Research Publications

2020 The ASXL1-G643W variant accelerates the development of CEBPA mutant acute myeloid leukemia.
D'Altri T, Wilhelmson AS, Schuster MB, Wenzel A, Kalvisa A, Pundhir S, Hansen AM, Porse BT.
Haematologica May 7:haematol.2019.235150 [PMID: 32381577] [PDF].
2020 Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans.
Nepal C, Taranta A, Hadzhiev Y, Pundhir S, Mydel P, Lenhard B, Müller F, Andersen JB.
iScience 23(4):101008 [PMID: 32268280] [PDF].
2019 The splicing factor RBM25 controls MYC activity in acute myeloid leukemia.
Ge Y, Schuster MB, Pundhir S, Rapin N, Bagger FO, Sidiropoulos N, Hashem N, Porse BT.
Nature Communications 10(1):172 [PMID: 30635567] [PDF].
2019 Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML.
Jakobsen JS, Laursen LG, Schuster MB, Pundhir S, Schoof E, Ge Y, d'Altri T, Vitting-Seerup K, Rapin N, Gentil C, Jendholm J, Theilgaard-Mönch K, Reckzeh K, Bullinger L, Döhner K, Hokland P, Fitzgibbon J, Porse BT.
Science Advances Jul 10;5(7):eaaw4304 [PMID: 31309149] [PDF].
2019 Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism.
Jacobsen MJ, Havgaard JH, Anthon C, Mentzel CMJ, Cirera S, Krogh PM, Pundhir S, Karlskov-Mortensen P, Bruun CS, Lesnik P, Guerin M, Gorodkin J, Jørgensen CB, Fredholm M, Barrès R.
Front Genet. 10:1268 [PMID: 31921306] [PDF].
2018 Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment.
Lauridsen FKB, Jensen TL, Rapin N, Aslan D, Wilhelmson AS, Pundhir S, Rehn M, Paul F, Giladi A, Hasemann MS, Serup P, Amit I, Porse BT.
Cell Reports 24(3):766-780 [PMID: 30021172] [PDF].
2018 Enhancer and transcription factor dynamics during myeloid differentiation reveal an early differentiation block in Cebpa null progenitors.
Pundhir S*, Lauridsen FB*, Schuster MB, Jakobsen J, Ge Y, Schoof E, Rapin N, Waage J, Hasemann M and Porse BT.
Cell Reports 23(9):2744-2757 [PMID: 29847803] [PDF] (*joint first authors).
2016 Peak-valley-peak pattern of histone modifications delineate active regulatory elements and their directionality.
Pundhir S, Bagger FO, Lauridsen FB, Rapin N and Porse BT.
Nucleic Acids Research 44:4037-4051 [PMID: 27095194] [PDF].
2016 BloodSpot: A database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis.
Bagger F, Sasivarevic D, Sohi S, Laursen L, Pundhir S, Sønderby C, Winther O, Rapin, N and Porse, B.
Nucleic Acids Research 44:D917-24 [PMID: 26507857] [PDF].
2015 Differential and coherent processing patterns from small RNAs.
Pundhir S and Gorodkin J.
Scientific Reports (Nature) 5:12062 [PMID: 26166713] [PDF].
2015 Emerging applications of read profiles towards the functional annotation of the genome.
Pundhir S, Poirazi Y and Gorodkin J.
Frontiers in Genetics 6:118 [PMID: 26042150] [PDF].
2014 EssOilDB: A database of essential oils reflecting terpene composition and variability in the plant kingdom.
Kumari S, Pundhir S, Priya P, Jeena G, Punetha A, Chawla K, Jafaree Z, Mondal S and Yadav G.
Database (Oxford) 2014:bau120 [PMID: 25534749] [PDF].
2014 Spatially conserved long non-coding RNA and cis-regulatory elements identified within Cd247 gene in human and mouse using high-throughput sequencing data from ENCODE project.
Pundhir S, Hannibal T, Bang-Berthelsen C, Wegener A, Pociot F, Holmberg D and Gorodkin J.
Gene 545(1):80-87 [PMID: 24797614] [PDF].
2014 Structured RNAs and synteny regions in the pig genome.
Anthon C, Tafer H, Havgaard J, Thomsen B, Hedegaard J, Seemann S, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen R, Fredholm M, Stadler P, Gorodkin J.
BMC Genomics 15:459 [PMID: 24917120] [PDF].
2013 MicroRNA discovery by similarity search to a database of RNA-seq profiles.
Pundhir S and Gorodkin J.
Frontiers in Genetics 4:133 [PMID: 23874353] [PDF].
2012 deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.
Langenberger D*, Pundhir S*, Ekstrøm C, Stadler P, Hoffmann S and Gorodkin J.
Bioinformatics 28(1):17-24 [PMID: 22053076] [PDF] (*joint first authors).
2012 SSPred: a prediction server based on SVM for the identification and classification of protein involved in bacterial secretion systems.
Pundhir S and Kumar A.
Bioinformation 6(10):380-382 [PMID: 21904425] [PDF].
2008 PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes.
Pundhir S, Vijaywargiya H and Kumar A.
In Silico Biology 8(3-4):223-234 [PMID: 19032158] [PDF].