LGT TAXIES WITH NOSE OVER EDGE OF RWY WHERE TOLD TO HOLD. SEEING POS; CAPT TAXIES ACROSS RWY. CTLR CLRS FOR 180 DEG TURN AND TKOF.

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AS WE BEGAN OUR TAXI; KENNEDY GND CLRED US 'RIGHT INNER; L HOTEL; R ON RWY 22; HOLD SHORT OF 31L ON RWY 22.' I READ IT BACK; AND THE CAPT REPEATED THE READBACK. AS WE TAXIED DOWN RWY 22; THERE WAS 1 ACFT ON TKOF ROLL. THERE WERE NO OTHER ACFT IN THE AREA; TAXIING OR HOLDING SHORT FOR DEP AHEAD OF US. CHKLISTS WERE DONE. I WOULD SAY THAT WE WERE TAXIING AT A REASONABLE MODEST SPD; BEING ON A RWY IT SEEMED SLOW ENOUGH. AS WE APCHED RWY 31L; IT SEEMED THAT WE WERE GOING A LITTLE TOO FAST TO HOLD SHORT COMFORTABLY; SO I SAID TO THE CAPT; 'THIS IS 31L COMING UP; WE'RE SUPPOSED TO HOLD SHORT.' HE HESITATED FOR A MOMENT; LOOKED L; THEN R; THEN APPLIED WHAT I WOULD CALL NORMAL BRAKING. WHEN WE CAME TO A STOP; THE NOSE OF THE ACFT WAS JUST SLIGHTLY OUT ON THE RWY. WHEN HE REALIZED WHERE WE WERE; HE IMMEDIATELY ADDED PWR; CROSSED THE RWY TO LEAVE IT CLR. THERE WAS NO CONFLICT; NO ONE ON FINAL; OR ANYWHERE CLOSE. GND CTL SAW WHAT WE HAD DONE; AND CLRED US FOR A 180 DEG TURN ON RWY 22. TWR CLRED US FOR TKOF AND WE DEPARTED. FIRST OF ALL; IF THE CAPT HAD APPLIED BRAKES IMMEDIATELY WITHOUT LOOKING AROUND; OR APPLIED BRAKES MORE FIRMLY; WE COULD HAVE STOPPED WELL SHORT. I BELIEVE HE WAS LOOKING FOR A HOLD LINE OR RWY MARKER AS EXPECTED WHEN ON A TAXIWAY. BEING ON THE CTRLINE OF RWY 22 THERE WAS NO HOLD LINE; AND THE RWY 31L MARKER; WHICH IS LOCATED TO BE SEEN FROM THE TAXIWAY AS WELL TO THE SIDE. I AM NOT SURE THAT HE REALIZED WHERE RWY 31L WAS UNTIL WE WERE FULLY STOPPED. I DO NOT KNOW WHY HE ELECTED TO CROSS THE RWY WITHOUT CLRNC; NOR DID I HAVE TIME TO REQUEST IT BEFORE WE WERE ACROSS.