojanovic MN, Lin Q.  2016.  Integrated Microfluidic Isolation of Aptamers Using Electrophoretic Oligonucleotide Manipulation. Sci Rep. 6:26139. Go to Pubmed
Hu X, Jing C, Xu X, Nakazawa N, Cornish VW, Margadant FMartin, Sheetz MP.  2016.  Cooperative Vinculin Binding to Talin Mapped by Time Resolved Super Resolution Microscopy. Nano Lett. Go to Pubmed
Lescarbeau RS, Lei L, Bakken KK, Sims PA, Sarkaria JN, Canoll P, White FM.  2016.  Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma. Mol Cancer Ther. Go to Pubmed
Sheng Z, Schramm CA, Connors M, Morris L, Mascola JR, Kwong PD, Shapiro L.  2016.  Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection. PLoS Comput Biol. 12(5):e1004940. Go to Pubmed
Goodman KMarie, Rubinstein R, Thu CAye, Bahna F, Mannepalli S, Ahlsen G, Rittenhouse C, Maniatis T, Honig B, Shapiro L.  2016.  Structural Basis of Diverse Homophilic Recognition by Clustered α- and β-Protocadherins. Neuron. 90(4):709-23. Go to Pubmed
Shimada K, Skouta R, Kaplan A, Yang WSeok, Hayano M, Dixon SJ, Brown LM, Valenzuela CA, Wolpaw AJ, Stockwell BR.  2016.  Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis. Nat Chem Biol. Go to Pubmed
Yang K-A, Pei R, Stojanovic MN.  2016.  In vitro selection and amplification protocols for isolation of aptameric sensors for small molecules. Methods. Go to Pubmed
Lachmann A, Giorgi FM, Alvarez MJ, Califano A.  2016.  Detection and removal of spatial bias in multiwell assays. Bioinformatics. Go to Pubmed
Lachmann A, Giorgi FM, Lopez G, Califano A.  2016.  ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. Bioinformatics. 32(14):2233-5. Go to Pubmed
Paganin M, Buldini B, Germano G, Seganfreddo E, di Meglio A, Magrin E, Grillo F, Pigazzi M, Rizzari C, Cazzaniga G et al.  2016.  A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia. Pediatr Blood Cancer. Go to Pubmed
Oren-Suissa M, Bayer EA, Hobert O.  2016.  Sex-specific pruning of neuronal synapses in Caenorhabditis elegans. Nature. Go to Pubmed
Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D.  2016.  A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proc Natl Acad Sci U S A. Go to Pubmed
Hobert O.  2016.  A map of terminal regulators of neuronal identity in Caenorhabditis elegans. Wiley Interdiscip Rev Dev Biol. Go to Pubmed
Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TMeir, Kathail P, Choi K, Bendall S, Friedman N, Pe'er D.  2016.  Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat Biotechnol. Go to Pubmed
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO.  2016.  Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Cell Syst. 2(4):260-71. Go to Pubmed
Kushwaha R, Jagadish N, Kustagi M, Mendiratta G, Seandel M, Soni R, Korkola JE, Thodima V, Califano A, Bosl GJ et al.  2016.  Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification. Stem Cell Reports. Go to Pubmed
Willems T, Gymrek M, G Poznik D, Tyler-Smith C, Erlich, iv Y.  2016.  Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet. Go to Pubmed
Toivanen R, Mohan A, Shen MM.  2016.  Basal Progenitors Contribute to Repair of the Prostate Epithelium Following Induced Luminal Anoikis. Stem Cell Reports. Go to Pubmed
Kaartokallio T, A Lokki I, Peterson H, Kivinen K, Hiltunen L, Salmela E, Lappalainen T, Maanselkä P, Heino S, Knuutila S et al.  2016.  Preeclampsia does not share common risk alleles in 9p21 with coronary artery disease and type 2 diabetes. Ann Med. :1-7. Go to Pubmed
G Poznik D, Xue Y, Mendez FL, Willems TF, Massaia A, Sayres MAWilson, Ayub Q, McCarthy SA, Narechania A, Kashin S et al.  2016.  Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. Go to Pubmed
Yang S, Carmi S, Pe'er I.  2016.  Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. J Comput Biol. Go to Pubmed
Gomes ALC, Wang HH.  2016.  The Role of Genome Accessibility in Transcription Factor Binding in Bacteria. PLoS Comput Biol. 12(4):e1004891. Go to Pubmed
Lao Y-H, Chi C-W, Friedrich SM, Peck K, Wang T-H, Leong KW, Chen L-C.  2016.  Signal-On Protein Detection via Dye Translocation between Aptamer and Quantum Dot. ACS Appl Mater Interfaces. Go to Pubmed
Beck DB, Cho MT, Millan F, Yates C, Hannibal M, O'Connor B, Shinawi M, Connolly AM, Waggoner D, Halbach S et al.  2016.  A recurrent de novo CTBP1 mutation is associated with developmental delay, hypotonia, ataxia, and tooth enamel defects. Neurogenetics. Go to Pubmed
Wang S, Xu Y, Chan HFai, Kim H-W, Wang Y, Leong KW, Chen M.  2016.  phicaNanoparticle-mediated inhibition of survivin to overcome drug resistance in cancer therapy. J Control Release. Go to Pubmed
Johns NI, Blazejewski T, Gomes ALc, Wang HH.  2016.  Principles for designing synthetic microbial communities. Curr Opin Microbiol. 31:146-153. Go to Pubmed
Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme K, Boutros PC et al.  2016.  Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement. Go to Pubmed
Merabet S, Mann RS.  2016.  To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins. Trends Genet. Go to Pubmed
Mason RD, Welles HC, Adams C, Chakrabarti BK, Gorman J, Zhou T, Nguyen R, O'Dell S, Lusvarghi S, Bewley CA et al.  2016.  Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability. PLoS Pathog. 12(4):e1005537. Go to Pubmed
Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich, iv Y, Joshi RS, Mittelman D, Sharp AJ.  2016.  Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids Res. Go to Pubmed
Patro R, Norel R, Prill RJ, Saez-Rodriguez J, Lorenz P, Steinbeck F, Ziems B, Luštrek M, Barbarini N, Tiengo A et al.  2016.  A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin. BMC Bioinformatics. 17:155. Go to Pubmed
C Westphalen B, Takemoto Y, Tanaka T, Macchini M, Jiang Z, Renz BW, Chen X, Ormanns S, Nagar K, Tailor Y et al.  2016.  Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis. Cell Stem Cell. 18(4):441-55. Go to Pubmed
Zaaijer S, Erlich, iv Y.  2016.  Using mobile sequencers in an academic classroom. Elife. 5 Go to Pubmed
Park M-J, Sheng R, Silkov A, Jung D-J, Wang Z-G, Xin Y, Kim H, Thiagarajan-Rosenkranz P, Song S, Yoon Y et al.  2016.  SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins. Mol Cell. 62(1):7-20. Go to Pubmed
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