• bioRxiv  ·  February 24, 2020  ·  Preprint

    An autoimmune disease risk variant has a trans master regulatory effect mediated by IRF1 under immune stimulation.

    Margot K Brandt, Sarah Kim-Hellmuth, Marcello Ziosi, Alper Gokden, Aaron Wolman, Nora Lam, Yocelyn Recinos, Veit K Hornung, Johannes Schumacher, Tuuli Lappalainen

    link out icon
  • Cell Reports  ·  March 3, 2020

    High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation.

    Legut M, Daniloski Z, Xue X, McKenzie D, Guo X, Wessels HH, Sanjana NE.

    link out icon
  • bioRxiv  ·  February 11, 2020  ·  Preprint

    Recent Ultra-rare Inherited Mutations Identify Novel Autism Candidate Risk Genes

    Amy B Wilfert, Tychele N Turner, Shwetha C Murali, PingHsun Hsieh, Arvis Sulovari, Tianyun Wang, Bradley P Coe, Hui Guo, Kendra Hoekzema, Trygve E Bakken, Lara H Winterkorn, Uday S Evani, Marta Byrska-Bishop, Rachel K Earl, Raphael A Bernier, The SPARK Consortium, Michael C Zody, Evan E Eichler

    link out icon
  • Nature  ·  February 6, 2020

    The evolutionary history of 2,658 cancers.

    PCAWG Evolution and Heterogeneity Working Group, PCAWG network (includes Imielinski M)

    link out icon
  • Nature  ·  February 5, 2020

    Pan-cancer analysis of whole genomes.

    The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (includes Marcin Imielinski & Xiaotong Yao)

    link out icon
  • Genome Biology  ·  December 23, 2019

    Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.

    Hafemeister C, Satija R.

    link out icon
  • Science Translational Medicine  ·  December 18, 2019

    Human genetics and neuropathology suggest a link between miR-218 and amyotrophic lateral sclerosis pathophysiology.

    Irit Reichenstein,*, Chen Eitan, Sandra Diaz-Garcia, Guy Haim, Iddo Magen, Aviad Siany, Mariah L. Hoye, Natali Rivkin, Tsviya Olender, Beata Toth, Revital Ravid, Amitai D. Mandelbaum, Eran Yanowski, Jing Liang, Jeffrey K. Rymer, Rivka Levy, Gilad Beck, Elena Ainbinder, Sali M. K. Farhan, Kimberly A. Lennox, Nicole M. Bode, Mark A. Behlke, Thomas Möller, Smita Saxena, Cristiane A. M. Moreno, Giancarlo Costaguta, Kristel R. van Eijk, Hemali Phatnani, Ammar Al-Chalabi, A. Nazli Başak, Leonard H. van den Berg, Orla Hardiman, John E. Landers, Jesus S. Mora, Karen E. Morrison, Pamela J. Shaw, Jan H. Veldink, Samuel L. Pfaff, Ofer Yizhar, Christina Gross, Robert H. Brown Jr., John M. Ravits, Matthew B. Harms, Timothy M. Miller and Eran Hornstein

    link out icon
  • Scientific Reports  ·  December 13, 2019

    Deep sequencing of 3 cancer cell lines on 2 sequencing platforms

    Kanika Arora, Minita Shah, Molly Johnson, Rashesh Sanghvi, Jennifer Shelton, Kshithija Nagulapalli, Dayna M Oschwald, Michael C Zody, Soren Germer, Vaidehi Jobanputra, Jade Carter, Nicolas Robine.

    link out icon
  • PLoS Genet  ·  December 13, 2019

    Leveraging allelic imbalance to refine fine-mapping for eQTL studies.

    Zou J, Hormozdiari F, Jew B, Castel SE, Lappalainen T, Ernst J, Sul JH, Eskin E.

    link out icon
  • Cell  ·  December 12, 2019

    Toward a Common Coordinate Framework for the Human Body.

    Jennifer E. Rood, Tim Stuart, Shila Ghazanfar, Tommaso Biancalani, Eyal Fisher, Andrew Butler, Anna Hupalowska, Leslie Gaffney, William Mauck, Gökçen Eraslan, John C. Marioni, Aviv Regev, Rahul Satija.

    link out icon
  • Nature Neuroscience  ·  November 25, 2019

    Exome sequencing in amyotrophic lateral sclerosis implicates a novel gene, DNAJC7, encoding a heat-shock protein.

    Farhan SMK, Howrigan DP, Abbott LE, Klim JR, Topp SD, Byrnes AE, Churchhouse C, Phatnani H, Smith BN, Rampersaud E, Wu G, Wuu J, Shatunov A, Iacoangeli A, Al Khleifat A, Mordes DA, Ghosh S; ALSGENS Consortium; FALS Consortium; Project MinE Consortium; CReATe Consortium, Eggan K, Rademakers R, McCauley JL, Schüle R, Züchner S, Benatar M, Taylor JP, Nalls M, Gotkine M, Shaw PJ, Morrison KE, Al-Chalabi A, Traynor B, Shaw CE, Goldstein DB, Harms MB, Daly MJ, Neale BM.

    link out icon
  • Genome Biology  ·  November 21, 2019

    EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation.

    Priscillia Lhoumaud, Gunjan Sethia, Izzo F, Sana Badri, MacIntosh Cornwell, Kim K-T, Landau D, Jane Skok
    link out icon
  • PNAS  ·  November 20, 2019

    Effects of ALS-associated TANK binding kinase 1 mutations on protein–protein interactions and kinase activity

    Junqiang Ye, Jonah Cheung, Valeria Gerbino, Göran Ahlsén, Christina Zimanyi, David Hirsh, and Tom Maniatis

    link out icon
  • bioRxiv  ·  November 18, 2019  ·  Preprint

    Genome-wide profiling of druggable active tumor defense mechanisms to enhance cancer immunotherapy

    Rigel J Kishton, Shashank J Patel, Suman K Vodnala, Amy K Decker, Yogin Patel, Madhusudhanan Sukumar, Tori N Yamamoto, Zhiya Yu, Michelle Ji, Amanda N Henning, Devikala Gurusamy, Douglas C Palmer, Winifred Lo, Anna Pasetto, Parisa Malekzadeh, Drew C Deniger, Kris C Wood, Neville E. Sanjana, Nicholas P Restifo

    link out icon
  • Journal of Heredity  ·  November 14, 2019

    Adaptive Radiation Genomics of Two Ecologically Divergent Hawai‘ian Honeycreepers: The ‘akiapōlā‘au and the Hawai‘i ‘amakihi.

    Michael G Campana, André Corvelo, Jennifer Shelton, Taylor E Callicrate, Karen L Bunting, Bridget Riley-Gillis, Frank Wos, Justin DeGrazia, Erich D Jarvis, Robert C Fleischer

    link out icon
  • Molecular Biology and Evolution  ·  November 8, 2019

    Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha.

    Irene Julca, Marina Marcet-Houben, Fernando Cruz, Carlos Vargas-Chavez, J Spencer Johnston, Jèssica Gómez-Garrido, Leonor Frias, André Corvelo, Damian Loska, Francisco Cámara, Marta Gut, Tyler Alioto, Amparo Latorre, Toni Gabaldón

    link out icon
  • bioRxiv  ·  November 7, 2019  ·  Preprint

    Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

    Netha Ulahannan, Matthew Pendleton, Aditya S Deshpande, Stefan Schwenk, Julie M Behr, Xiaoguang Dai, Carly Tyer, Priyesh Rughani, Sarah Kudman, Emily Adney, Huasong Tian, David Wilkes, Juan Miguel Mosquera, David Stoddart, Daniel J Turner, Sissel Juul, Eoghan Harrington, Marcin Imielinski

    link out icon
  • Genome Biology  ·  November 4, 2019

    Genetic regulation of gene expression and splicing during a 10-year period of human aging.

    Balliu B, Durrant M, Goede O, Abell N, Li X, Liu B, Gloudemans MJ, Cook NL, Smith KS, Knowles DA, Pala M, Cucca F, Schlessinger D, Jaiswal S, Sabatti C, Lind L, Ingelsson E, Montgomery SB.

    link out icon
  • Pigment Cell & Melanoma Research  ·  November 2, 2019

    Sequencing two Tyr::CreERT2 transgenic mouse lines.

    Aktary Z, Corvelo A, Estrin C, Larue L.

    link out icon
Decorative image color fade left Decorative image color fade right Decorative image color fade